DSpace Collection:
http://hdl.handle.net/10023/859
2016-02-06T00:26:47ZMagnetohydrostatic modelling of stellar coronae
http://hdl.handle.net/10023/8067
Abstract: We introduce to the stellar physics community a method of modelling stellar coronae that can be considered to be an extension of the potential field. In this approach, the magnetic field is coupled to the background atmosphere. The model is magnetohydrostatic and is a balance between the Lorentz force, the pressure gradient and gravity. Analytical solutions are possible and we consider a particular class of equilibria in this paper. The model contains two free parameters and the effects of these on both the geometry and topology of the coronal magnetic field are investigated. A demonstration of the approach is given using a magnetogram derived from Zeeman–Doppler imaging of the 0.75 M⊙ M-dwarf star GJ 182.2016-02-11T00:00:00ZMacTaggart, DavidGregory, ScottNeukirch, ThomasDonati, Jean-FrancoisWe introduce to the stellar physics community a method of modelling stellar coronae that can be considered to be an extension of the potential field. In this approach, the magnetic field is coupled to the background atmosphere. The model is magnetohydrostatic and is a balance between the Lorentz force, the pressure gradient and gravity. Analytical solutions are possible and we consider a particular class of equilibria in this paper. The model contains two free parameters and the effects of these on both the geometry and topology of the coronal magnetic field are investigated. A demonstration of the approach is given using a magnetogram derived from Zeeman–Doppler imaging of the 0.75 M⊙ M-dwarf star GJ 182.A single-station method for the detection, classification and location of fin whale calls using ocean-bottom seismic stations
http://hdl.handle.net/10023/8064
Abstract: Passive seismic monitoring in the oceans uses long-term deployments of Ocean Bottom Seismometers (OBSs). An OBS usually records the three components of ground motion and pressure, typically at 100Hz. This makes the OBS an ideal tool to investigate fin and blue whales that vocalize at frequencies below 45Hz. Previous applications of OBS data to locate whale calls have relied on single channel analyses that disregard the information that is conveyed by the horizontal seismic channels. Recently, Harris, Matias, Thomas, Harwood, and Geissler [J. Acoust. Soc. Am. 134, 3522-3535 (2013)] presented a method that used all four channels recorded by one OBS to derive the range and azimuth of fin whale calls. In this work, the detection, classification, and ranging of calls using this four-channel method were further investigated, focusing on methods to increase the accuracy of range estimates to direct path arrivals. Corrections to account for the influences of the sound speed in the water layer and the velocity structure in the top strata of the seabed were considered. The single station method discussed here is best implemented when OBSs have been deployed in deep water on top of seabed strata with low P-wave velocity. These conditions maximize the ability to detect and estimate ranges to fin whale calls.2015-07-01T00:00:00ZMatias, L.Harris, D.Passive seismic monitoring in the oceans uses long-term deployments of Ocean Bottom Seismometers (OBSs). An OBS usually records the three components of ground motion and pressure, typically at 100Hz. This makes the OBS an ideal tool to investigate fin and blue whales that vocalize at frequencies below 45Hz. Previous applications of OBS data to locate whale calls have relied on single channel analyses that disregard the information that is conveyed by the horizontal seismic channels. Recently, Harris, Matias, Thomas, Harwood, and Geissler [J. Acoust. Soc. Am. 134, 3522-3535 (2013)] presented a method that used all four channels recorded by one OBS to derive the range and azimuth of fin whale calls. In this work, the detection, classification, and ranging of calls using this four-channel method were further investigated, focusing on methods to increase the accuracy of range estimates to direct path arrivals. Corrections to account for the influences of the sound speed in the water layer and the velocity structure in the top strata of the seabed were considered. The single station method discussed here is best implemented when OBSs have been deployed in deep water on top of seabed strata with low P-wave velocity. These conditions maximize the ability to detect and estimate ranges to fin whale calls.An MHD avalanche in a multi-threaded coronal loop
http://hdl.handle.net/10023/8061
Abstract: For the first time, we demonstrate how an MHD avalanche might occur in a multi-threaded coronal loop. Considering 23 non-potential magnetic threads within a loop, we use 3D MHD simulations to show that only one thread needs to be unstable in order to start an avalanche even when the others are below marginal stability. This has significant implications for coronal heating in that it provides for energy dissipation with a trigger mechanism. The instability of the unstable thread follows the evolution determined in many earlier investigations. However, once one stable thread is disrupted, it coalesces with a neighbouring thread and this process disrupts other nearby threads. Coalescence with these disrupted threads then occurs leading to the disruption of yet more threads as the avalanche develops. Magnetic energy is released in discrete bursts as the surrounding stable threads are disrupted. The volume integrated heating, as a function of time, shows short spikes suggesting that the temporal form of the heating is more like that of \textit{nanoflares} than of constant heating.
Description: We acknowledge the financial support of STFC through the Consolidated grants to the University of St Andrews and the University of Manchester.2016-01-18T00:00:00ZHood, Alan WilliamCargill, PeterBrowning, PhilippaTam, KuanFor the first time, we demonstrate how an MHD avalanche might occur in a multi-threaded coronal loop. Considering 23 non-potential magnetic threads within a loop, we use 3D MHD simulations to show that only one thread needs to be unstable in order to start an avalanche even when the others are below marginal stability. This has significant implications for coronal heating in that it provides for energy dissipation with a trigger mechanism. The instability of the unstable thread follows the evolution determined in many earlier investigations. However, once one stable thread is disrupted, it coalesces with a neighbouring thread and this process disrupts other nearby threads. Coalescence with these disrupted threads then occurs leading to the disruption of yet more threads as the avalanche develops. Magnetic energy is released in discrete bursts as the surrounding stable threads are disrupted. The volume integrated heating, as a function of time, shows short spikes suggesting that the temporal form of the heating is more like that of \textit{nanoflares} than of constant heating.Using species proportions to quantify turnover in biodiversity
http://hdl.handle.net/10023/8033
Abstract: Quantifying species turnover is an important aspect of biodiversity monitoring. Turnover measures are usually based on species presence/absence data, reflecting the rate at which species are replaced. However, measures that reflect the rate at which individuals of a species are replaced by individuals of another species are far more sensitive to change. In this paper, we propose families of turnover measures that reflect changes in species proportions. We study the properties of our measures, and use simulation to assess their success in detecting turnover. Using data on the British farmland bird community from the breeding bird survey, we evaluate our measures to quantify temporal turnover and how it varies across the British mainland.
Description: We are very grateful to all the volunteers who have contributed to the BBS. Yuan was funded by EPSRC/NERC grant EP/1000917/1. Harrison was funded by the Scottish Government’s Centre of Expertise ClimateXChange (www.climatexchange.org.uk).2015-12-21T00:00:00ZYuan, YuanBuckland, Stephen TerrenceHarrison, PhilFoss, SergeyJohnston, AlisonQuantifying species turnover is an important aspect of biodiversity monitoring. Turnover measures are usually based on species presence/absence data, reflecting the rate at which species are replaced. However, measures that reflect the rate at which individuals of a species are replaced by individuals of another species are far more sensitive to change. In this paper, we propose families of turnover measures that reflect changes in species proportions. We study the properties of our measures, and use simulation to assess their success in detecting turnover. Using data on the British farmland bird community from the breeding bird survey, we evaluate our measures to quantify temporal turnover and how it varies across the British mainland.Particle acceleration at reconnecting separator current layers
http://hdl.handle.net/10023/8001
Abstract: The aim of this work is to investigate and characterise particle behaviour in a 3D MHD model of a reconnecting magnetic separator. We use a relativistic guiding-centre test-particle code to investigate electron and proton acceleration in snapshots from 3D MHD separator reconnection experiments, and compare the results with findings from an analytical separator reconnection model studied in a previous investigation. The behaviour (and acceleration) of large distributions of particles are examined in detail for both analytical and numerical separator reconnection models. Differences in acceleration sites are recovered and discussed, together with the dependence of final particle energy ranges upon the dimensions of the models and the stage of the (time-dependent) MHD reconnection event. We discuss the implications of these results for observed magnetic separators in the solar corona.2016-01-01T00:00:00ZThrelfall, J.E. H. Stevenson, J.E. Parnell, C.Neukirch, T.The aim of this work is to investigate and characterise particle behaviour in a 3D MHD model of a reconnecting magnetic separator. We use a relativistic guiding-centre test-particle code to investigate electron and proton acceleration in snapshots from 3D MHD separator reconnection experiments, and compare the results with findings from an analytical separator reconnection model studied in a previous investigation. The behaviour (and acceleration) of large distributions of particles are examined in detail for both analytical and numerical separator reconnection models. Differences in acceleration sites are recovered and discussed, together with the dependence of final particle energy ranges upon the dimensions of the models and the stage of the (time-dependent) MHD reconnection event. We discuss the implications of these results for observed magnetic separators in the solar corona.Well quasi-order in combinatorics : embeddings and homomorphisms
http://hdl.handle.net/10023/7963
Abstract: The notion of well quasi-order (wqo) from the theory of ordered sets often arises naturally in contexts where one deals with infinite collections of structures which can somehow be compared, and it then represents a useful discriminator between ‘tame’ and ‘wild’ such classes. In this article we survey such situations within combinatorics, and attempt to identify promising directions for further research. We argue that these are intimately linked with a more systematic and detailed study of homomorphisms in combinatorics.2015-07-01T00:00:00ZHuczynska, SophieRuskuc, NikThe notion of well quasi-order (wqo) from the theory of ordered sets often arises naturally in contexts where one deals with infinite collections of structures which can somehow be compared, and it then represents a useful discriminator between ‘tame’ and ‘wild’ such classes. In this article we survey such situations within combinatorics, and attempt to identify promising directions for further research. We argue that these are intimately linked with a more systematic and detailed study of homomorphisms in combinatorics.Expert elicitation of seasonal abundance of North Atlantic right whales Eubalaena glacialis in the mid-Atlantic
http://hdl.handle.net/10023/7921
Abstract: North Atlantic right whales (Eubalaena glacialis; henceforth right whales) are among the most endangered large whales. Although protected since 1935, their abundance has remained low. Right whales occupy the Atlantic Ocean from southern Greenland and the Gulf of St. Lawrence south to Florida. The highly industrialized mid-Atlantic region is part of the species’ migratory corridor. Gaps in knowledge of the species’ movements through the mid-Atlantic limit informed management of stressors to the species. To contribute to filling of these gaps, we elicited estimates of the relative abundance of adult right whales in the mid-Atlantic during four months, representing each season, from ten experts. We elicited the minimum, maximum, and mode as the number of individuals in a hypothetical population of 100 right whales, and confidence estimates as percentages. For each month-sex combination, we merged the ten experts’ answers into one distribution. The estimated modes of relative abundances of both sexes were highest in January and April (females, 29 and 59; males, 22 and 23) and lowest in July and October (females, five and nine; males, three and five). In some cases, our elicitation results were consistent with the results of studies based on sightings data. However, these studies generally did not adjust for sampling effort, which was low and likely variable. Our results supplement the results of these studies and will increase the accuracy of priors in complementary Bayesian models of right whale abundances and movements through the mid-Atlantic.
Description: This work was supported in part by US Office of Naval Research (ONR) grants to E.F.: N00014-09-1-0896 at University of California, Santa Barbara and N00014-12-1-0274 at University of California, Davis. This work was also supported by ONR grant N000141210286 to the University of St Andrews. In addition, we gratefully acknowledge funding for this work from The Marine Alliance for Science and Technology for Scotland (MASTS). MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.2015-11-04T00:00:00ZOedekoven, Cornelia SabrinaFleishman, EricaHamilton, PhilipClark, James S.Schick, Robert SchillingNorth Atlantic right whales (Eubalaena glacialis; henceforth right whales) are among the most endangered large whales. Although protected since 1935, their abundance has remained low. Right whales occupy the Atlantic Ocean from southern Greenland and the Gulf of St. Lawrence south to Florida. The highly industrialized mid-Atlantic region is part of the species’ migratory corridor. Gaps in knowledge of the species’ movements through the mid-Atlantic limit informed management of stressors to the species. To contribute to filling of these gaps, we elicited estimates of the relative abundance of adult right whales in the mid-Atlantic during four months, representing each season, from ten experts. We elicited the minimum, maximum, and mode as the number of individuals in a hypothetical population of 100 right whales, and confidence estimates as percentages. For each month-sex combination, we merged the ten experts’ answers into one distribution. The estimated modes of relative abundances of both sexes were highest in January and April (females, 29 and 59; males, 22 and 23) and lowest in July and October (females, five and nine; males, three and five). In some cases, our elicitation results were consistent with the results of studies based on sightings data. However, these studies generally did not adjust for sampling effort, which was low and likely variable. Our results supplement the results of these studies and will increase the accuracy of priors in complementary Bayesian models of right whale abundances and movements through the mid-Atlantic.Magneto-static modelling of the mixed plasma Beta solar atmosphere based on SUNRISE/IMaX data
http://hdl.handle.net/10023/7887
Abstract: Our aim is to model the 3D magnetic field structure of the upper solar atmosphere, including regions of non-negligible plasma beta. We use high-resolution photospheric magnetic field measurements from SUNRISE/IMaX as boundary condition for a magneto-static magnetic field model. The high resolution of IMaX allows us to resolve the interface region between photosphere and corona, but modelling this region is challenging for the following reasons. While the coronal magnetic field is thought to be force-free (the Lorentz-force vanishes), this is not the case in the mixed plasma β environment in the photosphere and lower chromosphere. In our model, pressure gradients and gravity forces are taken self-consistently into account and compensate the non-vanishing Lorentz-force. Above a certain height (about 2 Mm) the non-magnetic forces become very weak and consequently the magnetic field becomes almost force-free. Here we apply a linear approach, where the electric current density consists of a superposition of a field-line parallel current and a current perpendicular to the Sun’s gravity field. We illustrate the prospects and limitations of this approach and give an outlook for an extension towards a non-linear model.
Description: TN acknowledges support by the U.K.’s Science and Technology Facilities Council and would like to thank the MPS for its hospitality during a visit in December 2014.2015-12-01T00:00:00ZWiegelmann, ThomasNeukirch, ThomasNickeler, DieterSolanki, SamiMartinez Pillet, ValentinBorrero, Juan ManuleOur aim is to model the 3D magnetic field structure of the upper solar atmosphere, including regions of non-negligible plasma beta. We use high-resolution photospheric magnetic field measurements from SUNRISE/IMaX as boundary condition for a magneto-static magnetic field model. The high resolution of IMaX allows us to resolve the interface region between photosphere and corona, but modelling this region is challenging for the following reasons. While the coronal magnetic field is thought to be force-free (the Lorentz-force vanishes), this is not the case in the mixed plasma β environment in the photosphere and lower chromosphere. In our model, pressure gradients and gravity forces are taken self-consistently into account and compensate the non-vanishing Lorentz-force. Above a certain height (about 2 Mm) the non-magnetic forces become very weak and consequently the magnetic field becomes almost force-free. Here we apply a linear approach, where the electric current density consists of a superposition of a field-line parallel current and a current perpendicular to the Sun’s gravity field. We illustrate the prospects and limitations of this approach and give an outlook for an extension towards a non-linear model.Acoustic sequences in non-human animals : a tutorial review and prospectus
http://hdl.handle.net/10023/7848
Abstract: Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well-known example of birdsong, other animals such as insects, amphibians,and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise – let alone understand – the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near-future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning,quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, ‘Analysing vocal sequences in animals’. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field,across taxa and across disciplines. We also provide a tutorial-style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.2014-01-01T00:00:00ZKershenbaum, ArikBlumstein, DanRoch, MarieAkçay, ÇaglarBackus, GregoryBee, Mark A.Bohn, KirstenCao, YanCarter, GeraldCäsar, CristianeCoen, MichaelDe Ruiter, Stacy LynnDoyle, LauranceEdelman, ShimonFerrer-i-Cancho, RamonFreeberg, Todd M.Garland, Ellen ClareGustison, MorganHarley, Heidi E.Huetz, ChloéHughes, MelissaBruno, Julia HylandIlany, AmiyaalJin, Dezhe Z.Johnson, MichaelJu, ChenghuiKarnowski, JeremyLohr, BernardManser, MartaMcCowan, BrendaMercado III, EduardoNarins, Peter M.Piel, AlexRice, MeganSalmi, RobertaSasahara, KazutoshiSayigh, LaelaShiu, YuTaylor, CharlesVallejo, Edgar E.Waller, SaraZamora-Gutierrez, VeronicaAnimal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well-known example of birdsong, other animals such as insects, amphibians,and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise – let alone understand – the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near-future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning,quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, ‘Analysing vocal sequences in animals’. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field,across taxa and across disciplines. We also provide a tutorial-style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.Dose response severity functions for acoustic disturbance in cetaceans using recurrent event survival analysis
http://hdl.handle.net/10023/7845
Abstract: Behavioral response studies (BRSs) aim to enhance our understanding of the behavior changes made by animals in response to specific exposure levels of different stimuli, often presented in an increasing dosage. Here, we focus on BRSs that aim to understand behavioral responses of free-ranging whales and dolphins to manmade acoustic signals (although the methods are applicable more generally). One desired outcome of these studies is dose-response functions relevant to different species, signals and contexts. We adapted and applied recurrent event survival analysis (Cox proportional hazard models) to data from the 3S BRS project, where multiple behavioral responses of different severities had been observed per experimental exposure and per individual based upon expert scoring. We included species, signal type, exposure number and behavioral state prior to exposure as potential covariates. The best model included all main effect terms, with the exception of exposure number, as well as two interaction terms. The interactions between signal and behavioral state, and between species and behavioral state highlighted that the sensitivity of animals to different signal types (a 6–7 kHz upsweep sonar signal [MFAS] or a 1–2 kHz upsweep sonar signal [LFAS]) depended on their behavioral state (feeding or nonfeeding), and this differed across species. Of the three species included in this analysis (sperm whale [Physeter macrocephalus], killer whale [Orcinus orca] and long-finned pilot whale [Globicephala melas]), killer whales were consistently the most likely to exhibit behavioral responses to naval sonar exposure. We conclude that recurrent event survival analysis provides an effective framework for fitting dose-response severity functions to data from behavioral response studies. It can provide outputs that can help government and industry to evaluate the potential impacts of anthropogenic sound production in the ocean.2015-11-20T00:00:00ZHarris, Catriona MSadykova, DinaraDe Ruiter, Stacy LynnTyack, Peter LloydMiller, PatrickKvadsheim, PetterLam, Frans-PeterThomas, LenBehavioral response studies (BRSs) aim to enhance our understanding of the behavior changes made by animals in response to specific exposure levels of different stimuli, often presented in an increasing dosage. Here, we focus on BRSs that aim to understand behavioral responses of free-ranging whales and dolphins to manmade acoustic signals (although the methods are applicable more generally). One desired outcome of these studies is dose-response functions relevant to different species, signals and contexts. We adapted and applied recurrent event survival analysis (Cox proportional hazard models) to data from the 3S BRS project, where multiple behavioral responses of different severities had been observed per experimental exposure and per individual based upon expert scoring. We included species, signal type, exposure number and behavioral state prior to exposure as potential covariates. The best model included all main effect terms, with the exception of exposure number, as well as two interaction terms. The interactions between signal and behavioral state, and between species and behavioral state highlighted that the sensitivity of animals to different signal types (a 6–7 kHz upsweep sonar signal [MFAS] or a 1–2 kHz upsweep sonar signal [LFAS]) depended on their behavioral state (feeding or nonfeeding), and this differed across species. Of the three species included in this analysis (sperm whale [Physeter macrocephalus], killer whale [Orcinus orca] and long-finned pilot whale [Globicephala melas]), killer whales were consistently the most likely to exhibit behavioral responses to naval sonar exposure. We conclude that recurrent event survival analysis provides an effective framework for fitting dose-response severity functions to data from behavioral response studies. It can provide outputs that can help government and industry to evaluate the potential impacts of anthropogenic sound production in the ocean.A general framework for animal density estimation from acoustic detections across a fixed microphone array
http://hdl.handle.net/10023/7786
Abstract: Acoustic monitoring can be an efficient, cheap, non-invasive alternative to physical trapping of individuals. Spatially explicit capture-recapture (SECR) methods have been proposed to estimate calling animal abundance and density from data collected by a fixed array of microphones. However, these methods make some assumptions that are unlikely to hold in many situations, and the consequences of violating these are yet to be investigated. We generalize existing acoustic SECR methodology, enabling these methods to be used in a much wider variety of situations. We incorporate time-of-arrival (TOA) data collected by the microphone array, increasing the precision of calling animal density estimates. We use our method to estimate calling male density of the Cape Peninsula Moss Frog Arthroleptella lightfooti. Our method gives rise to an estimator of calling animal density that has negligible bias, and 95% confidence intervals with appropriate coverage. We show that using TOA information can substantially improve estimate precision. Our analysis of the A. lightfooti data provides the first statistically rigorous estimate of calling male density for an anuran population using a microphone array. This method fills a methodological gap in the monitoring of frog populations and is applicable to acoustic monitoring of other species that call or vocalize.
Description: Funding for the frog survey was received from the National Geographic Society/Waitt Grants Program (No. W184-11). The EPSRC and NERC helped to fund this research through a PhD grant (No. EP/I000917/1).2015-01-01T00:00:00ZStevenson, B.C.Borchers, D.L.Altwegg, R.Swift, R.J.Gillespie, D.M.Measey, G.J.Acoustic monitoring can be an efficient, cheap, non-invasive alternative to physical trapping of individuals. Spatially explicit capture-recapture (SECR) methods have been proposed to estimate calling animal abundance and density from data collected by a fixed array of microphones. However, these methods make some assumptions that are unlikely to hold in many situations, and the consequences of violating these are yet to be investigated. We generalize existing acoustic SECR methodology, enabling these methods to be used in a much wider variety of situations. We incorporate time-of-arrival (TOA) data collected by the microphone array, increasing the precision of calling animal density estimates. We use our method to estimate calling male density of the Cape Peninsula Moss Frog Arthroleptella lightfooti. Our method gives rise to an estimator of calling animal density that has negligible bias, and 95% confidence intervals with appropriate coverage. We show that using TOA information can substantially improve estimate precision. Our analysis of the A. lightfooti data provides the first statistically rigorous estimate of calling male density for an anuran population using a microphone array. This method fills a methodological gap in the monitoring of frog populations and is applicable to acoustic monitoring of other species that call or vocalize.Passive acoustic monitoring of beaked whale densities in the Gulf of Mexico
http://hdl.handle.net/10023/7779
Abstract: Beaked whales are deep diving elusive animals, difficult to census with conventional visual surveys. Methods are presented for the density estimation of beaked whales, using passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period during and following the Deepwater Horizon oil spill (2010–2013). Beaked whale species detected include: Gervais’ (Mesoplodon europaeus), Cuvier’s (Ziphius cavirostris), Blainville’s (Mesoplodon densirostris) and an unknown species of Mesoplodon sp. (designated as Beaked Whale Gulf — BWG). For Gervais’ and Cuvier’s beaked whales, we estimated weekly animal density using two methods, one based on the number of echolocation clicks, and another based on the detection of animal groups during 5 min time-bins. Density estimates derived from these two methods were in good general agreement. At two sites in the western GOM, Gervais’ beaked whales were present throughout the monitoring period, but Cuvier’s beaked whales were present only seasonally, with periods of low density during the summer and higher density in the winter. At an eastern GOM site, both Gervais’ and Cuvier’s beaked whales had a high density throughout the monitoring period.
Description: Funding to support the tag data was also received from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.2015-11-12T00:00:00ZHildebrand, JohnBaumann-Pickering, SimoneFrasier, KaitlinTrickey, JenniferMerkens, KarlinaWiggins, SeanMcDonald, MarkGarrison, LanceHarris, DanielleMarques, Tiago A.Thomas, LenBeaked whales are deep diving elusive animals, difficult to census with conventional visual surveys. Methods are presented for the density estimation of beaked whales, using passive acoustic monitoring data collected at sites in the Gulf of Mexico (GOM) from the period during and following the Deepwater Horizon oil spill (2010–2013). Beaked whale species detected include: Gervais’ (Mesoplodon europaeus), Cuvier’s (Ziphius cavirostris), Blainville’s (Mesoplodon densirostris) and an unknown species of Mesoplodon sp. (designated as Beaked Whale Gulf — BWG). For Gervais’ and Cuvier’s beaked whales, we estimated weekly animal density using two methods, one based on the number of echolocation clicks, and another based on the detection of animal groups during 5 min time-bins. Density estimates derived from these two methods were in good general agreement. At two sites in the western GOM, Gervais’ beaked whales were present throughout the monitoring period, but Cuvier’s beaked whales were present only seasonally, with periods of low density during the summer and higher density in the winter. At an eastern GOM site, both Gervais’ and Cuvier’s beaked whales had a high density throughout the monitoring period.Occurrence, distribution and abundance of cetaceans in Onslow Bay, North Carolina, USA
http://hdl.handle.net/10023/7772
Abstract: In this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.2014-01-01T00:00:00ZRead, Andrew, J.Barco, S.Bell, J.Borchers, David LouisBurt, M LouiseCummings, E.W.Dunn, J.Fougeres, J.Hazen, L.Williams-Hodge, L.E.Laura, A-M.McAlarney, R.J.Nilsson, P.Pabst, D.A.Paxton, Charles G. M.Schneider, S.Z.Urian, KimWaples, D.M.McLellan, W.A.In this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.Observational signatures of waves and flows in the solar corona
http://hdl.handle.net/10023/7722
Abstract: Propagating perturbations have been observed in extended coronal loop structures for a number of years, but the interpretation in terms of slow (propagating) magneto-acoustic waves and/or as quasi-periodic upflows remains unresolved. We used forward-modelling to construct observational signatures associated with a simple slow magneto-acoustic wave or periodic flow model. Observational signatures were computed for the 171 Å Fe ix and the 193 Å Fe xii spectral lines. Although there are many differences between the flow and wave models, we did not find any clear, robust observational characteristics that can be used in isolation (i.e. that do not rely on a comparison between the models). For the waves model, a relatively rapid change of the average line widths as a function of (shallow) line-of-sight angles was found, whereas the ratio of the line width amplitudes to the Doppler velocity amplitudes is relatively high for the flow model. The most robust observational signature found is that the ratio of the mean to the amplitudes of the Doppler velocity is always higher than one for the flow model. This ratio is substantially higher for flows than for waves, and for the flows model used in the study is exactly the same in the 171 Å Fe ix and the 193 Å Fe xii spectral lines. However, these potential observational signatures need to be treated cautiously because they are likely to be model-dependent.
Description: DM acknowledges support of a Royal Society University Research Fellowship and a KU Leuven Research Council senior research fellowship (SF/12/008). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet ). TVD has been sponsored by an Odysseus grant of the FWO Vlaanderen. The research was performed in the context of the IAP P7/08 CHARM (Belspo) and the GOA-2015-014 (KU Leuven). TVD acknowledges the funding from the FP7 ERG grant with number 276808.2015-02-01T00:00:00ZDe Moortel, I.Antolin, P.Van Doorsselaere, T.Propagating perturbations have been observed in extended coronal loop structures for a number of years, but the interpretation in terms of slow (propagating) magneto-acoustic waves and/or as quasi-periodic upflows remains unresolved. We used forward-modelling to construct observational signatures associated with a simple slow magneto-acoustic wave or periodic flow model. Observational signatures were computed for the 171 Å Fe ix and the 193 Å Fe xii spectral lines. Although there are many differences between the flow and wave models, we did not find any clear, robust observational characteristics that can be used in isolation (i.e. that do not rely on a comparison between the models). For the waves model, a relatively rapid change of the average line widths as a function of (shallow) line-of-sight angles was found, whereas the ratio of the line width amplitudes to the Doppler velocity amplitudes is relatively high for the flow model. The most robust observational signature found is that the ratio of the mean to the amplitudes of the Doppler velocity is always higher than one for the flow model. This ratio is substantially higher for flows than for waves, and for the flows model used in the study is exactly the same in the 171 Å Fe ix and the 193 Å Fe xii spectral lines. However, these potential observational signatures need to be treated cautiously because they are likely to be model-dependent.A description of LATTE outputs
http://hdl.handle.net/10023/7720
2015-10-30T00:00:00ZMarques, Tiago A.Thomas, LenAn exact collisionless equilibrium for the Force-Free Harris Sheet with low plasma beta
http://hdl.handle.net/10023/7691
Abstract: We present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution function in two of the velocity directions to a Maxwellian distribution.
Description: Funding: STFC Consolidated Grant [ST/K000950/1] (OA, TN & FW) and a Doctoral Training Grant [ST/K502327/1] (OA). EPSRC Doctoral Training Grant [EP/K503162/1] (ST).2015-10-01T00:00:00ZAllanson, Oliver DouglasNeukirch, ThomasWilson, FionaTroscheit, SaschaWe present a first discussion and analysis of the physical properties of a new exact collisionless equilibrium for a one-dimensional nonlinear force-free magnetic field, namely, the force-free Harris sheet. The solution allows any value of the plasma beta, and crucially below unity, which previous nonlinear force-free collisionless equilibria could not. The distribution function involves infinite series of Hermite polynomials in the canonical momenta, of which the important mathematical properties of convergence and non-negativity have recently been proven. Plots of the distribution function are presented for the plasma beta modestly below unity, and we compare the shape of the distribution function in two of the velocity directions to a Maxwellian distribution.A spatially explicit capture-recapture estimator for single-catch traps
http://hdl.handle.net/10023/7680
Abstract: 1. Single-catch traps are frequently used in live-trapping studies of small mammals. Thus far a likelihood for single-catch traps has proven elusive and usually the likelihood for multi-catch traps is used for spatially explicit capture-recapture (SECR) analyses of such data. Previous work found the multi-catch likelihood to provide a robust estimator of average density. 2. We build on a recently developed continuous-time model for SECR to derive a likelihood for single-catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multi-catch estimator for various scenarios with non-constant density surfaces. 3. While the multi-catch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height (but not range) of the detection function. By contrast, the single catch estimators of density, distribution and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance, so that despite the lower bias of the single-catch estimator of the density surface over space, its root mean squared error is similar to that of the multi-catch estimator. 4. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constantover the survey region, then the multi-catch estimator performs well with single-catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single-catch estimator when trap saturation is above about 60%. The estimator’s performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single-catch likelihood with unknown capture times remains intractable for now, researchers using single-catch traps should aim to incorporate timing devices with their traps.
Description: This work was part-funded by EPSRC grant EP/I000917/1.2015-11-01T00:00:00ZDistiller, GregBorchers, David Louis1. Single-catch traps are frequently used in live-trapping studies of small mammals. Thus far a likelihood for single-catch traps has proven elusive and usually the likelihood for multi-catch traps is used for spatially explicit capture-recapture (SECR) analyses of such data. Previous work found the multi-catch likelihood to provide a robust estimator of average density. 2. We build on a recently developed continuous-time model for SECR to derive a likelihood for single-catch traps. We use this to develop an estimator based on observed capture times and compare its performance by simulation to that of the multi-catch estimator for various scenarios with non-constant density surfaces. 3. While the multi-catch estimator is found to be a surprisingly robust estimator of average density, its performance deteriorates with high trap saturation and increasing density gradients. Moreover, it is found to be a poor estimator of the height (but not range) of the detection function. By contrast, the single catch estimators of density, distribution and detection function parameters are found to be unbiased or nearly unbiased in all scenarios considered. This gain comes at the cost of higher variance, so that despite the lower bias of the single-catch estimator of the density surface over space, its root mean squared error is similar to that of the multi-catch estimator. 4. If there is no interest in interpreting the detection function parameters themselves, and if density is expected to be fairly constantover the survey region, then the multi-catch estimator performs well with single-catch traps. However if accurate estimation of the detection function is of interest, or if density is expected to vary substantially in space, then there is merit in using the single-catch estimator when trap saturation is above about 60%. The estimator’s performance is improved if care is taken to place traps so as to span the range of variables that affect animal distribution. As a single-catch likelihood with unknown capture times remains intractable for now, researchers using single-catch traps should aim to incorporate timing devices with their traps.Homomorphic image orders on combinatorial structures
http://hdl.handle.net/10023/7679
Abstract: Combinatorial structures have been considered under various orders, including substructure order and homomorphism order. In this paper, we investigate the homomorphic image order, corresponding to the existence of a surjective homomorphism between two structures. We distinguish between strong and induced forms of the order and explore how they behave in the context of different common combinatorial structures. We focus on three aspects: antichains and partial well-order, the joint preimage property and the dual amalgamation property. The two latter properties are natural analogues of the well-known joint embedding property and amalgamation property, and are investigated here for the first time.2015-07-01T00:00:00ZHuczynska, SophieRuskuc, NikCombinatorial structures have been considered under various orders, including substructure order and homomorphism order. In this paper, we investigate the homomorphic image order, corresponding to the existence of a surjective homomorphism between two structures. We distinguish between strong and induced forms of the order and explore how they behave in the context of different common combinatorial structures. We focus on three aspects: antichains and partial well-order, the joint preimage property and the dual amalgamation property. The two latter properties are natural analogues of the well-known joint embedding property and amalgamation property, and are investigated here for the first time.The modelling and assessment of whale-watching impacts
http://hdl.handle.net/10023/7642
Abstract: In recent years there has been significant interest in modelling cumulative effects and the population consequences of individual changes in cetacean behaviour and physiology due to disturbance. One potential source of disturbance that has garnered particular interest is whale-watching. Though perceived as 'green' or eco-friendly tourism, there is evidence that whale-watching can result in statistically significant and biologically meaningful changes in cetacean behaviour, raising the question whether whale-watching is in fact a long term sustainable activity. However, an assessment of the impacts of whale-watching on cetaceans requires an understanding of the potential behavioural and physiological effects, data to effectively address the question and suitable modelling techniques. Here, we review the current state of knowledge on the viability of long-term whale-watching, as well as logistical limitations and potential opportunities. We conclude that an integrated, coordinated approach will be needed to further understanding of the possible effects of whale-watching on cetaceans.2015-10-01T00:00:00ZNew, Leslie FrancesHall, Ailsa JaneHarcourt, R.Kaufman, G.Parsons, E.C.M.Pearson, H.C.Cosentino, A.M.Schick, Robert SchillingIn recent years there has been significant interest in modelling cumulative effects and the population consequences of individual changes in cetacean behaviour and physiology due to disturbance. One potential source of disturbance that has garnered particular interest is whale-watching. Though perceived as 'green' or eco-friendly tourism, there is evidence that whale-watching can result in statistically significant and biologically meaningful changes in cetacean behaviour, raising the question whether whale-watching is in fact a long term sustainable activity. However, an assessment of the impacts of whale-watching on cetaceans requires an understanding of the potential behavioural and physiological effects, data to effectively address the question and suitable modelling techniques. Here, we review the current state of knowledge on the viability of long-term whale-watching, as well as logistical limitations and potential opportunities. We conclude that an integrated, coordinated approach will be needed to further understanding of the possible effects of whale-watching on cetaceans.Genetic censusing identifies an unexpectedly sizeable population of an endangered large mammal in a fragmented forest landscape
http://hdl.handle.net/10023/7614
Abstract: Background: As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments. Results: From 2011 through 2013, we noninvasively collected 865 chimpanzee fecal samples across 633 km2 and successfully genotyped 662 (77%) at up to 14 microsatellite loci. These genotypes corresponded to 182 chimpanzees, with a mean of 3.5 captures per individual. We obtained population size estimates of 256 (95% confidence interval 246-321) and 319 (288-357) chimpanzees using capture-with-replacement and spatially explicit capture-recapture models, respectively. The spatial clustering of associated genotypes suggests the presence of at least nine communities containing a minimum of 8-33 individuals each. Putative community distributions defined by the locations of associated genotypes correspond well with the distribution of 14 Y-chromosome haplotypes. Conclusions: These census figures are more than three times greater than a previous estimate based on an extrapolation from small-scale nest count surveys that tend to underestimate population size. The distribution of genotype clusters and Y-chromosome haplotypes together indicate the presence of numerous male philopatric chimpanzee communities throughout the corridor habitat. Our findings demonstrate that, despite extensive habitat loss and fragmentation, chimpanzees remain widely distributed and exhibit distinct community home ranges. Our results further imply that elusive and rare species may adapt to degraded habitats more successfully than previously believed. Their long-term persistence is unlikely, however, if protection is not afforded to them and habitat loss continues unabated.
Description: This study was funded by the American Society of Primatologists, the German Academic Exchange Service (DAAD), the Max Planck Society, the University of Southern California Jane Goodall Research Center and Dornsife College of Letters, Arts, and Sciences, the Nacey Maggioncalda Foundation, and Primate Conservation, Inc.2015-08-25T00:00:00ZMcCarthy, M.S.Lester, J.D.Howe, Eric JohnArandjelovic, M.Stanford, C.B.Vigilant, L.Background: As habitat degradation and fragmentation continue to impact wildlife populations around the world, it is critical to understand the behavioral flexibility of species in these environments. In Uganda, the mostly unprotected forest fragment landscape between the Budongo and Bugoma Forests is a potential corridor for chimpanzees, yet little is known about the status of chimpanzee populations in these fragments. Results: From 2011 through 2013, we noninvasively collected 865 chimpanzee fecal samples across 633 km2 and successfully genotyped 662 (77%) at up to 14 microsatellite loci. These genotypes corresponded to 182 chimpanzees, with a mean of 3.5 captures per individual. We obtained population size estimates of 256 (95% confidence interval 246-321) and 319 (288-357) chimpanzees using capture-with-replacement and spatially explicit capture-recapture models, respectively. The spatial clustering of associated genotypes suggests the presence of at least nine communities containing a minimum of 8-33 individuals each. Putative community distributions defined by the locations of associated genotypes correspond well with the distribution of 14 Y-chromosome haplotypes. Conclusions: These census figures are more than three times greater than a previous estimate based on an extrapolation from small-scale nest count surveys that tend to underestimate population size. The distribution of genotype clusters and Y-chromosome haplotypes together indicate the presence of numerous male philopatric chimpanzee communities throughout the corridor habitat. Our findings demonstrate that, despite extensive habitat loss and fragmentation, chimpanzees remain widely distributed and exhibit distinct community home ranges. Our results further imply that elusive and rare species may adapt to degraded habitats more successfully than previously believed. Their long-term persistence is unlikely, however, if protection is not afforded to them and habitat loss continues unabated.Particle energisation in a collapsing magnetic trap model : the relativistic regime
http://hdl.handle.net/10023/7603
Abstract: Context. In solar flares, a large number of charged particles is accelerated to high energies. By which physical processes this is achieved is one of the main open problems in solar physics. It has been suggested that during a flare, regions of the rapidly relaxing magnetic field can form a collapsing magnetic trap (CMT) and that this trap may contribute to particle energisation. Aims. In this Research Note we focus on a particular analytical CMT model based on kinematic magnetohydrodynamics. Previous investigations of particle acceleration for this CMT model focused on the non-relativistic energy regime. It is the specific aim of this Research Note to extend the previous work to relativistic particle energies. Methods. Particle orbits were calculated numerically using the relativistic guiding centre equations. We also calculated particle orbits using the non-relativistic guiding centre equations for comparison. Results. For mildly relativistic energies the relativistic and non-relativistic particle orbits mainly agree well, but clear deviations are seen for higher energies. In particular, the final particle energies obtained from the relativistic calculations are systematically lower than the energies reached from the corresponding non-relativistic calculations, and the mirror points of the relativistic orbits are systematically higher than for the corresponding non-relativistic orbits. Conclusions. While the overall behaviour of particle orbits in CMTs does not differ qualitatively when using the relativistic guiding centre equations, there are a few systematic quantitative differences between relativistic and non-relativistic particle dynamics.
Description: The authors acknowledge financial support by the UK’s Science and Technology Facilities Council through a Doctoral Training Grant (SEO) and Consolidated Grant ST/K000950/1 (SEO and TN).2014-07-01T00:00:00ZEradat Oskoui, S.Neukirch, T.Context. In solar flares, a large number of charged particles is accelerated to high energies. By which physical processes this is achieved is one of the main open problems in solar physics. It has been suggested that during a flare, regions of the rapidly relaxing magnetic field can form a collapsing magnetic trap (CMT) and that this trap may contribute to particle energisation. Aims. In this Research Note we focus on a particular analytical CMT model based on kinematic magnetohydrodynamics. Previous investigations of particle acceleration for this CMT model focused on the non-relativistic energy regime. It is the specific aim of this Research Note to extend the previous work to relativistic particle energies. Methods. Particle orbits were calculated numerically using the relativistic guiding centre equations. We also calculated particle orbits using the non-relativistic guiding centre equations for comparison. Results. For mildly relativistic energies the relativistic and non-relativistic particle orbits mainly agree well, but clear deviations are seen for higher energies. In particular, the final particle energies obtained from the relativistic calculations are systematically lower than the energies reached from the corresponding non-relativistic calculations, and the mirror points of the relativistic orbits are systematically higher than for the corresponding non-relativistic orbits. Conclusions. While the overall behaviour of particle orbits in CMTs does not differ qualitatively when using the relativistic guiding centre equations, there are a few systematic quantitative differences between relativistic and non-relativistic particle dynamics.Pairwise interaction point processes for modelling bivariate spatial point patterns in the presence of interaction uncertainty
http://hdl.handle.net/10023/7583
Abstract: Current ecological research seeks to understand the mechanisms that sustain biodiversity and allow a large number of species to coexist. Coexistence concerns inter-individual interactions. Consequently, there is an interest in identifying and quantifying interactions within and between species as reflected in the spatial pattern formed by the individuals. This study analyses the spatial pattern formed by the locations of plants in a community with high biodiversity from Western Australia. We fit a pairwise interaction Gibbs marked point process to the data using a Bayesian approach and quantify the inhibitory interactions within and between the two species. We quantitatively discriminate between competing models corresponding to different inter-specific and intraspecific interactions via posterior model probabilities. The analysis provides evidence that the intraspecific interactions for the two species of the genus Banksia are generally similar to those between the two species providing some evidence for mechanisms that sustain biodiversity.2015-09-01T00:00:00ZNightingale, Glenna FaithIllian, Janine BaerbelKing, RuthCurrent ecological research seeks to understand the mechanisms that sustain biodiversity and allow a large number of species to coexist. Coexistence concerns inter-individual interactions. Consequently, there is an interest in identifying and quantifying interactions within and between species as reflected in the spatial pattern formed by the individuals. This study analyses the spatial pattern formed by the locations of plants in a community with high biodiversity from Western Australia. We fit a pairwise interaction Gibbs marked point process to the data using a Bayesian approach and quantify the inhibitory interactions within and between the two species. We quantitatively discriminate between competing models corresponding to different inter-specific and intraspecific interactions via posterior model probabilities. The analysis provides evidence that the intraspecific interactions for the two species of the genus Banksia are generally similar to those between the two species providing some evidence for mechanisms that sustain biodiversity.Procedure description : using AUTEC’s hydrophones surrounding a DTAGed whale to obtain localizations
http://hdl.handle.net/10023/7523
2015-01-01T00:00:00ZMarques, Tiago A.Shaeffer, JessicaMoretti, DavidThomas, LenOn the theory of translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and magnetic shear
http://hdl.handle.net/10023/7484
Abstract: We present an improved formalism for translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and currents with a field aligned component. The derivation of a Grad-Shafranov type equation is given along with a constraint which links the shear field to the parallel pressure. The difficulties of the formalism are discussed and various methods of circumventing these difficulties are given. A simple example is then used to highlight the methods and difficulties involved.
Description: Funding: STFC Doctoral Training Grant ST/K502327/1 (Jonathan Hodgson) and STFC Consolidated Grant ST/K000950/1 (Thomas Neukirch)2015-09-02T00:00:00ZHodgson, Jonathan David BrockieNeukirch, ThomasWe present an improved formalism for translationally invariant magnetohydrodynamic equilibria with anisotropic pressure and currents with a field aligned component. The derivation of a Grad-Shafranov type equation is given along with a constraint which links the shear field to the parallel pressure. The difficulties of the formalism are discussed and various methods of circumventing these difficulties are given. A simple example is then used to highlight the methods and difficulties involved.Model-based distance sampling
http://hdl.handle.net/10023/7410
Abstract: Conventional distance sampling adopts a mixed approach, using model-based methods for the detection process, and design-based methods to estimate animal abundance in the study region, given estimated probabilities of detection. In recent years, there has been increasing interest in fully model-based methods. Model-based methods are less robust for estimating animal abundance than conventional methods, but offer several advantages: they allow the analyst to explore how animal density varies by habitat or topography; abundance can be estimated for any sub-region of interest; they provide tools for analysing data from designed distance sampling experiments, to assess treatment effects. We develop a common framework for model-based distance sampling, and show how the various model-based methods that have been proposed fit within this framework.
Description: CSO was part-funded by EPSRC/NERC Grant EP/1000917/1. Date of acceptance: 20/08/20152015-01-01T00:00:00ZBuckland, Stephen TerrenceOedekoven, Cornelia SabrinaBorchers, David LouisConventional distance sampling adopts a mixed approach, using model-based methods for the detection process, and design-based methods to estimate animal abundance in the study region, given estimated probabilities of detection. In recent years, there has been increasing interest in fully model-based methods. Model-based methods are less robust for estimating animal abundance than conventional methods, but offer several advantages: they allow the analyst to explore how animal density varies by habitat or topography; abundance can be estimated for any sub-region of interest; they provide tools for analysing data from designed distance sampling experiments, to assess treatment effects. We develop a common framework for model-based distance sampling, and show how the various model-based methods that have been proposed fit within this framework.Coronal heating in multiple magnetic threads
http://hdl.handle.net/10023/7259
Abstract: Context. Heating the solar corona to several million degrees requires the conversion of magnetic energy into thermal energy. In this paper, we investigate whether an unstable magnetic thread within a coronal loop can destabilise a neighbouring magnetic thread. Aims. By running a series of simulations, we aim to understand under what conditions the destabilisation of a single magnetic thread can also trigger a release of energy in a nearby thread. Methods. The 3D magnetohydrodynamics code, Lare3d, is used to simulate the temporal evolution of coronal magnetic fields during a kink instability and the subsequent relaxation process. We assume that a coronal magnetic loop consists of non-potential magnetic threads that are initially in an equilibrium state. Results. The non-linear kink instability in one magnetic thread forms a helical current sheet and initiates magnetic reconnection. The current sheet fragments, and magnetic energy is released throughout that thread. We find that, under certain conditions, this event can destabilise a nearby thread, which is a necessary requirement for starting an avalanche of energy release in magnetic threads. Conclusions. It is possible to initiate an energy release in a nearby, non-potential magnetic thread, because the energy released from one unstable magnetic thread can trigger energy release in nearby threads, provided that the nearby structures are close to marginal stability.
Description: We acknowledge the financial support of STFC through the Consolidated grant to the University of St Andrews.2015-08-01T00:00:00ZTam, Kuan VaiHood, Alan WilliamBrowning, PhilippaCargill, PeterContext. Heating the solar corona to several million degrees requires the conversion of magnetic energy into thermal energy. In this paper, we investigate whether an unstable magnetic thread within a coronal loop can destabilise a neighbouring magnetic thread. Aims. By running a series of simulations, we aim to understand under what conditions the destabilisation of a single magnetic thread can also trigger a release of energy in a nearby thread. Methods. The 3D magnetohydrodynamics code, Lare3d, is used to simulate the temporal evolution of coronal magnetic fields during a kink instability and the subsequent relaxation process. We assume that a coronal magnetic loop consists of non-potential magnetic threads that are initially in an equilibrium state. Results. The non-linear kink instability in one magnetic thread forms a helical current sheet and initiates magnetic reconnection. The current sheet fragments, and magnetic energy is released throughout that thread. We find that, under certain conditions, this event can destabilise a nearby thread, which is a necessary requirement for starting an avalanche of energy release in magnetic threads. Conclusions. It is possible to initiate an energy release in a nearby, non-potential magnetic thread, because the energy released from one unstable magnetic thread can trigger energy release in nearby threads, provided that the nearby structures are close to marginal stability.Large scale surveys for cetaceans : line transect assumptions, reliability of abundance estimates and improving survey efficiency – A response to MacLeod
http://hdl.handle.net/10023/7159
2014-02-01T00:00:00ZHammond, Philip StevenGillespie, Douglas MichaelLovell, PhilipSamarra, Filipa Isabel PereiraSwift, Rene JamesMacleod, KellyTasker, Mark LBerggren, PerBorchers, David LouisBurt, M LouisePaxton, Charles G. M.Canadas, AnaDesportes, GenevieveDonovan, Greg PGilles, AnitaLehnert, KristinaSiebert, UrsulaGordon, Jonathan Charles DavidLeaper, RussellLeopold, MardikScheidat, MeikeOien, NilsRidoux, VincentRogan, EmerSkov, HenrikTeilmann, JonasVan Canneyt, OlivierVazquez, Jose AntonioDetectability in audio-visual surveys of tropical rainforest birds : the influence of species, weather and habitat characteristics
http://hdl.handle.net/10023/7147
Abstract: Indices of relative abundance do not control for variation in detectability, which can bias density estimates such that ecological processes are difficult to infer. Distance sampling methods can be used to correct for detectability, but in rainforest, where dense vegetation and diverse assemblages complicate sampling, information is lacking about factors affecting their application. Rare species present an additional challenge, as data may be too sparse to fit detection functions. We present analyses of distance sampling data collected for a diverse tropical rainforest bird assemblage across broad elevational and latitudinal gradients in North Queensland, Australia. Using audio and visual detections, we assessed the influence of various factors on Effective Strip Width (ESW), an intuitively useful parameter, since it can be used to calculate an estimate of density from count data. Body size and species exerted the most important influence on ESW, with larger species detectable over greater distances than smaller species. Secondarily, wet weather and high shrub density decreased ESW for most species. ESW for several species also differed between summer and winter, possibly due to seasonal differences in calling behavior. Distance sampling proved logistically intensive in these environments, but large differences in ESW between species confirmed the need to correct for detection probability to obtain accurate density estimates. Our results suggest an evidence-based approach to controlling for factors influencing detectability, and avenues for further work including modeling detectability as a function of species characteristics such as body size and call characteristics. Such models may be useful in developing a calibration for non-distance sampling data and for estimating detectability of rare species.
Description: This research was funded by the Australian Government’s National Environmental Research Program, the Stuart Leslie Bird Research Award from Birds Australia (http://www.birdsaustralia.com.au/), the Earthwatch Institute (http://www.earthwatch.org/australia/), the Marine and Tropical Sciences Research Facility (MTSRF: http://www.rrrc.org.au/mtsrf). In addition, TAM was partially sponsored by national funds through the Fundação Nacional para a Ciência e Tecnologia, Portugal – FCT under the project (PEst-OE/MAT/UI0006/2011). Date of Acceptance: 27/04/20152015-06-25T00:00:00ZAnderson, Alexander S.Marques, Tiago A.Shoo, Luke P.Williams, Stephen E.Indices of relative abundance do not control for variation in detectability, which can bias density estimates such that ecological processes are difficult to infer. Distance sampling methods can be used to correct for detectability, but in rainforest, where dense vegetation and diverse assemblages complicate sampling, information is lacking about factors affecting their application. Rare species present an additional challenge, as data may be too sparse to fit detection functions. We present analyses of distance sampling data collected for a diverse tropical rainforest bird assemblage across broad elevational and latitudinal gradients in North Queensland, Australia. Using audio and visual detections, we assessed the influence of various factors on Effective Strip Width (ESW), an intuitively useful parameter, since it can be used to calculate an estimate of density from count data. Body size and species exerted the most important influence on ESW, with larger species detectable over greater distances than smaller species. Secondarily, wet weather and high shrub density decreased ESW for most species. ESW for several species also differed between summer and winter, possibly due to seasonal differences in calling behavior. Distance sampling proved logistically intensive in these environments, but large differences in ESW between species confirmed the need to correct for detection probability to obtain accurate density estimates. Our results suggest an evidence-based approach to controlling for factors influencing detectability, and avenues for further work including modeling detectability as a function of species characteristics such as body size and call characteristics. Such models may be useful in developing a calibration for non-distance sampling data and for estimating detectability of rare species.Double-observer line transect surveys with Markov-modulated Poisson process models for overdispersed animal availability
http://hdl.handle.net/10023/7085
Abstract: We develop maximum likelihood methods for line transect surveys in which animals go undetected at distance zero, either because they are stochastically unavailable while within view or because they are missed when they are available. These incorporate a Markov-modulated Poisson process model for animal availability, allowing more clustered availability events than is possible with Poisson availability models. They include a mark-recapture component arising from the independent-observer survey, leading to more accurate estimation of detection probability given availability. We develop models for situations in which (a) multiple detections of the same individual are possible and (b) some or all of the availability process parameters are estimated from the line transect survey itself, rather than from independent data. We investigate estimator performance by simulation, and compare the multiple-detection estimators with estimators that use only initial detections of individuals, and with a single-observer estimator. Simultaneous estimation of detection function parameters and availability model parameters is shown to be feasible from the line transect survey alone with multiple detections and double-observer data but not with single-observer data. Recording multiple detections of individuals improves estimator precision substantially when estimating the availability model parameters from survey data, and we recommend that these data be gathered. We apply the methods to estimate detection probability from a double-observer survey of North Atlantic minke whales, and find that double-observer data greatly improve estimator precision here too.2015-01-01T00:00:00ZBorchers, David LouisLangrock, RolandWe develop maximum likelihood methods for line transect surveys in which animals go undetected at distance zero, either because they are stochastically unavailable while within view or because they are missed when they are available. These incorporate a Markov-modulated Poisson process model for animal availability, allowing more clustered availability events than is possible with Poisson availability models. They include a mark-recapture component arising from the independent-observer survey, leading to more accurate estimation of detection probability given availability. We develop models for situations in which (a) multiple detections of the same individual are possible and (b) some or all of the availability process parameters are estimated from the line transect survey itself, rather than from independent data. We investigate estimator performance by simulation, and compare the multiple-detection estimators with estimators that use only initial detections of individuals, and with a single-observer estimator. Simultaneous estimation of detection function parameters and availability model parameters is shown to be feasible from the line transect survey alone with multiple detections and double-observer data but not with single-observer data. Recording multiple detections of individuals improves estimator precision substantially when estimating the availability model parameters from survey data, and we recommend that these data be gathered. We apply the methods to estimate detection probability from a double-observer survey of North Atlantic minke whales, and find that double-observer data greatly improve estimator precision here too.Chronic exposure to imidacloprid increases neuronal vulnerability to mitochondrial dysfunction in the bumblebee (Bombus terrestris)
http://hdl.handle.net/10023/6986
Abstract: The global decline in the abundance and diversity of insect pollinators could result from habitat loss, disease, and pesticide exposure. The contribution of the neonicotinoid insecticides (e.g., clothianidin and imidacloprid) to this decline is controversial, and key to understanding their risk is whether the astonishingly low levels found in the nectar and pollen of plants is sufficient to deliver neuroactive levels to their site of action: the bee brain. Here we show that bumblebees (Bombusterrestris audax) fed field levels [10 nM, 2.1 ppb (w/w)] of neonicotinoid accumulate between 4 and 10 nM in their brains within 3 days. Acute (minutes) exposure of cultured neurons to 10 nM clothianidin, but not imidacloprid, causes a nicotinic acetylcholine receptor-dependent rapid mitochondrial depolarization. However, a chronic (2 days) exposure to 1 nM imidacloprid leads to a receptor-dependent increased sensitivity to a normally innocuous level of acetylcholine, which now also causes rapid mitochondrial depolarization in neurons. Finally, colonies exposed to this level of imidacloprid show deficits in colony growth and nest condition compared with untreated colonies. These findings provide a mechanistic explanation for the poor navigation and foraging observed in neonicotinoid treated bumblebee colonies.
Description: This work was funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government, and The Wellcome Trust, under the Insect Pollinators Initiative (United Kingdom) Grant BB/ 1000313/1 (to C.N.C.).2015-05-01T00:00:00ZMoffat, C.Goncalves Pacheco, J.Sharpe, S.Samson, A.J.Bollan, K.A.Huang, J.Buckland, Stephen TerrenceConnolly, C.N.The global decline in the abundance and diversity of insect pollinators could result from habitat loss, disease, and pesticide exposure. The contribution of the neonicotinoid insecticides (e.g., clothianidin and imidacloprid) to this decline is controversial, and key to understanding their risk is whether the astonishingly low levels found in the nectar and pollen of plants is sufficient to deliver neuroactive levels to their site of action: the bee brain. Here we show that bumblebees (Bombusterrestris audax) fed field levels [10 nM, 2.1 ppb (w/w)] of neonicotinoid accumulate between 4 and 10 nM in their brains within 3 days. Acute (minutes) exposure of cultured neurons to 10 nM clothianidin, but not imidacloprid, causes a nicotinic acetylcholine receptor-dependent rapid mitochondrial depolarization. However, a chronic (2 days) exposure to 1 nM imidacloprid leads to a receptor-dependent increased sensitivity to a normally innocuous level of acetylcholine, which now also causes rapid mitochondrial depolarization in neurons. Finally, colonies exposed to this level of imidacloprid show deficits in colony growth and nest condition compared with untreated colonies. These findings provide a mechanistic explanation for the poor navigation and foraging observed in neonicotinoid treated bumblebee colonies.Estimating population sizes of lions Panthera leo and spotted hyaenas Crocuta crocuta in Uganda’s savannah parks, using lure count methods
http://hdl.handle.net/10023/6885
Abstract: Despite > 60 years of conservation in Uganda’s national parks the populations of lions and spotted hyaenas in these areas have never been estimated using a census method. Estimates for some sites have been extrapolated to other protected areas and educated guesses have been made but there has been nothing more definitive. We used a lure count analysis method of call-up counts to estimate populations of the lion Panthera leo and spotted hyaena Crocuta crocuta in the parks where reasonable numbers of these species exist: Queen Elizabeth Protected Area, Murchison Falls Conservation Area and Kidepo Valley National Park. We estimated a total of 408 lions and 324 hyaenas for these three conservation areas. It is unlikely that other conservation areas in Uganda host >10 lions or > 40 hyaenas. The Queen Elizabeth Protected Area had the largest populations of lions and hyaenas: 140 and 211, respectively. It is estimated that lion numbers have declined by 30% in this protected area since the late 1990s and there are increasing concerns for the long-term viability of both species in Uganda.
Description: Funding: United States Agency for International Development2014-07-01T00:00:00ZOmoya, Edward OkotMudumba, TutiloBuckland, Stephen TMulondo, PaulPlumptre, Andrew JDespite > 60 years of conservation in Uganda’s national parks the populations of lions and spotted hyaenas in these areas have never been estimated using a census method. Estimates for some sites have been extrapolated to other protected areas and educated guesses have been made but there has been nothing more definitive. We used a lure count analysis method of call-up counts to estimate populations of the lion Panthera leo and spotted hyaena Crocuta crocuta in the parks where reasonable numbers of these species exist: Queen Elizabeth Protected Area, Murchison Falls Conservation Area and Kidepo Valley National Park. We estimated a total of 408 lions and 324 hyaenas for these three conservation areas. It is unlikely that other conservation areas in Uganda host >10 lions or > 40 hyaenas. The Queen Elizabeth Protected Area had the largest populations of lions and hyaenas: 140 and 211, respectively. It is estimated that lion numbers have declined by 30% in this protected area since the late 1990s and there are increasing concerns for the long-term viability of both species in Uganda.Inflations of geometric grid classes of permutations
http://hdl.handle.net/10023/6862
Abstract: Geometric grid classes and the substitution decomposition have both been shown to be fundamental in the understanding of the structure of permutation classes. In particular, these are the two main tools in the recent classification of permutation classes of growth rate less than κ ≈ 2.20557 (a specific algebraic integer at which infinite antichains first appear). Using language- and order-theoretic methods, we prove that the substitution closures of geometric grid classes are well partially ordered, finitely based, and that all their subclasses have algebraic generating functions. We go on to show that the inflation of a geometric grid class by a strongly rational class is well partially ordered, and that all its subclasses have rational generating functions. This latter fact allows us to conclude that every permutation class with growth rate less than κ has a rational generating function. This bound is tight as there are permutation classes with growth rate κ which have nonrational generating functions.
Description: All three authors were partially supported by EPSRC via the grant EP/J006440/1.2015-02-01T00:00:00ZAlbert, M.D.Ruskuc, NikVatter, V.Geometric grid classes and the substitution decomposition have both been shown to be fundamental in the understanding of the structure of permutation classes. In particular, these are the two main tools in the recent classification of permutation classes of growth rate less than κ ≈ 2.20557 (a specific algebraic integer at which infinite antichains first appear). Using language- and order-theoretic methods, we prove that the substitution closures of geometric grid classes are well partially ordered, finitely based, and that all their subclasses have algebraic generating functions. We go on to show that the inflation of a geometric grid class by a strongly rational class is well partially ordered, and that all its subclasses have rational generating functions. This latter fact allows us to conclude that every permutation class with growth rate less than κ has a rational generating function. This bound is tight as there are permutation classes with growth rate κ which have nonrational generating functions.Subalgebras of FA-presentable algebras
http://hdl.handle.net/10023/6852
Abstract: Automatic presentations, also called FA-presentations, were introduced to extend finite model theory to infinite structures whilst retaining the solubility of fundamental decision problems. This paper studies FA-presentable algebras. First, an example is given to show that the class of finitely generated FA-presentable algebras is not closed under forming finitely generated subalgebras, even within the class of algebras with only unary operations. In contrast, a finitely generated subalgebra of an FA-presentable algebra with a single unary operation is itself FA-presentable. Furthermore, it is proven that the class of unary FA-presentable algebras is closed under forming finitely generated subalgebras and that the membership problem for such subalgebras is decidable.2014-06-01T00:00:00ZCain, A.J.Ruskuc, NikAutomatic presentations, also called FA-presentations, were introduced to extend finite model theory to infinite structures whilst retaining the solubility of fundamental decision problems. This paper studies FA-presentable algebras. First, an example is given to show that the class of finitely generated FA-presentable algebras is not closed under forming finitely generated subalgebras, even within the class of algebras with only unary operations. In contrast, a finitely generated subalgebra of an FA-presentable algebra with a single unary operation is itself FA-presentable. Furthermore, it is proven that the class of unary FA-presentable algebras is closed under forming finitely generated subalgebras and that the membership problem for such subalgebras is decidable.Excitation and damping of broadband kink waves in the solar corona
http://hdl.handle.net/10023/6839
Abstract: Context. Observations such as those by the Coronal Multi-Channel Polarimeter (CoMP) have revealed that broadband kink oscillations are ubiquitous in the solar corona. Aims. We consider footpoint-driven kink waves propagating in a low β coronal plasma with a cylindrical density structure. We investigate the excitation and damping of propagating kink waves by a broadband driver, including the effects of different spatial profiles for the driver. Methods. We employ a general spatial damping profile in which the initial stage of the damping envelope is approximated by a Gaussian profile and the asymptotic state by an exponential one. We develop a method of accounting for the presence of these different damping regimes and test it using data from numerical simulations. Results. Strongly damped oscillations in low density coronal loops are more accurately described by a Gaussian spatial damping profile than an exponential profile. The consequences for coronal seismology are investigated and applied to observational data for the ubiquitous broadband waves observed by CoMP. Current data cannot distinguish between the exponential and Gaussian profiles because of the levels of noise. We demonstrate the importance of the spatial profile of the driver on the resulting damping profile. Furthermore, we show that a small-scale turbulent driver is inefficient at exciting propagating kink waves
Description: D.J.P. acknowledges financial support from STFC. I.D.M. acknowledges support of a Royal Society University Research Fellowship. The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/ 2007−2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).2015-06-01T00:00:00ZPascoe, David JamesWright, Andrew NicholasDe Moortel, InekeHood, Alan WilliamContext. Observations such as those by the Coronal Multi-Channel Polarimeter (CoMP) have revealed that broadband kink oscillations are ubiquitous in the solar corona. Aims. We consider footpoint-driven kink waves propagating in a low β coronal plasma with a cylindrical density structure. We investigate the excitation and damping of propagating kink waves by a broadband driver, including the effects of different spatial profiles for the driver. Methods. We employ a general spatial damping profile in which the initial stage of the damping envelope is approximated by a Gaussian profile and the asymptotic state by an exponential one. We develop a method of accounting for the presence of these different damping regimes and test it using data from numerical simulations. Results. Strongly damped oscillations in low density coronal loops are more accurately described by a Gaussian spatial damping profile than an exponential profile. The consequences for coronal seismology are investigated and applied to observational data for the ubiquitous broadband waves observed by CoMP. Current data cannot distinguish between the exponential and Gaussian profiles because of the levels of noise. We demonstrate the importance of the spatial profile of the driver on the resulting damping profile. Furthermore, we show that a small-scale turbulent driver is inefficient at exciting propagating kink wavesDeveloping and enhancing biodiversity monitoring programmes : a collaborative assessment of priorities
http://hdl.handle.net/10023/6756
Abstract: Biodiversity is changing at unprecedented rates, and it is increasingly important that these changes are quantified through monitoring programmes. Previous recommendations for developing or enhancing these programmes focus either on the end goals, that is the intended use of the data, or on how these goals are achieved, for example through volunteer involvement in citizen science, but not both. These recommendations are rarely prioritized. We used a collaborative approach, involving 52 experts in biodiversity monitoring in the UK, to develop a list of attributes of relevance to any biodiversity monitoring programme and to order these attributes by their priority. We also ranked the attributes according to their importance in monitoring biodiversity in the UK. Experts involved included data users, funders, programme organizers and participants in data collection. They covered expertise in a wide range of taxa. We developed a final list of 25 attributes of biodiversity monitoring schemes, ordered from the most elemental (those essential for monitoring schemes; e.g. articulate the objectives and gain sufficient participants) to the most aspirational (e.g. electronic data capture in the field, reporting change annually). This ordered list is a practical framework which can be used to support the development of monitoring programmes. People's ranking of attributes revealed a difference between those who considered attributes with benefits to end users to be most important (e.g. people from governmental organizations) and those who considered attributes with greatest benefit to participants to be most important (e.g. people involved with volunteer biological recording schemes). This reveals a distinction between focussing on aims and the pragmatism in achieving those aims. Synthesis and applications. The ordered list of attributes developed in this study will assist in prioritizing resources to develop biodiversity monitoring programmes (including citizen science). The potential conflict between end users of data and participants in data collection that we discovered should be addressed by involving the diversity of stakeholders at all stages of programme development. This will maximize the chance of successfully achieving the goals of biodiversity monitoring programmes.
Description: This work was supported by the UK Department for Environment, Food and Rural Affairs (Defra) [grant number WC1014] and the Natural Environment Research Council through National Capability funding to the Centre for Ecology and Hydrology.2015-06-01T00:00:00ZPocock, Michael J. O.Newson, Stuart E.Henderson, Ian G.Peyton, JodeySutherland, William J.Noble, David G.Ball, Stuart G.Beckmann, Björn C.Biggs, JeremyBrereton, TomBullock, David J.Buckland, Stephen T.Edwards, MikeEaton, Mark A.Harvey, Martin C.Hill, Mark O.Horlock, MartinHubble, David S.Julian, Angela M.Mackey, Edward C.Mann, Darren J.Marshall, Matthew J.Medlock, Jolyon M.O'Mahony, Elaine M.Pacheco, MarinaPorter, KeithPrentice, SteveProcter, Deborah A.Roy, Helen E.Southway, Sue E.Shortall, Chris R.Stewart, Alan J. A.Wembridge, David E.Wright, Mark A.Roy, David B.Biodiversity is changing at unprecedented rates, and it is increasingly important that these changes are quantified through monitoring programmes. Previous recommendations for developing or enhancing these programmes focus either on the end goals, that is the intended use of the data, or on how these goals are achieved, for example through volunteer involvement in citizen science, but not both. These recommendations are rarely prioritized. We used a collaborative approach, involving 52 experts in biodiversity monitoring in the UK, to develop a list of attributes of relevance to any biodiversity monitoring programme and to order these attributes by their priority. We also ranked the attributes according to their importance in monitoring biodiversity in the UK. Experts involved included data users, funders, programme organizers and participants in data collection. They covered expertise in a wide range of taxa. We developed a final list of 25 attributes of biodiversity monitoring schemes, ordered from the most elemental (those essential for monitoring schemes; e.g. articulate the objectives and gain sufficient participants) to the most aspirational (e.g. electronic data capture in the field, reporting change annually). This ordered list is a practical framework which can be used to support the development of monitoring programmes. People's ranking of attributes revealed a difference between those who considered attributes with benefits to end users to be most important (e.g. people from governmental organizations) and those who considered attributes with greatest benefit to participants to be most important (e.g. people involved with volunteer biological recording schemes). This reveals a distinction between focussing on aims and the pragmatism in achieving those aims. Synthesis and applications. The ordered list of attributes developed in this study will assist in prioritizing resources to develop biodiversity monitoring programmes (including citizen science). The potential conflict between end users of data and participants in data collection that we discovered should be addressed by involving the diversity of stakeholders at all stages of programme development. This will maximize the chance of successfully achieving the goals of biodiversity monitoring programmes.Bayesian methods for hierarchical distance sampling models
http://hdl.handle.net/10023/6714
Abstract: The few distance sampling studies that use Bayesian methods typically consider only line transect sampling with a half-normal detection function. We present a Bayesian approach to analyse distance sampling data applicable to line and point transects, exact and interval distance data and any detection function possibly including covariates affecting detection probabilities. We use an integrated likelihood which combines the detection and count models. For the latter, counts are related to covariates in a log-linear mixed effect Poisson model which accommodates correlated counts. We use a Metropolis-Hastings algorithm for updating parameters and a reversible jump algorithm to include model selection for both the detection function and count models. The approach is applied to a large-scale experimental design study of northern bobwhite coveys where the interest was to assess the effect of establishing herbaceous buffers around agricultural fields in several states in the US on bird densities. Results were compared with those from an existing maximum likelihood approach that analyses the detection and count models in two stages. Both methods revealed an increase of covey densities on buffered fields. Our approach gave estimates with higher precision even though it does not condition on a known detection function for the count model.
Description: Cornelia S. Oedekoven was supported by a studentship jointly funded by the University of St Andrews and EPSRC (EPSRC grant EP/C522702/1), through the National Centre for Statistical Ecology.2014-06-01T00:00:00ZOedekoven, Cornelia SabrinaBuckland, Stephen TerrenceMacKenzie, Monique LeaKing, RuthEvans, KristineBurger, WesThe few distance sampling studies that use Bayesian methods typically consider only line transect sampling with a half-normal detection function. We present a Bayesian approach to analyse distance sampling data applicable to line and point transects, exact and interval distance data and any detection function possibly including covariates affecting detection probabilities. We use an integrated likelihood which combines the detection and count models. For the latter, counts are related to covariates in a log-linear mixed effect Poisson model which accommodates correlated counts. We use a Metropolis-Hastings algorithm for updating parameters and a reversible jump algorithm to include model selection for both the detection function and count models. The approach is applied to a large-scale experimental design study of northern bobwhite coveys where the interest was to assess the effect of establishing herbaceous buffers around agricultural fields in several states in the US on bird densities. Results were compared with those from an existing maximum likelihood approach that analyses the detection and count models in two stages. Both methods revealed an increase of covey densities on buffered fields. Our approach gave estimates with higher precision even though it does not condition on a known detection function for the count model.Using accelerometers to determine the calling behavior of tagged baleen whales
http://hdl.handle.net/10023/6623
Abstract: Low-frequency acoustic signals generated by baleen whales can propagate over vast distances, making the assignment of calls to specific individuals problematic. Here, we report the novel use of acoustic recording tags equipped with high-resolution accelerometers to detect vibrations from the surface of two tagged fin whales that directly match the timing of recorded acoustic signals. A tag deployed on a buoy in the vicinity of calling fin whales and a recording from a tag that had just fallen off a whale were able to detect calls acoustically but did not record corresponding accelerometer signals that were measured on calling individuals. Across the hundreds of calls measured on two tagged fin whales, the accelerometer response was generally anisotropic across all three axes, appeared to depend on tag placement and increased with the level of received sound. These data demonstrate that high-sample rate accelerometry can provide important insights into the acoustic behavior of baleen whales that communicate at low frequencies. This method helps identify vocalizing whales, which in turn enables the quantification of call rates, a fundamental component of models used to estimate baleen whale abundance and distribution from passive acoustic monitoring.2014-07-15T00:00:00ZGoldbogen, JeremyDe Ruiter, Stacy LynnStimpert, AlisonCalambokidis, JohnFriedlaender, AriSchorr, GregMoretti, DavidTyack, Peter LloydSouthall, BrandonLow-frequency acoustic signals generated by baleen whales can propagate over vast distances, making the assignment of calls to specific individuals problematic. Here, we report the novel use of acoustic recording tags equipped with high-resolution accelerometers to detect vibrations from the surface of two tagged fin whales that directly match the timing of recorded acoustic signals. A tag deployed on a buoy in the vicinity of calling fin whales and a recording from a tag that had just fallen off a whale were able to detect calls acoustically but did not record corresponding accelerometer signals that were measured on calling individuals. Across the hundreds of calls measured on two tagged fin whales, the accelerometer response was generally anisotropic across all three axes, appeared to depend on tag placement and increased with the level of received sound. These data demonstrate that high-sample rate accelerometry can provide important insights into the acoustic behavior of baleen whales that communicate at low frequencies. This method helps identify vocalizing whales, which in turn enables the quantification of call rates, a fundamental component of models used to estimate baleen whale abundance and distribution from passive acoustic monitoring.The effect of animal movement on line transect estimates of abundance
http://hdl.handle.net/10023/6466
Abstract: Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.
Description: This work was supported by the University of St Andrews (http://www.st-andrews.ac.uk/; RG, STB, LT) and by a summer scholarship and PhD grant from The Carnegie Trust for the Universities of Scotland (http://www.carnegie-trust.org/) to RG.2015-03-23T00:00:00ZGlennie, R.Buckland, S.T.Thomas, L.Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.Mixture models for distance sampling detection functions
http://hdl.handle.net/10023/6463
Abstract: We present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.
Description: Funding: EPSRC DTG2015-03-20T00:00:00ZMiller, David LawrenceThomas, LenWe present a new class of models for the detection function in distance sampling surveys of wildlife populations, based on finite mixtures of simple parametric key functions such as the half-normal. The models share many of the features of the widely-used “key function plus series adjustment” (K+A) formulation: they are flexible, produce plausible shapes with a small number of parameters, allow incorporation of covariates in addition to distance and can be fitted using maximum likelihood. One important advantage over the K+A approach is that the mixtures are automatically monotonic non-increasing and non-negative, so constrained optimization is not required to ensure distance sampling assumptions are honoured. We compare the mixture formulation to the K+A approach using simulations to evaluate its applicability in a wide set of challenging situations. We also re-analyze four previously problematic real-world case studies. We find mixtures outperform K+A methods in many cases, particularly spiked line transect data (i.e., where detectability drops rapidly at small distances) and larger sample sizes. We recommend that current standard model selection methods for distance sampling detection functions are extended to include mixture models in the candidate set.Bayesian hierarchical modelling of continuous non-negative longitudinal data with a spike at zero : an application to a study of birds visiting gardens in winter
http://hdl.handle.net/10023/6164
Abstract: The development of methods for dealing with continuous data with a spike at zero has lagged behind those for overdispersed or zero-inflated count data. We consider longitudinal ecological data corresponding to an annual average of 26 weekly maximum counts of birds, and are hence effectively continuous, bounded below by zero but also with a discrete mass at zero. We develop a Bayesian hierarchical Tweedie regression model that can directly accommodate the excess number of zeros common to this type of data, whilst accounting for both spatial and temporal correlation. Implementation of the model is conducted in a Markov chain Monte Carlo (MCMC) framework, using reversible jump MCMC to explore uncertainty across both parameter and model spaces. This regression modelling framework is very flexible and removes the need to make strong assumptions about mean-variance relationships a priori. It can also directly account for the spike at zero, whilst being easily applicable to other types of data and other model formulations. Whilst a correlative study such as this cannot prove causation, our results suggest that an increase in an avian predator may have led to an overall decrease in the number of one of its prey species visiting garden feeding stations in the United Kingdom. This may reflect a change in behaviour of house sparrows to avoid feeding stations frequented by sparrowhawks, or a reduction in house sparrow population size as a result of sparrowhawk increase.2015-01-01T00:00:00ZSwallow, Benjamin ThomasBuckland, Stephen TerrenceKing, RuthToms, MikeThe development of methods for dealing with continuous data with a spike at zero has lagged behind those for overdispersed or zero-inflated count data. We consider longitudinal ecological data corresponding to an annual average of 26 weekly maximum counts of birds, and are hence effectively continuous, bounded below by zero but also with a discrete mass at zero. We develop a Bayesian hierarchical Tweedie regression model that can directly accommodate the excess number of zeros common to this type of data, whilst accounting for both spatial and temporal correlation. Implementation of the model is conducted in a Markov chain Monte Carlo (MCMC) framework, using reversible jump MCMC to explore uncertainty across both parameter and model spaces. This regression modelling framework is very flexible and removes the need to make strong assumptions about mean-variance relationships a priori. It can also directly account for the spike at zero, whilst being easily applicable to other types of data and other model formulations. Whilst a correlative study such as this cannot prove causation, our results suggest that an increase in an avian predator may have led to an overall decrease in the number of one of its prey species visiting garden feeding stations in the United Kingdom. This may reflect a change in behaviour of house sparrows to avoid feeding stations frequented by sparrowhawks, or a reduction in house sparrow population size as a result of sparrowhawk increase.Statistical ecology comes of age
http://hdl.handle.net/10023/6128
Abstract: The desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1 –4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.2014-12-24T00:00:00ZGimenez, OlivierBuckland, Stephen TerrenceMorgan, Byron J. T.Bez, NicolasBertrand, SophieChoquet, RemiDray, StephaneEtienne, Marie-PierreFewster, RachelGosselin, FredericMerigot, BastienMonestiez, PascalMorales, Juan M.Mortier, FredericMunoz, FrancoisOvaskainen, OtsoPavoine, SandrinePradel, RogerSchurr, Frank M.Thomas, LenThuiller, WilfriedTrenkel, Verenade Valpine, PerryRexstad, EricThe desire to predict the consequences of global environmental change has been the driver towards more realistic models embracing the variability and uncertainties inherent in ecology. Statistical ecology has gelled over the past decade as a discipline that moves away from describing patterns towards modelling the ecological processes that generate these patterns. Following the fourth International Statistical Ecology Conference (1 –4 July 2014) in Montpellier, France, we analyse current trends in statistical ecology. Important advances in the analysis of individual movement, and in the modelling of population dynamics and species distributions, are made possible by the increasing use of hierarchical and hidden process models. Exciting research perspectives include the development of methods to interpret citizen science data and of efficient, flexible computational algorithms for model fitting. Statistical ecology has come of age: it now provides a general and mathematically rigorous framework linking ecological theory and empirical data.Statistical evidence for the existence of Alfvénic turbulence in solar coronal loops
http://hdl.handle.net/10023/5987
Abstract: Recent observations have demonstrated that waves capable of carrying large amounts of energy are ubiquitous throughout the solar corona. However, the question of how this wave energy is dissipated (on which timescales and length scales) and released into the plasma remains largely unanswered. Both analytic and numerical models have previously shown that Alfvénic turbulence may play a key role not only in the generation of the fast solar wind, but in the heating of coronal loops. In an effort to bridge the gap between theory and observations, we expand on a recent study by analyzing 37 clearly isolated coronal loops using data from the Coronal Multi-channel Polarimeter instrument.We observe Alfvénic perturbations with phase speeds which range from 250 to 750 km s-1 and periods from 140 to 270 s for the chosen loops. While excesses of high-frequency wave power are observed near the apex of some loops (tentatively supporting the onset of Alfvénic turbulence), we show that this excess depends on loop length and the wavelength of the observed oscillations. In deriving a proportional relationship between the loop length/wavelength ratio and the enhanced wave power at the loop apex, and from the analysis of the line widths associated with these loops, our findings are supportive of the existence of Alfvénic turbulence in coronal loops.
Description: The authors acknowledge support from NASA contracts NNX08BA99G, NNX11AN98G, NNM12AB40P, NNG09FA40C (IRIS), and NNM07AA01C (Hinode). The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).2014-12-10T00:00:00ZLiu, J.Mcintosh, S.W.De Moortel, I.Threlfall, J.Bethge, C.Recent observations have demonstrated that waves capable of carrying large amounts of energy are ubiquitous throughout the solar corona. However, the question of how this wave energy is dissipated (on which timescales and length scales) and released into the plasma remains largely unanswered. Both analytic and numerical models have previously shown that Alfvénic turbulence may play a key role not only in the generation of the fast solar wind, but in the heating of coronal loops. In an effort to bridge the gap between theory and observations, we expand on a recent study by analyzing 37 clearly isolated coronal loops using data from the Coronal Multi-channel Polarimeter instrument.We observe Alfvénic perturbations with phase speeds which range from 250 to 750 km s-1 and periods from 140 to 270 s for the chosen loops. While excesses of high-frequency wave power are observed near the apex of some loops (tentatively supporting the onset of Alfvénic turbulence), we show that this excess depends on loop length and the wavelength of the observed oscillations. In deriving a proportional relationship between the loop length/wavelength ratio and the enhanced wave power at the loop apex, and from the analysis of the line widths associated with these loops, our findings are supportive of the existence of Alfvénic turbulence in coronal loops.Analysing mark-recapture-recovery data in the presence of missing covariate data via multiple imputation
http://hdl.handle.net/10023/5932
Abstract: We consider mark–recapture–recovery data with additional individual time-varying continuous covariate data. For such data it is common to specify the model parameters, and in particular the survival probabilities, as a function of these covariates to incorporate individual heterogeneity. However, an issue arises in relation to missing covariate values, for (at least) the times when an individual is not observed, leading to an analytically intractable likelihood. We propose a two-step multiple imputation approach to obtain estimates of the demographic parameters. Firstly, a model is fitted to only the observed covariate values. Conditional on the fitted covariate model, multiple “complete” datasets are generated (i.e. all missing covariate values are imputed). Secondly, for each complete dataset, a closed form complete data likelihood can be maximised to obtain estimates of the model parameters which are subsequently combined to obtain an overall estimate of the parameters. Associated standard errors and 95 % confidence intervals are obtained using a non-parametric bootstrap. A simulation study is undertaken to assess the performance of the proposed two-step approach. We apply the method to data collected on a well-studied population of Soay sheep and compare the results with a Bayesian data augmentation approach. Supplementary materials accompanying this paper appear on-line.2015-03-01T00:00:00ZWorthington, HannahKing, RuthBuckland, Stephen TerrenceWe consider mark–recapture–recovery data with additional individual time-varying continuous covariate data. For such data it is common to specify the model parameters, and in particular the survival probabilities, as a function of these covariates to incorporate individual heterogeneity. However, an issue arises in relation to missing covariate values, for (at least) the times when an individual is not observed, leading to an analytically intractable likelihood. We propose a two-step multiple imputation approach to obtain estimates of the demographic parameters. Firstly, a model is fitted to only the observed covariate values. Conditional on the fitted covariate model, multiple “complete” datasets are generated (i.e. all missing covariate values are imputed). Secondly, for each complete dataset, a closed form complete data likelihood can be maximised to obtain estimates of the model parameters which are subsequently combined to obtain an overall estimate of the parameters. Associated standard errors and 95 % confidence intervals are obtained using a non-parametric bootstrap. A simulation study is undertaken to assess the performance of the proposed two-step approach. We apply the method to data collected on a well-studied population of Soay sheep and compare the results with a Bayesian data augmentation approach. Supplementary materials accompanying this paper appear on-line.Backward wave cyclotron-maser emission in the auroral magnetosphere
http://hdl.handle.net/10023/5802
Abstract: In this Letter, we present theory and particle-in-cell simulations describing cyclotron radio emission from Earth's auroral region and similar phenomena in other astrophysical environments. In particular, we find that the radiation, generated by a down-going electron horseshoe distribution is due to a backward wave cyclotron-maser emission process. The backward wave nature of the radiation contributes to upward refraction of the radiation that is also enhanced by a density inhomogeneity. We also show that the radiation is preferentially amplified along the auroral oval rather than transversely. The results are in agreement with recent Cluster observations.
Description: This work was supported by EPSRC Grant No. EP/G04239X/1.2014-10-07T00:00:00ZSpeirs, D. C.Bingham, R.Cairns, R. A.Vorgul, I.Kellett, B. J.Phelps, A. D. R.Ronald, K.In this Letter, we present theory and particle-in-cell simulations describing cyclotron radio emission from Earth's auroral region and similar phenomena in other astrophysical environments. In particular, we find that the radiation, generated by a down-going electron horseshoe distribution is due to a backward wave cyclotron-maser emission process. The backward wave nature of the radiation contributes to upward refraction of the radiation that is also enhanced by a density inhomogeneity. We also show that the radiation is preferentially amplified along the auroral oval rather than transversely. The results are in agreement with recent Cluster observations.A unifying model for capture-recapture and distance sampling surveys of wildlife populations
http://hdl.handle.net/10023/5797
Abstract: Spatially explicit capture-recapture (SECR) methods extend traditional capture-recapture methods for estimating population density by using information contained in the location of traps. The The central feature of the improvement is estimation from the locations of traps at which animals were and were not captured to estimate of the distance over which animals are susceptible to capture. We show that standard SECR models are a special case of a more general class of model in which animal detection is not certain, but some information is available about the location of detected animals. The model class accommodates a range of spatial data types and includes as a special case mark-recapture distance sampling, where distances to detected animals are recorded by multiple observers. Other examples of additional information that can be included are bearing to detected animals, strength of acoustic signals received from detected animals, and time of arrival of acoustic signals at detectors. Errors in variables are easily incorporated. We illustrate the versatility of the model and method through a number of applications, in each case using real and simulated data, and comparing our results with those from previous studies where these are available.
Description: Funding: Part-funded by Fundacao Nacional para a Cienca e Technologia, Portugal (FCT) under the project PEst OE/MAT/UI0006/2011 (Marques) and the UK Engineering and Physical Sciences Research Council EP/I000917/12015-01-01T00:00:00ZBorchers, D. L.Stevenson, B.C.Kidney, D.Thomas, L.Marques, T.A.Spatially explicit capture-recapture (SECR) methods extend traditional capture-recapture methods for estimating population density by using information contained in the location of traps. The The central feature of the improvement is estimation from the locations of traps at which animals were and were not captured to estimate of the distance over which animals are susceptible to capture. We show that standard SECR models are a special case of a more general class of model in which animal detection is not certain, but some information is available about the location of detected animals. The model class accommodates a range of spatial data types and includes as a special case mark-recapture distance sampling, where distances to detected animals are recorded by multiple observers. Other examples of additional information that can be included are bearing to detected animals, strength of acoustic signals received from detected animals, and time of arrival of acoustic signals at detectors. Errors in variables are easily incorporated. We illustrate the versatility of the model and method through a number of applications, in each case using real and simulated data, and comparing our results with those from previous studies where these are available.Acoustic and foraging behavior of a Baird’s beaked whale, Berardius bairdii, exposed to simulated sonar
http://hdl.handle.net/10023/5787
Abstract: Beaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe the underwater behavior of a Baird's beaked whale (Berardius bairdii) from the first deployment of a multi-sensor acoustic tag on this species. The animal exhibited shallow (23 ± 15 m max depth), intermediate (324 ± 49 m), and deep (1138 ± 243 m) dives. Echolocation clicks were produced with a mean inter-click interval of approximately 300 ms and peak frequency of 25 kHz. Two deep dives included presumed foraging behavior, with echolocation pulsed sounds (presumed prey capture attempts) associated with increased maneuvering, and sustained inverted swimming during the bottom phase of the dive. A controlled exposure to simulated mid-frequency active sonar (3.5–4 kHz) was conducted 4 hours after tag deployment, and within 3 minutes of exposure onset, the tagged whale increased swim speed and body movement, and continued to show unusual dive behavior for each of its next three dives, one of each type. These are the first data on the acoustic foraging behavior in this largest beaked whale species, and the first experimental demonstration of a response to simulated sonar.
Description: Research was supported by the US Navy Chief of Naval Operations, Environmental Readiness Program, the Office of Naval Research, the Naval Postgraduate School, and the National Research Council.2014-11-13T00:00:00ZStimpert, AlisonDe Ruiter, Stacy LynnSouthall, BrandonMoretti, DavidFalcone, ErinGoldbogen, JeremyFriedlaender, AriSchorr, GregCalambokidis, JohnBeaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe the underwater behavior of a Baird's beaked whale (Berardius bairdii) from the first deployment of a multi-sensor acoustic tag on this species. The animal exhibited shallow (23 ± 15 m max depth), intermediate (324 ± 49 m), and deep (1138 ± 243 m) dives. Echolocation clicks were produced with a mean inter-click interval of approximately 300 ms and peak frequency of 25 kHz. Two deep dives included presumed foraging behavior, with echolocation pulsed sounds (presumed prey capture attempts) associated with increased maneuvering, and sustained inverted swimming during the bottom phase of the dive. A controlled exposure to simulated mid-frequency active sonar (3.5–4 kHz) was conducted 4 hours after tag deployment, and within 3 minutes of exposure onset, the tagged whale increased swim speed and body movement, and continued to show unusual dive behavior for each of its next three dives, one of each type. These are the first data on the acoustic foraging behavior in this largest beaked whale species, and the first experimental demonstration of a response to simulated sonar.The nature of separator current layers in MHS equilibria I. Current parallel to the separator
http://hdl.handle.net/10023/5785
Abstract: Separators, which are in many ways the three-dimensional equivalent to two-dimensional nulls, are important sites for magnetic reconnection. Magnetic reconnection occurs in strong current layers which have very short length scales. The aim of this work is to explore the nature of current layers around separators. A separator is a special field line which lies along the intersection of two separatrix surfaces and forms the boundary between four topologically distinct flux domains. In particular, here the current layer about a separator that joins two 3D nulls and lies along the intersection of their separatrix surfaces is investigated. A magnetic configuration containing a single separator embedded in a uniform plasma with a uniform electric current parallel to the separator is considered. This initial magnetic setup, which is not in equilibrium, relaxes in a non-resistive manner to form an equilibrium. The relaxation is achieved using the 3D MHD code, Lare3d, with resistivity set to zero. A series of experiments with varying initial current are run to investigate the characteristics of the resulting current layers present in the final (quasi-) equilibrium states. In each experiment, the separator collapses and a current layer forms along it. The dimensions and strength of the current layer increase with initial current. It is found that separator current layers formed from current parallel to the separator are twisted. Also the collapse of the separator is a process that evolves like an infinite-time singularity where the length, width and peak current in the layer grow slowly whilst the depth of the current layer decreases.
Description: JEHS would like to thank STFC for financial support during her Ph.D and CEP acknowledges support from the STFC consolidated grant.2015-01-01T00:00:00ZStevenson, Julie Elizabeth HelenParnell, Clare ElizabethPriest, Eric RonaldHaynes, Andrew LewisSeparators, which are in many ways the three-dimensional equivalent to two-dimensional nulls, are important sites for magnetic reconnection. Magnetic reconnection occurs in strong current layers which have very short length scales. The aim of this work is to explore the nature of current layers around separators. A separator is a special field line which lies along the intersection of two separatrix surfaces and forms the boundary between four topologically distinct flux domains. In particular, here the current layer about a separator that joins two 3D nulls and lies along the intersection of their separatrix surfaces is investigated. A magnetic configuration containing a single separator embedded in a uniform plasma with a uniform electric current parallel to the separator is considered. This initial magnetic setup, which is not in equilibrium, relaxes in a non-resistive manner to form an equilibrium. The relaxation is achieved using the 3D MHD code, Lare3d, with resistivity set to zero. A series of experiments with varying initial current are run to investigate the characteristics of the resulting current layers present in the final (quasi-) equilibrium states. In each experiment, the separator collapses and a current layer forms along it. The dimensions and strength of the current layer increase with initial current. It is found that separator current layers formed from current parallel to the separator are twisted. Also the collapse of the separator is a process that evolves like an infinite-time singularity where the length, width and peak current in the layer grow slowly whilst the depth of the current layer decreases.The probability of generating a finite simple group
http://hdl.handle.net/10023/5658
Abstract: We study the probability of generating a finite simple group, together with its generalisation PG,socG(d), the conditional probability of generating an almost simple finite group G by d elements, given that these elements generate G/ socG. We prove that PG,socG(2) ⩾ 53/90, with equality if and only if G is A6 or S6, and establish a similar result for PG,socG(3). Positive answers to longstanding questions of Wiegold on direct products, and of Mel’nikov on profinite groups, follow easily from our results.2013-11-01T00:00:00ZMenezes, Nina EmmaQuick, MartynRoney-Dougal, Colva MaryWe study the probability of generating a finite simple group, together with its generalisation PG,socG(d), the conditional probability of generating an almost simple finite group G by d elements, given that these elements generate G/ socG. We prove that PG,socG(2) ⩾ 53/90, with equality if and only if G is A6 or S6, and establish a similar result for PG,socG(3). Positive answers to longstanding questions of Wiegold on direct products, and of Mel’nikov on profinite groups, follow easily from our results.The cooling of coronal plasmas. IV. Catastrophic cooling of loops
http://hdl.handle.net/10023/5503
Abstract: We examine the radiative cooling of coronal loops and demonstrate that the recently identified catastrophic cooling is due to the inability of a loop to sustain radiative/enthalpy cooling below a critical temperature, which can be >1 MK in flares, 0.5-1 MK in active regions, and 0.1 MK in long tenuous loops. Catastrophic cooling is characterized by a rapid fall in coronal temperature, while the coronal density changes by a small amount. Analytic expressions for the critical temperature are derived and show good agreement with numerical results. This effect considerably limits the lifetime of coronal plasmas below the critical temperature.2013-07-20T00:00:00ZCargill, P.J.Bradshaw, S.J.We examine the radiative cooling of coronal loops and demonstrate that the recently identified catastrophic cooling is due to the inability of a loop to sustain radiative/enthalpy cooling below a critical temperature, which can be >1 MK in flares, 0.5-1 MK in active regions, and 0.1 MK in long tenuous loops. Catastrophic cooling is characterized by a rapid fall in coronal temperature, while the coronal density changes by a small amount. Analytic expressions for the critical temperature are derived and show good agreement with numerical results. This effect considerably limits the lifetime of coronal plasmas below the critical temperature.Recurrent explosive eruptions and the "sigmoid-to-arcade" transformation in the Sun driven by dynamical magnetic flux emergence
http://hdl.handle.net/10023/5319
Abstract: We report on three-dimensional MHD simulations of recurrent mini coronal mass ejection (CME)-like eruptions in a small active region (AR), which is formed by the dynamical emergence of a twisted (not kink unstable) flux tube from the solar interior. The eruptions develop as a result of the repeated formation and expulsion of new flux ropes due to continuous emergence and reconnection of sheared field lines along the polarity inversion line of the AR. The acceleration of the eruptions is triggered by tether-cutting reconnection at the current sheet underneath the erupting field. We find that each explosive eruption is followed by reformation of a sigmoidal structure and a subsequent "sigmoid-to-flare arcade" transformation in the AR. These results might have implications for recurrent CMEs and eruptive sigmoids/flares observations and theoretical studies.
Description: The authors acknowledge support by EU (IEF-272549 grant) and the Royal Society.2014-05-10T00:00:00ZArchontis, V.Hood, A.W.Tsinganos, K.We report on three-dimensional MHD simulations of recurrent mini coronal mass ejection (CME)-like eruptions in a small active region (AR), which is formed by the dynamical emergence of a twisted (not kink unstable) flux tube from the solar interior. The eruptions develop as a result of the repeated formation and expulsion of new flux ropes due to continuous emergence and reconnection of sheared field lines along the polarity inversion line of the AR. The acceleration of the eruptions is triggered by tether-cutting reconnection at the current sheet underneath the erupting field. We find that each explosive eruption is followed by reformation of a sigmoidal structure and a subsequent "sigmoid-to-flare arcade" transformation in the AR. These results might have implications for recurrent CMEs and eruptive sigmoids/flares observations and theoretical studies.Observations of a hybrid double-streamer/pseudostreamer in the solar corona
http://hdl.handle.net/10023/5318
Abstract: We report on the first observation of a single hybrid magnetic structure that contains both a pseudostreamer and a double streamer. This structure was originally observed by the SWAP instrument on board the PROBA2 satellite between 2013 May 5 and 10. It consists of a pair of filament channels near the south pole of the Sun. On the western edge of the structure, the magnetic morphology above the filaments is that of a side-by-side double streamer, with open field between the two channels. On the eastern edge, the magnetic morphology is that of a coronal pseudostreamer without the central open field. We investigated this structure with multiple observations and modeling techniques. We describe the topology and dynamic consequences of such a unified structure.
Description: D.B.S. and L.A.R. acknowledge support from the Belgian Federal Science Policy Office (BELSPO) through the ESA-PRODEX program, grant No. 4000103240. S.J.P. acknowledges the financial support of the Isle of Man Government.2014-05-20T00:00:00ZRachmeler, L.A.Platten, S.J.Bethge, C.Seaton, D.B.Yeates, A.R.We report on the first observation of a single hybrid magnetic structure that contains both a pseudostreamer and a double streamer. This structure was originally observed by the SWAP instrument on board the PROBA2 satellite between 2013 May 5 and 10. It consists of a pair of filament channels near the south pole of the Sun. On the western edge of the structure, the magnetic morphology above the filaments is that of a side-by-side double streamer, with open field between the two channels. On the eastern edge, the magnetic morphology is that of a coronal pseudostreamer without the central open field. We investigated this structure with multiple observations and modeling techniques. We describe the topology and dynamic consequences of such a unified structure.Active region emission measure distributions and implications for nanoflare heating
http://hdl.handle.net/10023/5305
Abstract: The temperature dependence of the emission measure (EM) in the core of active regions coronal loops is an important diagnostic of heating processes. Observations indicate that EM(T) ~ T a below approximately 4 MK, with 2 < a < 5. Zero-dimensional hydrodynamic simulations of nanoflare trains are used to demonstrate the dependence of a on the time between individual nanoflares (NT) and the distribution of nanoflare energies. If TN is greater than a few thousand seconds, a < 3. For smaller values, trains of equally spaced nanoflares cannot account for the observed range of a if the distribution of nanoflare energies is either constant, randomly distributed, or a power law. Power law distributions where there is a delay between consecutive nanoflares proportional to the energy of the second nanoflare do lead to the observed range of a. However, TN must then be of the order of hundreds to no more than a few thousand seconds. If a nanoflare leads to the relaxation of a stressed coronal field to a near-potential state, the time taken to build up the required magnetic energy is thus too long to account for the EM measurements. Instead, it is suggested that a nanoflare involves the relaxation from one stressed coronal state to another, dissipating only a small fraction of the available magnetic energy. A consequence is that nanoflare energies may be smaller than previously envisioned.2014-03-20T00:00:00ZCargill, P.J.The temperature dependence of the emission measure (EM) in the core of active regions coronal loops is an important diagnostic of heating processes. Observations indicate that EM(T) ~ T a below approximately 4 MK, with 2 < a < 5. Zero-dimensional hydrodynamic simulations of nanoflare trains are used to demonstrate the dependence of a on the time between individual nanoflares (NT) and the distribution of nanoflare energies. If TN is greater than a few thousand seconds, a < 3. For smaller values, trains of equally spaced nanoflares cannot account for the observed range of a if the distribution of nanoflare energies is either constant, randomly distributed, or a power law. Power law distributions where there is a delay between consecutive nanoflares proportional to the energy of the second nanoflare do lead to the observed range of a. However, TN must then be of the order of hundreds to no more than a few thousand seconds. If a nanoflare leads to the relaxation of a stressed coronal field to a near-potential state, the time taken to build up the required magnetic energy is thus too long to account for the EM measurements. Instead, it is suggested that a nanoflare involves the relaxation from one stressed coronal state to another, dissipating only a small fraction of the available magnetic energy. A consequence is that nanoflare energies may be smaller than previously envisioned.The solar cycle variation of topological structures in the global solar corona
http://hdl.handle.net/10023/5271
Abstract: Context. The complicated distribution of magnetic flux across the solar photosphere results in a complex web of coronal magnetic field structures. To understand this complexity, the magnetic skeleton of the coronal field can be calculated. The skeleton highlights the (separatrix) surfaces that divide the field into topologically distinct regions, allowing open-field regions on the solar surface to be located. Furthermore, separatrix surfaces and their intersections with other separatrix surfaces (i.e., separators) are important likely energy release sites. Aims. The aim of this paper is to investigate, throughout the solar cycle, the nature of coronal magnetic-field topologies that arise under the potential-field source-surface approximation. In particular, we characterise the typical global fields at solar maximum and minimum. Methods. Global magnetic fields are extrapolated from observed Kitt Peak and SOLIS synoptic magnetograms, from Carrington rotations 1645 to 2144, using the potential-field source-surface model. This allows the variations in the coronal skeleton to be studied over three solar cycles. Results. The main building blocks which make up magnetic fields are identified and classified according to the nature of their separatrix surfaces. The magnetic skeleton reveals that, at solar maximum, the global coronal field involves a multitude of topological structures at all latitudes criss-crossing throughout the atmosphere. Many open-field regions exist originating anywhere on the photosphere. At solar minimum, the coronal topology is heavily influenced by the solar magnetic dipole. A strong dipole results in a simple large-scale structure involving just two large polar open-field regions, but, at short radial distances between ± 60° latitude, the small-scale topology is complex. If the solar magnetic dipole if weak, as in the recent minimum, then the low-latitude quiet-sun magnetic fields may be globally significant enough to create many disconnected open-field regions between ± 60° latitude, in addition to the two polar open-field regions.
Description: S.J.P. acknowledges financial support from the Isle of Man Government. E.R.P. is grateful to the Leverhulme Trust for his emeritus fellowship. The research leading to these results has received funding from the European Commission’s Seventh Framework Programme (FP7/2007-2013) under the grant agreement SWIFF (project No. 263340, www.swiff.eu).2014-05-01T00:00:00ZPlatten, S.J.Parnell, C.E.Haynes, A.L.Priest, E.R.MacKay, D.H.Context. The complicated distribution of magnetic flux across the solar photosphere results in a complex web of coronal magnetic field structures. To understand this complexity, the magnetic skeleton of the coronal field can be calculated. The skeleton highlights the (separatrix) surfaces that divide the field into topologically distinct regions, allowing open-field regions on the solar surface to be located. Furthermore, separatrix surfaces and their intersections with other separatrix surfaces (i.e., separators) are important likely energy release sites. Aims. The aim of this paper is to investigate, throughout the solar cycle, the nature of coronal magnetic-field topologies that arise under the potential-field source-surface approximation. In particular, we characterise the typical global fields at solar maximum and minimum. Methods. Global magnetic fields are extrapolated from observed Kitt Peak and SOLIS synoptic magnetograms, from Carrington rotations 1645 to 2144, using the potential-field source-surface model. This allows the variations in the coronal skeleton to be studied over three solar cycles. Results. The main building blocks which make up magnetic fields are identified and classified according to the nature of their separatrix surfaces. The magnetic skeleton reveals that, at solar maximum, the global coronal field involves a multitude of topological structures at all latitudes criss-crossing throughout the atmosphere. Many open-field regions exist originating anywhere on the photosphere. At solar minimum, the coronal topology is heavily influenced by the solar magnetic dipole. A strong dipole results in a simple large-scale structure involving just two large polar open-field regions, but, at short radial distances between ± 60° latitude, the small-scale topology is complex. If the solar magnetic dipole if weak, as in the recent minimum, then the low-latitude quiet-sun magnetic fields may be globally significant enough to create many disconnected open-field regions between ± 60° latitude, in addition to the two polar open-field regions.Resistive magnetohydrodynamic reconnection : resolving long-term, chaotic dynamics
http://hdl.handle.net/10023/5233
Abstract: In this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.
Description: We acknowledge financial support from the EC FP7/2007-2013 Grant Agreement SWIFF (No. 263340) and from project GOA/2009/009 (KU Leuven). This research has been funded by the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office (IAP P7/08 CHARM). Part of the simulations used the infrastructure of the VSC-Flemish Supercomputer Center, funded by the Hercules Foundation and the Flemish Government-Department EWI. Another part of the simulations was done at the former Danish Center for Scientific Computing at Copenhagen University which is now part of DeIC Danish e-Infrastructure Cooperation.2013-09-13T00:00:00ZKeppens, R.Porth, O.Galsgaard, K.Frederiksen, J.T.Restante, A.L.Lapenta, G.Parnell, C.In this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.Effect of collisions on amplification of laser beams by Brillouin scattering in plasmas
http://hdl.handle.net/10023/5173
Abstract: We report on particle in cell simulations of energy transfer between a laser pump beam and a counter-propagating seed beam using the Brillouin scattering process in uniform plasma including collisions. The results presented show that the ion acoustic waves excited through naturally occurring Brillouin scattering of the pump field are preferentially damped without affecting the driven Brillouin scattering process resulting from the beating of the pump and seed fields together. We find that collisions, including the effects of Landau damping, allow for a more efficient transfer of energy between the laser beams, and a significant reduction in the amount of seed pre-pulse produced.
Description: Authors KH, RT, DCS, RAC, RB were supported by EPSRC grant EP/G04239X/1.2013-10-01T00:00:00ZHumphrey, K. A.Trines, R. M. G. M.Fiuza, F.Speirs, D. C.Norreys, P.Cairns, R. A.Silva, L. O.Bingham, R.We report on particle in cell simulations of energy transfer between a laser pump beam and a counter-propagating seed beam using the Brillouin scattering process in uniform plasma including collisions. The results presented show that the ion acoustic waves excited through naturally occurring Brillouin scattering of the pump field are preferentially damped without affecting the driven Brillouin scattering process resulting from the beating of the pump and seed fields together. We find that collisions, including the effects of Landau damping, allow for a more efficient transfer of energy between the laser beams, and a significant reduction in the amount of seed pre-pulse produced.First comparison of wave observations from CoMP and AIA/SDO
http://hdl.handle.net/10023/5153
Abstract: Context. Waves have long been thought to contribute to the heating of the solar corona and the generation of the solar wind. Recent observations have demonstrated evidence of quasi-periodic longitudinal disturbances and ubiquitous transverse wave propagation in many different coronal environments. Aims. This paper investigates signatures of different types of oscillatory behaviour, both above the solar limb and on-disk, by comparing findings from the Coronal Multi-channel Polarimeter (CoMP) and the Atmospheric Imaging Assembly (AIA) on-board the Solar Dynamics Observatory (SDO) for the same active region. Methods. We study both transverse and longitudinal motion by comparing and contrasting time-distance images of parallel and perpendicular cuts along/across active region fan loops. Comparisons between parallel space-time diagram features in CoMP Doppler velocity and transverse oscillations in AIA images are made, together with space-time analysis of propagating quasi-periodic intensity features seen near the base of loops in AIA. Results. Signatures of transverse motions are observed along the same magnetic structure using CoMP Doppler velocity (vphase = 600 → 750 km s-1, P = 3 → 6 min) and in AIA/SDO above the limb (P = 3 → 8 min). Quasi-periodic intensity features (vphase = 100 → 200 km s-1, P = 6 → 11 min) also travel along the base of the same structure. On the disk, signatures of both transverse and longitudinal intensity features were observed by AIA, and both show similar properties to signatures found along structures anchored in the same active region three days earlier above the limb. Correlated features are recovered by space-time analysis of neighbouring tracks over perpendicular distances of ≲2.6 Mm.
Description: I.D.M. acknowledges support of a Royal Society University Research Fellowship. The research leading to these results has also received funding from the European Commission Seventh Framework Programme (FP7/2007-2013) under the grant agreements SOLSPANET (project No. 269299, www.solspanet.eu/solspanet).2013-08-01T00:00:00ZThrelfall, James WilliamDe Moortel, InekeMcIntosh, ScottBethge, ChristianContext. Waves have long been thought to contribute to the heating of the solar corona and the generation of the solar wind. Recent observations have demonstrated evidence of quasi-periodic longitudinal disturbances and ubiquitous transverse wave propagation in many different coronal environments. Aims. This paper investigates signatures of different types of oscillatory behaviour, both above the solar limb and on-disk, by comparing findings from the Coronal Multi-channel Polarimeter (CoMP) and the Atmospheric Imaging Assembly (AIA) on-board the Solar Dynamics Observatory (SDO) for the same active region. Methods. We study both transverse and longitudinal motion by comparing and contrasting time-distance images of parallel and perpendicular cuts along/across active region fan loops. Comparisons between parallel space-time diagram features in CoMP Doppler velocity and transverse oscillations in AIA images are made, together with space-time analysis of propagating quasi-periodic intensity features seen near the base of loops in AIA. Results. Signatures of transverse motions are observed along the same magnetic structure using CoMP Doppler velocity (vphase = 600 → 750 km s-1, P = 3 → 6 min) and in AIA/SDO above the limb (P = 3 → 8 min). Quasi-periodic intensity features (vphase = 100 → 200 km s-1, P = 6 → 11 min) also travel along the base of the same structure. On the disk, signatures of both transverse and longitudinal intensity features were observed by AIA, and both show similar properties to signatures found along structures anchored in the same active region three days earlier above the limb. Correlated features are recovered by space-time analysis of neighbouring tracks over perpendicular distances of ≲2.6 Mm.Fitting models of multiple-hypotheses to partial population data : investigating the causes of cycles in red grouse
http://hdl.handle.net/10023/5119
Abstract: There are two postulated causes for the observed periodic fluctuations (cycles) in red grouse (Lagopus lagopus scoticus). The first involves interaction with the parasitic nematode Trichostrongylus tenuis. The second invokes delayed regulation through the effect of male aggressiveness on territoriality. Empirical evidence exists to support both hypotheses, and each hypothesis has been modeled deterministically. However, little effort has gone into looking at the combined effects of the two mechanisms or formally fitting the corresponding models to field data. Here we present a model for red grouse dynamics that includes both parasites and territoriality. To explore the single and combined hypotheses, we specify three versions of this model and fit them to data using Bayesian state-space modeling, a method that allows statistical inference to be performed on mechanistic models such as ours. Output from the three models is then examined to determine their goodness of fit and the biological plausibility of the parameter values required by each to fit the population data. While all three models are capable of emulating the observed cyclic dynamics, only the model including both aggression and parasites does so under consistently realistic parameter values, providing theoretical support for the idea that both mechanisms shape red grouse cycles.2009-09-01T00:00:00ZNew, LMatthiopoulos, JasonRedpath, SBuckland, Stephen TerrenceThere are two postulated causes for the observed periodic fluctuations (cycles) in red grouse (Lagopus lagopus scoticus). The first involves interaction with the parasitic nematode Trichostrongylus tenuis. The second invokes delayed regulation through the effect of male aggressiveness on territoriality. Empirical evidence exists to support both hypotheses, and each hypothesis has been modeled deterministically. However, little effort has gone into looking at the combined effects of the two mechanisms or formally fitting the corresponding models to field data. Here we present a model for red grouse dynamics that includes both parasites and territoriality. To explore the single and combined hypotheses, we specify three versions of this model and fit them to data using Bayesian state-space modeling, a method that allows statistical inference to be performed on mechanistic models such as ours. Output from the three models is then examined to determine their goodness of fit and the biological plausibility of the parameter values required by each to fit the population data. While all three models are capable of emulating the observed cyclic dynamics, only the model including both aggression and parasites does so under consistently realistic parameter values, providing theoretical support for the idea that both mechanisms shape red grouse cycles.conting : an R package for Bayesian analysis of complete and incomplete contingency tables
http://hdl.handle.net/10023/5050
Abstract: The aim of this paper is to demonstrate the R package conting for the Bayesian analysis of complete and incomplete contingency tables using hierarchical log-linear models. This package allows a user to identify interactions between categorical factors (via complete contingency tables) and to estimate closed population sizes using capture-recapture studies (via incomplete contingency tables). The models are fitted using Markov chain Monte Carlo methods. In particular, implementations of the Metropolis-Hastings and reversible jump algorithms appropriate for log-linear models are employed. The conting package is demonstrated on four real examples.2014-06-01T00:00:00ZOverstall, AntonyKing, RuthThe aim of this paper is to demonstrate the R package conting for the Bayesian analysis of complete and incomplete contingency tables using hierarchical log-linear models. This package allows a user to identify interactions between categorical factors (via complete contingency tables) and to estimate closed population sizes using capture-recapture studies (via incomplete contingency tables). The models are fitted using Markov chain Monte Carlo methods. In particular, implementations of the Metropolis-Hastings and reversible jump algorithms appropriate for log-linear models are employed. The conting package is demonstrated on four real examples.Using hidden Markov models to deal with availability bias on line transect surveys
http://hdl.handle.net/10023/5017
Abstract: We develop estimators for line transect surveys of animals that are stochastically unavailable for detection while within detection range. The detection process is formulated as a hidden Markov model with a binary state-dependent observation model that depends on both perpendicular and forward distances. This provides a parametric method of dealing with availability bias when estimates of availability process parameters are available even if series of availability events themselves are not. We apply the estimators to an aerial and a shipboard survey of whales, and investigate their properties by simulation. They are shown to be more general and more flexible than existing estimators based on parametric models of the availability process. We also find that methods using availability correction factors can be very biased when surveys are not close to being instantaneous, as can estimators that assume temporal independence in availability when there is temporal dependence.
Description: This work was supported by EPSRC grant EP/I000917/12013-01-01T00:00:00ZBorchers, David LouisZucchini, WalterHeide-Jørgensen, M.P.Cañadas, A.Langrock, RolandWe develop estimators for line transect surveys of animals that are stochastically unavailable for detection while within detection range. The detection process is formulated as a hidden Markov model with a binary state-dependent observation model that depends on both perpendicular and forward distances. This provides a parametric method of dealing with availability bias when estimates of availability process parameters are available even if series of availability events themselves are not. We apply the estimators to an aerial and a shipboard survey of whales, and investigate their properties by simulation. They are shown to be more general and more flexible than existing estimators based on parametric models of the availability process. We also find that methods using availability correction factors can be very biased when surveys are not close to being instantaneous, as can estimators that assume temporal independence in availability when there is temporal dependence.J J Thomson and the Discovery of the Electron
http://hdl.handle.net/10023/4991
Abstract: One experiment, more than any other, is often associated with the `discovery of the electron' in 1897. This is J J Thomson's determination of the mass to charge ratio (m/e) of cathode rays by deflecting them in magnetic and electric fields. Yet this experiment was performed two months after Thomson first announced that cathode rays were very small, negatively charged particles. So why was it important? I look at Thomson's route to, and conduct of, the experiment, and then at how his ideas were received.1999-01-01T00:00:00ZFalconer, Isobel JessieOne experiment, more than any other, is often associated with the `discovery of the electron' in 1897. This is J J Thomson's determination of the mass to charge ratio (m/e) of cathode rays by deflecting them in magnetic and electric fields. Yet this experiment was performed two months after Thomson first announced that cathode rays were very small, negatively charged particles. So why was it important? I look at Thomson's route to, and conduct of, the experiment, and then at how his ideas were received.Injecting drug users in Scotland, 2006 : listing, number, demography, and opiate-related death-rates
http://hdl.handle.net/10023/4904
Abstract: Using Bayesian capture–recapture analysis, we estimated the number of current injecting drug users (IDUs) in Scotland in 2006 from the cross-counts of 5670 IDUs listed on four data-sources: social enquiry reports (901 IDUs listed), hospital records (953), drug treatment agencies (3504), and recent Hepatitis C virus (HCV) diagnoses (827 listed as IDU-risk). Further, we accessed exact numbers of opiate-related drugs-related deaths (DRDs) in 2006 and 2007 to improve estimation of Scotland's DRD rates per 100 current IDUs. Using all four data-sources, and model-averaging of standard hierarchical log-linear models to allow for pairwise interactions between data-sources and/or demographic classifications, Scotland had an estimated 31700 IDUs in 2006 (95% credible interval: 24900–38700); but 25000 IDUs (95% CI: 20700–35000) by excluding recent HCV diagnoses whose IDU-risk can refer to past injecting. Only in the younger age-group (15–34 years) were Scotland's opiate-related DRD rates significantly lower for females than males. Older males’ opiate-related DRD rate was 1.9 (1.24–2.40) per 100 current IDUs without or 1.3 (0.94–1.64) with inclusion of recent HCV diagnoses. If, indeed, Scotland had only 25000 current IDUs in 2006, with only 8200 of them aged 35+ years, the opiate-related DRD rate is higher among this older age group than has been appreciated hitherto. There is counter-balancing good news for the public health: the hitherto sharp increase in older current IDUs had stalled by 2006.2013-06-01T00:00:00ZKing, RuthBird, SheilaOverstall, AntonyHay, GordonHutchinson, SharonUsing Bayesian capture–recapture analysis, we estimated the number of current injecting drug users (IDUs) in Scotland in 2006 from the cross-counts of 5670 IDUs listed on four data-sources: social enquiry reports (901 IDUs listed), hospital records (953), drug treatment agencies (3504), and recent Hepatitis C virus (HCV) diagnoses (827 listed as IDU-risk). Further, we accessed exact numbers of opiate-related drugs-related deaths (DRDs) in 2006 and 2007 to improve estimation of Scotland's DRD rates per 100 current IDUs. Using all four data-sources, and model-averaging of standard hierarchical log-linear models to allow for pairwise interactions between data-sources and/or demographic classifications, Scotland had an estimated 31700 IDUs in 2006 (95% credible interval: 24900–38700); but 25000 IDUs (95% CI: 20700–35000) by excluding recent HCV diagnoses whose IDU-risk can refer to past injecting. Only in the younger age-group (15–34 years) were Scotland's opiate-related DRD rates significantly lower for females than males. Older males’ opiate-related DRD rate was 1.9 (1.24–2.40) per 100 current IDUs without or 1.3 (0.94–1.64) with inclusion of recent HCV diagnoses. If, indeed, Scotland had only 25000 current IDUs in 2006, with only 8200 of them aged 35+ years, the opiate-related DRD rate is higher among this older age group than has been appreciated hitherto. There is counter-balancing good news for the public health: the hitherto sharp increase in older current IDUs had stalled by 2006.Standing kink modes in three-dimensional coronal loops
http://hdl.handle.net/10023/4745
Abstract: So far, the straight flux tube model proposed by Edwin & Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers. The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.
Description: I.D.M. acknowledges support from a Royal Society University Research Fellowship. The computational work for this paper was carried out at the joint STFC and SFC (SRIF)-fundedclusterattheUniversityofStAndrews(UK). The research leading to these results has also received funding from the European Commissions Seventh Framework Programme (FP7/2007-2013) under the grant agreement SOLSPANET (project No. 269299;www.solspanet.eu/solspanet).2014-03-11T00:00:00ZDe Moortel, InekePascoe, David JamesSo far, the straight flux tube model proposed by Edwin & Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers. The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.Potential Evidence for the Onset of Alfvénic Turbulence in Trans-equatorial Coronal Loops
http://hdl.handle.net/10023/4740
Abstract: This study investigates Coronal Multi-channel Polarimeter Doppler-shift observations of a large, off-limb, trans-equatorial loop system observed on 2012 April 10-11. Doppler-shift oscillations with a broad range of frequencies are found to propagate along the loop with a speed of about 500 km s–1. The power spectrum of perturbations travelling up from both loop footpoints is remarkably symmetric, probably due to the almost perfect north-south alignment of the loop system. Compared to the power spectrum at the footpoints of the loop, the Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. We suggest this excess high-frequency power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvénic) turbulence.2014-02-10T00:00:00ZDe Moortel, InekeMcIntosh, ScottThrelfall, James WilliamBethge, ChristianLiu, JThis study investigates Coronal Multi-channel Polarimeter Doppler-shift observations of a large, off-limb, trans-equatorial loop system observed on 2012 April 10-11. Doppler-shift oscillations with a broad range of frequencies are found to propagate along the loop with a speed of about 500 km s–1. The power spectrum of perturbations travelling up from both loop footpoints is remarkably symmetric, probably due to the almost perfect north-south alignment of the loop system. Compared to the power spectrum at the footpoints of the loop, the Fourier power at the apex appears to be higher in the high-frequency part of the spectrum than expected from theoretical models. We suggest this excess high-frequency power could be tentative evidence for the onset of a cascade of the low-to-mid frequency waves into (Alfvénic) turbulence.On the commutator lengths of certain classes of finitely presented groups
http://hdl.handle.net/10023/4719
Abstract: For a finite group G = 〈X〉 (X ≠ G), the least positive integer ML(G) is called the maximum length of G with respect to the generating set X if every element of G maybe represented as a product of at most ML(G) elements of X. The maximum length of G, denoted by ML (G), is defined to be the minimum of {ML(G) G = 〈X〉, X ≠ G, X ≠ G - {1}}. The well-known commutator length of a group G, denoted by c (G), satisfies the inequality c (G) ≤ ML(G′), where G′ is the derived subgroup of G. In this paper we study the properties of ML (G) and by using this inequality we give upper bounds for the commutator lengths of certain classes of finite groups. In some cases these upper bounds involve the interesting sequences of Fibonacci and Lucas numbers.2006-01-01T00:00:00ZDoostie, H.Campbell, P.P.For a finite group G = 〈X〉 (X ≠ G), the least positive integer ML(G) is called the maximum length of G with respect to the generating set X if every element of G maybe represented as a product of at most ML(G) elements of X. The maximum length of G, denoted by ML (G), is defined to be the minimum of {ML(G) G = 〈X〉, X ≠ G, X ≠ G - {1}}. The well-known commutator length of a group G, denoted by c (G), satisfies the inequality c (G) ≤ ML(G′), where G′ is the derived subgroup of G. In this paper we study the properties of ML (G) and by using this inequality we give upper bounds for the commutator lengths of certain classes of finite groups. In some cases these upper bounds involve the interesting sequences of Fibonacci and Lucas numbers.An approximate Bayesian method applied to estimating the trajectories of four British grey seal (Halichoerus grypus) populations from pup counts.
http://hdl.handle.net/10023/4688
Abstract: 1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about population structure; this is straightforward when populations are growing exponentially, but not when growth slows, since it is unclear whether density dependence affects pup survival or fecundity. 2. We present an approximate Bayesian method for fitting pup trajectories, estimating adult population size and investigating alternative biological models. The method is equivalent to fitting a density dependent Leslie matrix model, within a Bayesian framework, but with the forms of the density dependent effects as outputs rather than assumptions. 3. This approach requires fewer assumptions than the state space models currently used, and produces similar estimates. The simplifications made the models easier to fit, reducing their computational intensity and allowing regional differences in demographic parameters to be considered. 4. The approach is not restricted to situations where only a single component of the population is observable, but, particularly in those cases, provides a practical method for extracting information from limited datasets. 5. We discuss the potential and limitations of the method and suggest that this approach provides a useful tool for at least the preliminary analysis of similar datasets.2011-01-01T00:00:00ZLonergan, Michael EdwardThompson, DavidThomas, Leonard JosephDuck, Callan David1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about population structure; this is straightforward when populations are growing exponentially, but not when growth slows, since it is unclear whether density dependence affects pup survival or fecundity. 2. We present an approximate Bayesian method for fitting pup trajectories, estimating adult population size and investigating alternative biological models. The method is equivalent to fitting a density dependent Leslie matrix model, within a Bayesian framework, but with the forms of the density dependent effects as outputs rather than assumptions. 3. This approach requires fewer assumptions than the state space models currently used, and produces similar estimates. The simplifications made the models easier to fit, reducing their computational intensity and allowing regional differences in demographic parameters to be considered. 4. The approach is not restricted to situations where only a single component of the population is observable, but, particularly in those cases, provides a practical method for extracting information from limited datasets. 5. We discuss the potential and limitations of the method and suggest that this approach provides a useful tool for at least the preliminary analysis of similar datasets.Modelling group dynamic animal movement
http://hdl.handle.net/10023/4555
Abstract: 1). Group dynamics are a fundamental aspect of many species' movements. The need to adequately model individuals' interactions with other group members has been recognized, particularly in order to differentiate the role of social forces in individual movement from environmental factors. However, to date, practical statistical methods, which can include group dynamics in animal movement models, have been lacking. 2). We consider a flexible modelling framework that distinguishes a group-level model, describing the movement of the group's centre, and an individual-level model, such that each individual makes its movement decisions relative to the group centroid. The basic idea is framed within the flexible class of hidden Markov models, extending previous work on modelling animal movement by means of multistate random walks. 3). While in simulation experiments parameter estimators exhibit some bias in non-ideal scenarios, we show that generally the estimation of models of this type is both feasible and ecologically informative. 4). We illustrate the approach using real movement data from 11 reindeer (Rangifer tarandus). Results indicate a directional bias towards a group centroid for reindeer in an encamped state. Though the attraction to the group centroid is relatively weak, our model successfully captures group-influenced movement dynamics. Specifically, as compared to a regular mixture of correlated random walks, the group dynamic model more accurately predicts the non-diffusive behaviour of a cohesive mobile group. 5). As technology continues to develop, it will become easier and less expensive to tag multiple individuals within a group in order to follow their movements. Our work provides a first inferential framework for understanding the relative influences of individual versus group-level movement decisions. This framework can be extended to include covariates corresponding to environmental influences or body condition. As such, this framework allows for a broader understanding of the many internal and external factors that can influence an individual's movement.2014-02-01T00:00:00ZLangrock, RolandHopcraft, GrantBlackwell, PaulGoodall, VictoriaKing, RuthNiu, MuPatterson, TobyPedersen, MartinSkarin, AnnaSchick, Robert Schilling1). Group dynamics are a fundamental aspect of many species' movements. The need to adequately model individuals' interactions with other group members has been recognized, particularly in order to differentiate the role of social forces in individual movement from environmental factors. However, to date, practical statistical methods, which can include group dynamics in animal movement models, have been lacking. 2). We consider a flexible modelling framework that distinguishes a group-level model, describing the movement of the group's centre, and an individual-level model, such that each individual makes its movement decisions relative to the group centroid. The basic idea is framed within the flexible class of hidden Markov models, extending previous work on modelling animal movement by means of multistate random walks. 3). While in simulation experiments parameter estimators exhibit some bias in non-ideal scenarios, we show that generally the estimation of models of this type is both feasible and ecologically informative. 4). We illustrate the approach using real movement data from 11 reindeer (Rangifer tarandus). Results indicate a directional bias towards a group centroid for reindeer in an encamped state. Though the attraction to the group centroid is relatively weak, our model successfully captures group-influenced movement dynamics. Specifically, as compared to a regular mixture of correlated random walks, the group dynamic model more accurately predicts the non-diffusive behaviour of a cohesive mobile group. 5). As technology continues to develop, it will become easier and less expensive to tag multiple individuals within a group in order to follow their movements. Our work provides a first inferential framework for understanding the relative influences of individual versus group-level movement decisions. This framework can be extended to include covariates corresponding to environmental influences or body condition. As such, this framework allows for a broader understanding of the many internal and external factors that can influence an individual's movement.Living on the edge : Roe deer (Capreolus capreolus) density in the margins of Its geographical range
http://hdl.handle.net/10023/4523
Abstract: Over the last decades roe deer (Capreolus capreolus) populations have increased in number and distribution throughout Europe. Such increases have profound impacts on ecosystems, both positive and negative. Therefore monitoring roe deer populations is essential for the appropriate management of this species, in order to achieve a balance between conservation and mitigation of the negative impacts. Despite being required for an effective management plan, the study of roe deer ecology in Portugal is at an early stage, and hence there is still a complete lack of knowledge of roe deer density within its known range. Distance sampling of pellet groups coupled with production and decay rates for pellet groups provided density estimates for roe deer in northeastern Portugal (Lombada National Hunting Area - LNHA, Serra de Montesinho – SM and Serra da Nogueira – SN; LNHA and SM located in Montesinho Natural Park). The estimated roe deer density using a stratified detection function was 1.23/100 ha for LNHA, 4.87/100 ha for SM and 4.25/100 ha in SN, with 95% confidence intervals (CI) of 0.68 to 2.21, 3.08 to 7.71 and 2.25 to 8.03, respectively. For the entire area, the estimated density was about 3.51/100 ha (95% CI - 2.26–5.45). This method can provide estimates of roe deer density, which will ultimately support management decisions. However, effective monitoring should be based on long-term studies that are able to detect population fluctuations. This study represents the initial phase of roe deer monitoring at the edge of its European range and intends to fill the gap in this species ecology, as the gathering of similar data over a number of years will provide the basis for stronger inferences. Monitoring should be continued, although the study area should be increased to evaluate the accuracy of estimates and assess the impact of management actions.2014-02-01T00:00:00ZValente, Ana M.Fonseca, CarlosMarques, Tiago A.Santos, João P.Rodrigues, RogérioTorres, Rita TinocoOver the last decades roe deer (Capreolus capreolus) populations have increased in number and distribution throughout Europe. Such increases have profound impacts on ecosystems, both positive and negative. Therefore monitoring roe deer populations is essential for the appropriate management of this species, in order to achieve a balance between conservation and mitigation of the negative impacts. Despite being required for an effective management plan, the study of roe deer ecology in Portugal is at an early stage, and hence there is still a complete lack of knowledge of roe deer density within its known range. Distance sampling of pellet groups coupled with production and decay rates for pellet groups provided density estimates for roe deer in northeastern Portugal (Lombada National Hunting Area - LNHA, Serra de Montesinho – SM and Serra da Nogueira – SN; LNHA and SM located in Montesinho Natural Park). The estimated roe deer density using a stratified detection function was 1.23/100 ha for LNHA, 4.87/100 ha for SM and 4.25/100 ha in SN, with 95% confidence intervals (CI) of 0.68 to 2.21, 3.08 to 7.71 and 2.25 to 8.03, respectively. For the entire area, the estimated density was about 3.51/100 ha (95% CI - 2.26–5.45). This method can provide estimates of roe deer density, which will ultimately support management decisions. However, effective monitoring should be based on long-term studies that are able to detect population fluctuations. This study represents the initial phase of roe deer monitoring at the edge of its European range and intends to fill the gap in this species ecology, as the gathering of similar data over a number of years will provide the basis for stronger inferences. Monitoring should be continued, although the study area should be increased to evaluate the accuracy of estimates and assess the impact of management actions.A risk function for behavioral disruption of Blainville’s beaked whales (Mesoplodon densirostris) from mid-frequency active sonar
http://hdl.handle.net/10023/4522
Abstract: There is increasing concern about the potential effects of noise pollution on marine life in the world’s oceans. For marine mammals, anthropogenic sounds may cause behavioral disruption, and this can be quantified using a risk function that relates sound exposure to a measured behavioral response. Beaked whales are a taxon of deep diving whales that may be particularly susceptible to naval sonar as the species has been associated with sonar-related mass stranding events. Here we derive the first empirical risk function for Blainville’s beaked whales (Mesoplodon densirostris) by combining in situ data from passive acoustic monitoring of animal vocalizations and navy sonar operations with precise ship tracks and sound field modeling. The hydrophone array at the Atlantic Undersea Test and Evaluation Center, Bahamas, was used to locate vocalizing groups of Blainville’s beaked whales and identify sonar transmissions before, during, and after Mid-Frequency Active (MFA) sonar operations. Sonar transmission times and source levels were combined with ship tracks using a sound propagation model to estimate the received level (RL) at each hydrophone. A generalized additive model was fitted to data to model the presence or absence of the start of foraging dives in 30-minute periods as a function of the corresponding sonar RL at the hydrophone closest to the center of each group. This model was then used to construct a risk function that can be used to estimate the probability of a behavioral change (cessation of foraging) the individual members of a Blainville’s beaked whale population might experience as a function of sonar RL. The function predicts a 0.5 probability of disturbance at a RL of 150dBrms re µPa (CI: 144 to 155) This is 15dB lower than the level used historically by the US Navy in their risk assessments but 10 dB higher than the current 140 dB step-function2014-01-01T00:00:00ZMoretti, DavidThomas, LenMarques, Tiago A.Harwood, JohnDilley, AshleyNeales, BertShaffer, JessicaMccarthy, ENew, Leslie FrancesJarvis, SMorrissey, RonThere is increasing concern about the potential effects of noise pollution on marine life in the world’s oceans. For marine mammals, anthropogenic sounds may cause behavioral disruption, and this can be quantified using a risk function that relates sound exposure to a measured behavioral response. Beaked whales are a taxon of deep diving whales that may be particularly susceptible to naval sonar as the species has been associated with sonar-related mass stranding events. Here we derive the first empirical risk function for Blainville’s beaked whales (Mesoplodon densirostris) by combining in situ data from passive acoustic monitoring of animal vocalizations and navy sonar operations with precise ship tracks and sound field modeling. The hydrophone array at the Atlantic Undersea Test and Evaluation Center, Bahamas, was used to locate vocalizing groups of Blainville’s beaked whales and identify sonar transmissions before, during, and after Mid-Frequency Active (MFA) sonar operations. Sonar transmission times and source levels were combined with ship tracks using a sound propagation model to estimate the received level (RL) at each hydrophone. A generalized additive model was fitted to data to model the presence or absence of the start of foraging dives in 30-minute periods as a function of the corresponding sonar RL at the hydrophone closest to the center of each group. This model was then used to construct a risk function that can be used to estimate the probability of a behavioral change (cessation of foraging) the individual members of a Blainville’s beaked whale population might experience as a function of sonar RL. The function predicts a 0.5 probability of disturbance at a RL of 150dBrms re µPa (CI: 144 to 155) This is 15dB lower than the level used historically by the US Navy in their risk assessments but 10 dB higher than the current 140 dB step-functionOptimizing sampling design to deal with mist-net avoidance in Amazonian birds and bats
http://hdl.handle.net/10023/4520
Abstract: Mist netting is a widely used technique to sample bird and bat assemblages. However, captures often decline with time because animals learn and avoid the locations of nets. This avoidance or net shyness can substantially decrease sampling efficiency. We quantified the day-to-day decline in captures of Amazonian birds and bats with mist nets set at the same location for four consecutive days. We also evaluated how net avoidance influences the efficiency of surveys under different logistic scenarios using re-sampling techniques. Net avoidance caused substantial declines in bird and bat captures, although more accentuated in the latter. Most of the decline occurred between the first and second days of netting: 28% in birds and 47% in bats. Captures of commoner species were more affected. The numbers of species detected also declined. Moving nets daily to minimize the avoidance effect increased captures by 30% in birds and 70% in bats. However, moving the location of nets may cause a reduction in netting time and captures. When moving the nets caused the loss of one netting day it was no longer advantageous to move the nets frequently. In bird surveys that could even decrease the number of individuals captured and species detected. Net avoidance can greatly affect sampling efficiency but adjustments in survey design can minimize this. Whenever nets can be moved without losing netting time and the objective is to capture many individuals, they should be moved daily. If the main objective is to survey species present then nets should still be moved for bats, but not for birds. However, if relocating nets causes a significant loss of netting time, moving them to reduce effects of shyness will not improve sampling efficiency in either group. Overall, our findings can improve the design of mist netting sampling strategies in other tropical areas.2013-09-18T00:00:00ZMarques, Joao TiagoRamos Pereira, Maria J.Marques, Tiago A.Santos, Carlos DavidSantana, JoanaBeja, PedroPalmeirim, Jorge M.Mist netting is a widely used technique to sample bird and bat assemblages. However, captures often decline with time because animals learn and avoid the locations of nets. This avoidance or net shyness can substantially decrease sampling efficiency. We quantified the day-to-day decline in captures of Amazonian birds and bats with mist nets set at the same location for four consecutive days. We also evaluated how net avoidance influences the efficiency of surveys under different logistic scenarios using re-sampling techniques. Net avoidance caused substantial declines in bird and bat captures, although more accentuated in the latter. Most of the decline occurred between the first and second days of netting: 28% in birds and 47% in bats. Captures of commoner species were more affected. The numbers of species detected also declined. Moving nets daily to minimize the avoidance effect increased captures by 30% in birds and 70% in bats. However, moving the location of nets may cause a reduction in netting time and captures. When moving the nets caused the loss of one netting day it was no longer advantageous to move the nets frequently. In bird surveys that could even decrease the number of individuals captured and species detected. Net avoidance can greatly affect sampling efficiency but adjustments in survey design can minimize this. Whenever nets can be moved without losing netting time and the objective is to capture many individuals, they should be moved daily. If the main objective is to survey species present then nets should still be moved for bats, but not for birds. However, if relocating nets causes a significant loss of netting time, moving them to reduce effects of shyness will not improve sampling efficiency in either group. Overall, our findings can improve the design of mist netting sampling strategies in other tropical areas.Laboratory astrophysics : investigation of planetary and astrophysical maser emission
http://hdl.handle.net/10023/4494
Abstract: This paper describes a model for cyclotron maser emission applicable to planetary auroral radio emission, the stars UV Ceti and CU Virginus, blazar jets and astrophysical shocks. These emissions may be attributed to energetic electrons moving into convergent magnetic fields that are typically found in association with dipole like planetary magnetospheres or shocks. It is found that magnetic compression leads to the formation of a velocity distribution having a horseshoe shape as a result of conservation of the electron magnetic moment. Under certain plasma conditions where the local electron plasma frequency ωpe is much less than the cyclotron frequency ωce the distribution is found to be unstable to maser type radiation emission. We have established a laboratory-based facility that has verified many of the details of our original theoretical description and agrees well with numerical simulations. The experiment has demonstrated that the horseshoe distribution produces cyclotron emission at a frequency just below the local electron cyclotron frequency, with polarisation close to X-mode and propagating nearly perpendicularly to the electron beam motion. We discuss recent developments in the theory and simulation of the instability including addressing radiation escape problems, and relate these to the laboratory, space, and astrophysical observations. The experiments showed strong narrow band EM emissions at frequencies just below the cold-plasma cyclotron frequency as predicted by the theory. Measurements of the conversion efficiency, mode and spectral content were in close agreement with the predictions of numerical simulations undertaken using a particle-in-cell code and also with satellite observations confirming the horseshoe maser as an important emission mechanism in geophysical/astrophysical plasmas. In each case we address how the radiation can escape the plasma without suffering strong absorption at the second harmonic layer.2013-01-01T00:00:00ZSpeirs, DavidCairns, R AlanKellett, BarryVorgul, IrenaMcConville, SandraCross, AdrianPhelps, AlanRonald, KevinBingham, RobertThis paper describes a model for cyclotron maser emission applicable to planetary auroral radio emission, the stars UV Ceti and CU Virginus, blazar jets and astrophysical shocks. These emissions may be attributed to energetic electrons moving into convergent magnetic fields that are typically found in association with dipole like planetary magnetospheres or shocks. It is found that magnetic compression leads to the formation of a velocity distribution having a horseshoe shape as a result of conservation of the electron magnetic moment. Under certain plasma conditions where the local electron plasma frequency ωpe is much less than the cyclotron frequency ωce the distribution is found to be unstable to maser type radiation emission. We have established a laboratory-based facility that has verified many of the details of our original theoretical description and agrees well with numerical simulations. The experiment has demonstrated that the horseshoe distribution produces cyclotron emission at a frequency just below the local electron cyclotron frequency, with polarisation close to X-mode and propagating nearly perpendicularly to the electron beam motion. We discuss recent developments in the theory and simulation of the instability including addressing radiation escape problems, and relate these to the laboratory, space, and astrophysical observations. The experiments showed strong narrow band EM emissions at frequencies just below the cold-plasma cyclotron frequency as predicted by the theory. Measurements of the conversion efficiency, mode and spectral content were in close agreement with the predictions of numerical simulations undertaken using a particle-in-cell code and also with satellite observations confirming the horseshoe maser as an important emission mechanism in geophysical/astrophysical plasmas. In each case we address how the radiation can escape the plasma without suffering strong absorption at the second harmonic layer.Incomplete contingency tables with censored cells with application to estimating the number of people who inject drugs in Scotland
http://hdl.handle.net/10023/4433
Abstract: Estimating the size of hidden or difficult to reach populations is often of interest for economic, sociological or public health reasons. In order to estimate such populations, administrative data lists are often collated to form multi-list cross-counts and displayed in the form of an incomplete contingency table. Log-linear models are typically fitted to such data to obtain an estimate of the total population size by estimating the number of individuals not observed by any of the data-sources. This approach has been taken to estimate the current number of people who inject drugs (PWID) in Scotland, with the Hepatitis C virus (HCV) diagnosis database used as one of the data-sources to identify PWID. However, the HCV diagnosis data-source does not distinguish between current and former PWID, which, if ignored, will lead to over-estimation of the total population size of current PWID. We extend the standard model-fitting approach to allow for a data-source which contains a mixture of target and non-target individuals (i.e. in this case; current and former PWID). We apply the proposed approach to data for PWID in Scotland in 2003, 2006 and 2009 and compare to the results from standard log-linear models.2014-04-30T00:00:00ZOverstall, AntonyKing, RuthBird, SheilaHutchinson, SharonHay, GordonEstimating the size of hidden or difficult to reach populations is often of interest for economic, sociological or public health reasons. In order to estimate such populations, administrative data lists are often collated to form multi-list cross-counts and displayed in the form of an incomplete contingency table. Log-linear models are typically fitted to such data to obtain an estimate of the total population size by estimating the number of individuals not observed by any of the data-sources. This approach has been taken to estimate the current number of people who inject drugs (PWID) in Scotland, with the Hepatitis C virus (HCV) diagnosis database used as one of the data-sources to identify PWID. However, the HCV diagnosis data-source does not distinguish between current and former PWID, which, if ignored, will lead to over-estimation of the total population size of current PWID. We extend the standard model-fitting approach to allow for a data-source which contains a mixture of target and non-target individuals (i.e. in this case; current and former PWID). We apply the proposed approach to data for PWID in Scotland in 2003, 2006 and 2009 and compare to the results from standard log-linear models.Magnetohydrodynamics dynamical relaxation of coronal magnetic fields : I. Parallel untwisted magnetic fields in 2D
http://hdl.handle.net/10023/4378
Abstract: Context. For the last thirty years, most of the studies on the relaxation of stressed magnetic fields in the solar environment have only considered the Lorentz force, neglecting plasma contributions, and therefore, limiting every equilibrium to that of a force-free field. Aims: Here we begin a study of the non-resistive evolution of finite beta plasmas and their relaxation to magnetohydrostatic states, where magnetic forces are balanced by plasma-pressure gradients, by using a simple 2D scenario involving a hydromagnetic disturbance to a uniform magnetic field. The final equilibrium state is predicted as a function of the initial disturbances, with aims to demonstrate what happens to the plasma during the relaxation process and to see what effects it has on the final equilibrium state. Methods: A set of numerical experiments are run using a full MHD code, with the relaxation driven by magnetoacoustic waves damped by viscous effects. The numerical results are compared with analytical calculations made within the linear regime, in which the whole process must remain adiabatic. Particular attention is paid to the thermodynamic behaviour of the plasma during the relaxation. Results: The analytical predictions for the final non force-free equilibrium depend only on the initial perturbations and the total pressure of the system. It is found that these predictions hold surprisingly well even for amplitudes of the perturbation far outside the linear regime. Conclusions: Including the effects of a finite plasma beta in relaxation experiments leads to significant differences from the force-free case.2010-05-01T00:00:00ZFuentes Fernandez, JorgeParnell, Clare ElizabethHood, Alan WilliamContext. For the last thirty years, most of the studies on the relaxation of stressed magnetic fields in the solar environment have only considered the Lorentz force, neglecting plasma contributions, and therefore, limiting every equilibrium to that of a force-free field. Aims: Here we begin a study of the non-resistive evolution of finite beta plasmas and their relaxation to magnetohydrostatic states, where magnetic forces are balanced by plasma-pressure gradients, by using a simple 2D scenario involving a hydromagnetic disturbance to a uniform magnetic field. The final equilibrium state is predicted as a function of the initial disturbances, with aims to demonstrate what happens to the plasma during the relaxation process and to see what effects it has on the final equilibrium state. Methods: A set of numerical experiments are run using a full MHD code, with the relaxation driven by magnetoacoustic waves damped by viscous effects. The numerical results are compared with analytical calculations made within the linear regime, in which the whole process must remain adiabatic. Particular attention is paid to the thermodynamic behaviour of the plasma during the relaxation. Results: The analytical predictions for the final non force-free equilibrium depend only on the initial perturbations and the total pressure of the system. It is found that these predictions hold surprisingly well even for amplitudes of the perturbation far outside the linear regime. Conclusions: Including the effects of a finite plasma beta in relaxation experiments leads to significant differences from the force-free case.Flux emergence and coronal eruption
http://hdl.handle.net/10023/4376
Abstract: Aims. Our aim is to study the photospheric flux distribution of a twisted flux tube that emerges from the solar interior. We also report on the eruption of a new flux rope when the emerging tube rises into a pre-existing magnetic field in the corona. Methods. To study the evolution, we use 3D numerical simulations by solving the time-dependent and resistive MHD equations. We qualitatively compare our numerical results with MDI magnetograms of emerging flux at the solar surface. Results. We find that the photospheric magnetic flux distribution consists of two regions of opposite polarities and elongated magnetic tails on the two sides of the polarity inversion line (PIL), depending on the azimuthal nature of the emerging field lines and the initial field strength of the rising tube. Their shape is progressively deformed due to plasma motions towards the PIL. Our results are in qualitative agreement with observational studies of magnetic flux emergence in active regions (ARs). Moreover, if the initial twist of the emerging tube is small, the photospheric magnetic field develops an undulating shape and does not possess tails. In all cases, we find that a new flux rope is formed above the original axis of the emerging tube that may erupt into the corona, depending on the strength of the ambient field.2010-05-01T00:00:00ZArchontis, VasilisHood, Alan WilliamAims. Our aim is to study the photospheric flux distribution of a twisted flux tube that emerges from the solar interior. We also report on the eruption of a new flux rope when the emerging tube rises into a pre-existing magnetic field in the corona. Methods. To study the evolution, we use 3D numerical simulations by solving the time-dependent and resistive MHD equations. We qualitatively compare our numerical results with MDI magnetograms of emerging flux at the solar surface. Results. We find that the photospheric magnetic flux distribution consists of two regions of opposite polarities and elongated magnetic tails on the two sides of the polarity inversion line (PIL), depending on the azimuthal nature of the emerging field lines and the initial field strength of the rising tube. Their shape is progressively deformed due to plasma motions towards the PIL. Our results are in qualitative agreement with observational studies of magnetic flux emergence in active regions (ARs). Moreover, if the initial twist of the emerging tube is small, the photospheric magnetic field develops an undulating shape and does not possess tails. In all cases, we find that a new flux rope is formed above the original axis of the emerging tube that may erupt into the corona, depending on the strength of the ambient field.Pelagic movements of pacific leatherback turtles (Dermochelys coriacea) reveal the complex role of prey and ocean currents
http://hdl.handle.net/10023/4356
Abstract: Background: Leatherback turtles are renowned for their trans-oceanic migrations. However, despite numerous movement studies, the precise drivers of movement patterns in leatherbacks remain elusive. Many previous studies of leatherback turtles as well as other diving marine predators have analyzed surface movement patterns using only surface covariates. Since turtles and other marine predators spend the vast majority of their time diving under water, an analysis of movement patterns at depth should yield insight into what drives their movements. Results: We analyzed the movement paths of 15 post-nesting adult female Pacific leatherback turtles, which were caught and tagged on three nesting beaches in Mexico. The temporal length of the tracks ranged from 32 to 436 days, and the spatial distance covered ranged from 1,532 km to 13,097 km. We analyzed these tracks using a movement model designed to yield inference on the parameters driving movement. Because the telemetry data included diving depths, we extended an earlier version of the model that examined surface only movements, and here analyze movements in 3-dimensions. We tested the effect of dynamic environmental covariates from a coupled biophysical oceanographic model on patch choice in diving leatherback turtles, and compared the effects of parameters measured at the surface and at depth. The covariates included distance to future patch, temperature, salinity, meridional current velocity (current in the north–south direction), zonal current velocity (current in the east–west direction), phytoplankton density, diatom density, micro-plankton density, and meso-zooplankton density. We found significant, i.e. non-zero, correlation between movement and the parameters for oceanic covariates in 8 of the tracks. Of particular note, for one turtle we observed a lack of correlation between movements and a modeled index of zooplankton at the surface, but a significant correlation between movements and zooplankton at depth. Two of the turtles express a preference for patches at depth with elevated diatoms, and 2 turtles prefer patches with higher mezozooplankton values at depth. In contrast, 4 turtles expressed a preference for elevated zooplankton patches at the surface, but not at depth. We suggest that our understanding of a marine predator’s response to the environment may change significantly depending upon the analytical frame of reference, i.e. whether relationships are examined at the surface, at depth, or at different temporal resolutions. Lastly, we tested the effects of accounting for ocean currents on the movement patterns and found that for 13 of the 15 turtles, the parameter governing distance to the next patch decreased. Conclusions: Our results suggest that relationships derived from the analysis of surface tracks may not entirely explain movement patterns of this highly migratory species. Accounting for choices in the water column has shown that for certain individual turtles, what appears to be favourable habitat at depth is quantitatively different from that at the surface. This has implications for the analysis of the movements and diving behaviour of any top marine predator. The leatherback turtle is a deep diving reptile, and it is important to understand the subsurface variables that influence their movements if we are to precisely map the spatial dimensions of favorable leatherback habitat. These results present a new view into the drivers of diving patterns in turtles, and in particular represent a way of analyzing movements at depth that can be extended to other diving species.
Description: APC paid through BIS OA funds.2013-11-01T00:00:00ZSchick, Robert SchillingRoberts, JasonEckert, ScottClark, JamesBailey, HelenChai, FeiShi, LiHalpin, PatrickBackground: Leatherback turtles are renowned for their trans-oceanic migrations. However, despite numerous movement studies, the precise drivers of movement patterns in leatherbacks remain elusive. Many previous studies of leatherback turtles as well as other diving marine predators have analyzed surface movement patterns using only surface covariates. Since turtles and other marine predators spend the vast majority of their time diving under water, an analysis of movement patterns at depth should yield insight into what drives their movements. Results: We analyzed the movement paths of 15 post-nesting adult female Pacific leatherback turtles, which were caught and tagged on three nesting beaches in Mexico. The temporal length of the tracks ranged from 32 to 436 days, and the spatial distance covered ranged from 1,532 km to 13,097 km. We analyzed these tracks using a movement model designed to yield inference on the parameters driving movement. Because the telemetry data included diving depths, we extended an earlier version of the model that examined surface only movements, and here analyze movements in 3-dimensions. We tested the effect of dynamic environmental covariates from a coupled biophysical oceanographic model on patch choice in diving leatherback turtles, and compared the effects of parameters measured at the surface and at depth. The covariates included distance to future patch, temperature, salinity, meridional current velocity (current in the north–south direction), zonal current velocity (current in the east–west direction), phytoplankton density, diatom density, micro-plankton density, and meso-zooplankton density. We found significant, i.e. non-zero, correlation between movement and the parameters for oceanic covariates in 8 of the tracks. Of particular note, for one turtle we observed a lack of correlation between movements and a modeled index of zooplankton at the surface, but a significant correlation between movements and zooplankton at depth. Two of the turtles express a preference for patches at depth with elevated diatoms, and 2 turtles prefer patches with higher mezozooplankton values at depth. In contrast, 4 turtles expressed a preference for elevated zooplankton patches at the surface, but not at depth. We suggest that our understanding of a marine predator’s response to the environment may change significantly depending upon the analytical frame of reference, i.e. whether relationships are examined at the surface, at depth, or at different temporal resolutions. Lastly, we tested the effects of accounting for ocean currents on the movement patterns and found that for 13 of the 15 turtles, the parameter governing distance to the next patch decreased. Conclusions: Our results suggest that relationships derived from the analysis of surface tracks may not entirely explain movement patterns of this highly migratory species. Accounting for choices in the water column has shown that for certain individual turtles, what appears to be favourable habitat at depth is quantitatively different from that at the surface. This has implications for the analysis of the movements and diving behaviour of any top marine predator. The leatherback turtle is a deep diving reptile, and it is important to understand the subsurface variables that influence their movements if we are to precisely map the spatial dimensions of favorable leatherback habitat. These results present a new view into the drivers of diving patterns in turtles, and in particular represent a way of analyzing movements at depth that can be extended to other diving species.Energy dissipation and resolution of steep gradients in one-dimensional Burgers flows
http://hdl.handle.net/10023/4333
Abstract: Traveling-wave solutions of the inviscid Burgers equation having smooth initial wave profiles of suitable shapes are known to develop shocks (infinite gradients) in finite times. Such singular solutions are characterized by energy spectra that scale with the wave number k as k−2. In the presence of viscosity ν>0, no shocks can develop, and smooth solutions remain so for all times t>0, eventually decaying to zero as t→∞. At peak energy dissipation, say t = t∗, the spectrum of such a smooth solution extends to a finite dissipation wave number kν and falls off more rapidly, presumably exponentially, for k>kν. The number N of Fourier modes within the so-called inertial range is proportional to kν. This represents the number of modes necessary to resolve the dissipation scale and can be thought of as the system’s number of degrees of freedom. The peak energy dissipation rate ϵ remains positive and becomes independent of ν in the inviscid limit. In this study, we carry out an analysis which verifies the dynamical features described above and derive upper bounds for ϵ and N. It is found that ϵ satisfies ϵ ≤ ν2α−1‖u∗‖∞2(1−α)‖(−Δ)α/2u∗‖2, where α<1 and u∗ = u(x,t∗) is the velocity field at t = t∗. Given ϵ>0 in the limit ν→0, this implies that the energy spectrum remains no steeper than k−2 in that limit. For the critical k−2 scaling, the bound for ϵ reduces to ϵ ≤ k0‖u0‖∞‖u0‖2, where k0 marks the lower end of the inertial range and u0 = u(x,0). This implies N ≤ L‖u0‖∞/ν, where L is the domain size, which is shown to coincide with a rigorous estimate for the number of degrees of freedom defined in terms of local Lyapunov exponents. We demonstrate both analytically and numerically an instance, where the k−2 scaling is uniquely realizable. The numerics also return ϵ and t∗, consistent with analytic values derived from the corresponding limiting weak solution.2010-03-01T00:00:00ZTran, Chuong VanDritschel, David GerardTraveling-wave solutions of the inviscid Burgers equation having smooth initial wave profiles of suitable shapes are known to develop shocks (infinite gradients) in finite times. Such singular solutions are characterized by energy spectra that scale with the wave number k as k−2. In the presence of viscosity ν>0, no shocks can develop, and smooth solutions remain so for all times t>0, eventually decaying to zero as t→∞. At peak energy dissipation, say t = t∗, the spectrum of such a smooth solution extends to a finite dissipation wave number kν and falls off more rapidly, presumably exponentially, for k>kν. The number N of Fourier modes within the so-called inertial range is proportional to kν. This represents the number of modes necessary to resolve the dissipation scale and can be thought of as the system’s number of degrees of freedom. The peak energy dissipation rate ϵ remains positive and becomes independent of ν in the inviscid limit. In this study, we carry out an analysis which verifies the dynamical features described above and derive upper bounds for ϵ and N. It is found that ϵ satisfies ϵ ≤ ν2α−1‖u∗‖∞2(1−α)‖(−Δ)α/2u∗‖2, where α<1 and u∗ = u(x,t∗) is the velocity field at t = t∗. Given ϵ>0 in the limit ν→0, this implies that the energy spectrum remains no steeper than k−2 in that limit. For the critical k−2 scaling, the bound for ϵ reduces to ϵ ≤ k0‖u0‖∞‖u0‖2, where k0 marks the lower end of the inertial range and u0 = u(x,0). This implies N ≤ L‖u0‖∞/ν, where L is the domain size, which is shown to coincide with a rigorous estimate for the number of degrees of freedom defined in terms of local Lyapunov exponents. We demonstrate both analytically and numerically an instance, where the k−2 scaling is uniquely realizable. The numerics also return ϵ and t∗, consistent with analytic values derived from the corresponding limiting weak solution.Maximum likelihood estimation of mark-recapture-recovery models in the presence of continuous covariates
http://hdl.handle.net/10023/4073
Abstract: We consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.
Description: Supplementary material: R code for model fitting. Sample R code for simulating MRR data and fitting the corresponding model using the HMM-based approach (with MRR model as described in Section 3). Digital Object Identifier: doi:10.1214/13-AOAS644SUPP2013-01-01T00:00:00ZLangrock, RolandKing, RuthWe consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.Prioritizing global marine mammal habitats using density maps in place of range maps
http://hdl.handle.net/10023/4068
Abstract: Despite lessons from terrestrial systems, conservation efforts in marine systems continue to focus on identifying priority sites for protection based on high species richness inferred from range maps. Range maps oversimplify spatial variability in animal distributions by assuming uniform distribution within range and de facto giving equal weight to critical and marginal habitats. We used Marxan ver. 2.43 to compare species richness-based systematic reserve network solutions using information about marine mammal range and relative abundance. At a global scale, reserve network solutions were strongly sensitive to model inputs and assumptions. Solutions based on different input data overlapped by a third at most, with agreement as low as 10% in some cases. At a regional scale, species richness was inversely related to density, such that species richness hotspots excluded highest-density areas for all species. Based on these findings, we caution that species-richness estimates derived from range maps and used as input in conservation planning exercises may inadvertently lead to protection of largely marginal habitat.
Description: RW was supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme FP7-PEOPLE-2009-IIF2014-03-01T00:00:00ZWilliams, RobertGrand, JoannaHooker, Sascha KateBuckland, Stephen TerrenceReeves, Randall R.Rojas-Bracho, LorenzoSandilands, DougKaschner, KristinDespite lessons from terrestrial systems, conservation efforts in marine systems continue to focus on identifying priority sites for protection based on high species richness inferred from range maps. Range maps oversimplify spatial variability in animal distributions by assuming uniform distribution within range and de facto giving equal weight to critical and marginal habitats. We used Marxan ver. 2.43 to compare species richness-based systematic reserve network solutions using information about marine mammal range and relative abundance. At a global scale, reserve network solutions were strongly sensitive to model inputs and assumptions. Solutions based on different input data overlapped by a third at most, with agreement as low as 10% in some cases. At a regional scale, species richness was inversely related to density, such that species richness hotspots excluded highest-density areas for all species. Based on these findings, we caution that species-richness estimates derived from range maps and used as input in conservation planning exercises may inadvertently lead to protection of largely marginal habitat.Spatial models for distance sampling data : recent developments and future directions
http://hdl.handle.net/10023/4046
Abstract: Our understanding of a biological population can be greatly enhanced by modelling their distribution in space and as a function of environmental covariates. Density surface models consist of a spatial model of the abundance of a biological population which has been corrected for uncertain detection via distance sampling methods. We offer a comparison of recent advances in the field and consider the likely directions of future research. In particular we consider spatial modelling techniques that may be advantageous to applied ecologists such as quantification of uncertainty in a two-stage model and smoothing in areas with complex boundaries. The methods discussed are available in an \textsf{R} package developed by the authors and are largely implemented in the popular Windows package Distance (or are soon to be incorporated). Density surface modelling enables applied ecologists to reliably estimate abundances and create maps of animal/plant distribution. Such models can also be used to investigate the relationships between distribution and environmental covariates.2013-11-01T00:00:00ZMiller, David LawrenceBurt, M LouiseRexstad, EricThomas, LenOur understanding of a biological population can be greatly enhanced by modelling their distribution in space and as a function of environmental covariates. Density surface models consist of a spatial model of the abundance of a biological population which has been corrected for uncertain detection via distance sampling methods. We offer a comparison of recent advances in the field and consider the likely directions of future research. In particular we consider spatial modelling techniques that may be advantageous to applied ecologists such as quantification of uncertainty in a two-stage model and smoothing in areas with complex boundaries. The methods discussed are available in an \textsf{R} package developed by the authors and are largely implemented in the popular Windows package Distance (or are soon to be incorporated). Density surface modelling enables applied ecologists to reliably estimate abundances and create maps of animal/plant distribution. Such models can also be used to investigate the relationships between distribution and environmental covariates.A default prior distribution for contingency tables with dependent factor levels
http://hdl.handle.net/10023/4042
Abstract: A default prior distribution is proposed for the Bayesian analysis of contingency tables. The prior is specified to allow for dependence between levels of the factors. Different dependence structures are considered, including conditional autoregressive and distance correlation structures. To demonstrate the prior distribution, a dataset is considered involving estimating the number of injecting drug users in the eleven National Health Service board regions of Scotland using an incomplete contingency table where the dependence structure relates to geographical regions.
Description: Both authors were partly funded by MRC-funded addictions cluster, NIQUAD (Grant No. G1000021).2014-01-01T00:00:00ZOverstall, AntonyKing, RuthA default prior distribution is proposed for the Bayesian analysis of contingency tables. The prior is specified to allow for dependence between levels of the factors. Different dependence structures are considered, including conditional autoregressive and distance correlation structures. To demonstrate the prior distribution, a dataset is considered involving estimating the number of injecting drug users in the eleven National Health Service board regions of Scotland using an incomplete contingency table where the dependence structure relates to geographical regions.Combining individual animal movement and ancillary biotelemetry data to investigate population-level activity budgets
http://hdl.handle.net/10023/3993
Abstract: Recent technological advances have permitted the collection of detailed animal location and ancillary biotelemetry data that facilitate inference about animal movement and associated behaviors. However, these rich sources of individual information, location, and biotelemetry data, are typically analyzed independently, with population-level inferences remaining largely post hoc. We describe a hierarchical modeling approach, which is able to integrate location and ancillary biotelemetry (e.g., physiological or accelerometer) data from many individuals. We can thus obtain robust estimates of (1) population-level movement parameters and (2) activity budgets for a set of behaviors among which animals transition as they respond to changes in their internal and external environment. Measurement error and missing data are easily accommodated using a state-space formulation of the proposed hierarchical model. Using Bayesian analysis methods, we demonstrate our modeling approach with location and dive activity data from 17 harbor seals (Phoca vitulina) in the United Kingdom. Based jointly on movement and diving activity, we identified three distinct movement behavior states: resting, foraging, and transit, and estimated population-level activity budgets to these three states. Because harbor seals are known to dive for both foraging and transit (but not usually for resting), we compared these results to a similar population level analysis utilizing only location data. We found that a large proportion of time steps were mischaracterized when behavior states were inferred from horizontal trajectory alone, with 33% of time steps exhibiting a majority of dive activity assigned to the resting state. Only 1% of these time steps were assigned to resting when inferred from both trajectory and dive activity data using our integrated modeling approach. There is mounting evidence of the potential perils of inferring animal behavior based on trajectory alone, but there fortunately now exist many flexible analytical techniques for extracting more out of the increasing wealth of information afforded by recent advances in biologging technology.2013-04-01T00:00:00ZMcClintock, Brett ThomasRussell, Deborah Jill FraserMatthiopoulos, JasonKing, RuthRecent technological advances have permitted the collection of detailed animal location and ancillary biotelemetry data that facilitate inference about animal movement and associated behaviors. However, these rich sources of individual information, location, and biotelemetry data, are typically analyzed independently, with population-level inferences remaining largely post hoc. We describe a hierarchical modeling approach, which is able to integrate location and ancillary biotelemetry (e.g., physiological or accelerometer) data from many individuals. We can thus obtain robust estimates of (1) population-level movement parameters and (2) activity budgets for a set of behaviors among which animals transition as they respond to changes in their internal and external environment. Measurement error and missing data are easily accommodated using a state-space formulation of the proposed hierarchical model. Using Bayesian analysis methods, we demonstrate our modeling approach with location and dive activity data from 17 harbor seals (Phoca vitulina) in the United Kingdom. Based jointly on movement and diving activity, we identified three distinct movement behavior states: resting, foraging, and transit, and estimated population-level activity budgets to these three states. Because harbor seals are known to dive for both foraging and transit (but not usually for resting), we compared these results to a similar population level analysis utilizing only location data. We found that a large proportion of time steps were mischaracterized when behavior states were inferred from horizontal trajectory alone, with 33% of time steps exhibiting a majority of dive activity assigned to the resting state. Only 1% of these time steps were assigned to resting when inferred from both trajectory and dive activity data using our integrated modeling approach. There is mounting evidence of the potential perils of inferring animal behavior based on trajectory alone, but there fortunately now exist many flexible analytical techniques for extracting more out of the increasing wealth of information afforded by recent advances in biologging technology.Population status of Pan troglodytes verus in Lagoas de Cufada Natural Park, Guinea-Bissau
http://hdl.handle.net/10023/3974
Abstract: The western chimpanzee, Pan troglodytes verus, has been classified as Endangered on the IUCN Red List since 1988. Intensive agriculture, commercial plantations, logging, and mining have eliminated or degraded the habitats suitable for P. t. verus over a large part of its range. In this study we assessed the effect of land-use change on the population size and density of chimpanzees at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau. We further explored chimpanzee distribution in relation to landscape-level proxies of human disturbance. Nest count and distance-sampling methods were employed along 11 systematically placed linear transects in 2010 and 2011. Estimated nest decay rate was 293.9 days (%CV = 58.8). Based on this estimate of decay time and using the Standing-Crop Nest Count Method, we obtained a habitat-weighted average chimpanzee density estimate for 2011 of 0.22 nest building chimpanzees/km2 (95% CI 0.08–0.62), corresponding to 137 (95% CI 51.0–390.0) chimpanzees for LCNP. Human disturbance had a negative influence on chimpanzee distribution as nests were built farther away from human settlements, roads, and rivers than if they were randomly distributed, coinciding with the distribution of the remaining patches of dense canopy forest. We conclude that the continuous disappearance of suitable habitat (e.g. the replacement of LCNP's dense forests by monocultures of cashew plantations) may be compromising the future of one of the most threatened Guinean coastal chimpanzee populations. We discuss strategies to ensure long-term conservation in this important refuge for this chimpanzee subspecies at its westernmost margin of geographic distribution.2013-08-01T00:00:00ZCarvalho, Joana S.Marques, Tiago A.Vicente, LuisThe western chimpanzee, Pan troglodytes verus, has been classified as Endangered on the IUCN Red List since 1988. Intensive agriculture, commercial plantations, logging, and mining have eliminated or degraded the habitats suitable for P. t. verus over a large part of its range. In this study we assessed the effect of land-use change on the population size and density of chimpanzees at Lagoas de Cufada Natural Park (LCNP), Guinea-Bissau. We further explored chimpanzee distribution in relation to landscape-level proxies of human disturbance. Nest count and distance-sampling methods were employed along 11 systematically placed linear transects in 2010 and 2011. Estimated nest decay rate was 293.9 days (%CV = 58.8). Based on this estimate of decay time and using the Standing-Crop Nest Count Method, we obtained a habitat-weighted average chimpanzee density estimate for 2011 of 0.22 nest building chimpanzees/km2 (95% CI 0.08–0.62), corresponding to 137 (95% CI 51.0–390.0) chimpanzees for LCNP. Human disturbance had a negative influence on chimpanzee distribution as nests were built farther away from human settlements, roads, and rivers than if they were randomly distributed, coinciding with the distribution of the remaining patches of dense canopy forest. We conclude that the continuous disappearance of suitable habitat (e.g. the replacement of LCNP's dense forests by monocultures of cashew plantations) may be compromising the future of one of the most threatened Guinean coastal chimpanzee populations. We discuss strategies to ensure long-term conservation in this important refuge for this chimpanzee subspecies at its westernmost margin of geographic distribution.A generalised likelihood framework for partially observed capture-recapture-recovery models
http://hdl.handle.net/10023/3877
Abstract: We provide a closed form likelihood expression for multi-state mark-recapture-recovery data when the state of an individual may be only partially observed. The corresponding su cient statistics are presented in addition to a matrix formulation which facilitates an e cient calculation of the likelihood. This likelihood framework provides a consistent and uni ed framework with many standard models applied to mark-recapture-recovery data as special cases.2014-01-01T00:00:00ZKing, RuthMcCrea, R SWe provide a closed form likelihood expression for multi-state mark-recapture-recovery data when the state of an individual may be only partially observed. The corresponding su cient statistics are presented in addition to a matrix formulation which facilitates an e cient calculation of the likelihood. This likelihood framework provides a consistent and uni ed framework with many standard models applied to mark-recapture-recovery data as special cases.Estimating resource acquisition and at-sea body condition of a marine predator
http://hdl.handle.net/10023/3867
Abstract: (1) Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. (2) However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. (3) Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. (4) We found that physiological condition significantly impacted lipid gain at two time-scales – daily and at departure from the colony – that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. (5) We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.
Description: This article was made open access through BIS OA funding.2013-01-01T00:00:00ZSchick, Robert SchillingNew, LeslieThomas, LenCosta, DanielHindell, MarkMcMahon, CliveRobinson, PatrickSimmons, SamanthaThums, MicheleHarwood, JohnClark, James(1) Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. (2) However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. (3) Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. (4) We found that physiological condition significantly impacted lipid gain at two time-scales – daily and at departure from the colony – that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. (5) We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.Using hierarchical bayes to understand movement, health, and survival in the endangered North Atlantic right whale
http://hdl.handle.net/10023/3860
Abstract: Body condition is an indicator of health, and it plays a key role in many vital processes for mammalian species. While evidence of individual body condition can be obtained, these observations provide just brief glimpses into the health state of the animal. An analytical framework is needed for understanding how health of animals changes over space and time.Through knowledge of individual health we can better understand the status of populations. This is particularly important in endangered species, where the consequences of disruption of critical biological functions can push groups of animals rapidly toward extinction. Here we built a state-space model that provides estimates of movement, health, and survival. We assimilated 30+ years of photographic evidence of body condition and three additional visual health parameters in individual North Atlantic right whales, together with survey data, to infer the true health status as it changes over space and time. We also included the effect of reproductive status and entanglement status on health. At the population level, we estimated differential movement patterns in males and females. At the individual level, we estimated the likely animal locations each month. We estimated the relationship between observed and latent health status. Observations of body condition, skin condition, cyamid infestation on the blowholes, and rake marks all provided measures of the true underlying health. The resulting time series of individual health highlight both normal variations in health status and how anthropogenic stressors can affect the health and, ultimately, the survival of individuals. This modeling approach provides information for monitoring of health in right whales, as well as a framework for integrating observational data at the level of individuals up through the health status of the population. This framework can be broadly applied to a variety of systems – terrestrial and marine – where sporadic observations of individuals exist.
Description: This article was made open access through BIS OA funding.2013-06-01T00:00:00ZSchick, Robert SchillingKraus, Scott D.Rolland, Rosalind M.Knowlton, Amy R.Hamilton, Philip K.Pettis, Heather M.Kenney, Robert D.Clark, James S.Body condition is an indicator of health, and it plays a key role in many vital processes for mammalian species. While evidence of individual body condition can be obtained, these observations provide just brief glimpses into the health state of the animal. An analytical framework is needed for understanding how health of animals changes over space and time.Through knowledge of individual health we can better understand the status of populations. This is particularly important in endangered species, where the consequences of disruption of critical biological functions can push groups of animals rapidly toward extinction. Here we built a state-space model that provides estimates of movement, health, and survival. We assimilated 30+ years of photographic evidence of body condition and three additional visual health parameters in individual North Atlantic right whales, together with survey data, to infer the true health status as it changes over space and time. We also included the effect of reproductive status and entanglement status on health. At the population level, we estimated differential movement patterns in males and females. At the individual level, we estimated the likely animal locations each month. We estimated the relationship between observed and latent health status. Observations of body condition, skin condition, cyamid infestation on the blowholes, and rake marks all provided measures of the true underlying health. The resulting time series of individual health highlight both normal variations in health status and how anthropogenic stressors can affect the health and, ultimately, the survival of individuals. This modeling approach provides information for monitoring of health in right whales, as well as a framework for integrating observational data at the level of individuals up through the health status of the population. This framework can be broadly applied to a variety of systems – terrestrial and marine – where sporadic observations of individuals exist.Cetacean abundance and distribution in European Atlantic shelf waters to inform conservation and management
http://hdl.handle.net/10023/3859
Abstract: The European Union (EU) Habitats Directive requires Member States to monitor and maintain at favourable conservation status those species identified to be in need of protection, including all cetaceans. In July 2005 we surveyed the entire EU Atlantic continental shelf to generate robust estimates of abundance for harbour porpoise and other cetacean species. The survey used line transect sampling methods and purpose built data collection equipment designed to minimise bias in estimates of abundance. Shipboard transects covered 19,725 km in sea conditions ⩽Beaufort 4 in an area of 1,005,743 km2. Aerial transects covered 15,802 km in good/moderate conditions (⩽Beaufort 3) in an area of 364,371 km2. Thirteen cetacean species were recorded; abundance was estimated for harbour porpoise (375,358; CV = 0.197), bottlenose dolphin (16,485; CV = 0.422), white-beaked dolphin (16,536; CV = 0.303), short-beaked common dolphin (56,221; CV = 0.234) and minke whale (18,958; CV = 0.347). Abundance in 2005 was similar to that estimated in July 1994 for harbour porpoise, white-beaked dolphin and minke whale in a comparable area. However, model-based density surfaces showed a marked difference in harbour porpoise distribution between 1994 and 2005. Our results allow EU Member States to discharge their responsibilities under the Habitats Directive and inform other international organisations concerning the assessment of conservation status of cetaceans and the impact of bycatch at a large spatial scale. The lack of evidence for a change in harbour porpoise abundance in EU waters as a whole does not exclude the possibility of an impact of bycatch in some areas. Monitoring bycatch and estimation of abundance continue to be essential.
Description: This article was made open access through BIS OA funding.2013-08-01T00:00:00ZHammond, Philip StevenMacleod, KellyBerggren, PerBorchers, David LouisBurt, M LouiseCañadas, AnaDesportes, GenevieveDonovan, Greg PGilles, AnitaGillespie, Douglas MichaelGordon, Jonathan Charles DavidHiby, LexKuklik, IwonaLeaper, RussellLehnert, KristinaLeopold, MardikLovell, PhilipØien, NilsPaxton, Charles G. M.Ridoux, VincentRogan, EmerSamarra, Filipa Isabel PereiraScheidat, MeikeSequeira, MarinaSiebert, UrsulaSkov, HenrikSwift, Rene JamesTasker, MarkTeilmann, JonasVan Canneyt, OlivierVázquez, José AntonioThe European Union (EU) Habitats Directive requires Member States to monitor and maintain at favourable conservation status those species identified to be in need of protection, including all cetaceans. In July 2005 we surveyed the entire EU Atlantic continental shelf to generate robust estimates of abundance for harbour porpoise and other cetacean species. The survey used line transect sampling methods and purpose built data collection equipment designed to minimise bias in estimates of abundance. Shipboard transects covered 19,725 km in sea conditions ⩽Beaufort 4 in an area of 1,005,743 km2. Aerial transects covered 15,802 km in good/moderate conditions (⩽Beaufort 3) in an area of 364,371 km2. Thirteen cetacean species were recorded; abundance was estimated for harbour porpoise (375,358; CV = 0.197), bottlenose dolphin (16,485; CV = 0.422), white-beaked dolphin (16,536; CV = 0.303), short-beaked common dolphin (56,221; CV = 0.234) and minke whale (18,958; CV = 0.347). Abundance in 2005 was similar to that estimated in July 1994 for harbour porpoise, white-beaked dolphin and minke whale in a comparable area. However, model-based density surfaces showed a marked difference in harbour porpoise distribution between 1994 and 2005. Our results allow EU Member States to discharge their responsibilities under the Habitats Directive and inform other international organisations concerning the assessment of conservation status of cetaceans and the impact of bycatch at a large spatial scale. The lack of evidence for a change in harbour porpoise abundance in EU waters as a whole does not exclude the possibility of an impact of bycatch in some areas. Monitoring bycatch and estimation of abundance continue to be essential.Magnetohydrodynamic simulations of the ejection of a magnetic flux rope
http://hdl.handle.net/10023/3855
Abstract: Context. Coronal mass ejections (CME’s) are one of the most violent phenomena found on the Sun. One model to explain their occurrence is the flux rope ejection model. In this model, magnetic flux ropes form slowly over time periods of days to weeks. They then lose equilibrium and are ejected from the solar corona over a few hours. The contrasting time scales of formation and ejection pose a serious problem for numerical simulations. Aims. We simulate the whole life span of a flux rope from slow formation to rapid ejection and investigate whether magnetic flux ropes formed from a continuous magnetic field distribution, during a quasi-static evolution, can erupt to produce a CME. Methods. To model the full life span of magnetic flux ropes we couple two models. The global non-linear force-free field (GNLFFF) evolution model is used to follow the quasi-static formation of a flux rope. The MHD code ARMVAC is used to simulate the production of a CME through the loss of equilibrium and ejection of this flux rope. Results. We show that the two distinct models may be successfully coupled and that the flux rope is ejected out of our simulation box, where the outer boundary is placed at 2.5 R⊙. The plasma expelled during the flux rope ejection travels outward at a speed of 100 km s-1, which is consistent with the observed speed of CMEs in the low corona. Conclusions. Our work shows that flux ropes formed in the GNLFFF can lead to the ejection of a mass loaded magnetic flux rope in full MHD simulations. Coupling the two distinct models opens up a new avenue of research to investigate phenomena where different phases of their evolution occur on drastically different time scales.2013-06-01T00:00:00ZPagano, PaoloMackay, Duncan HendryPoedts, StefaanContext. Coronal mass ejections (CME’s) are one of the most violent phenomena found on the Sun. One model to explain their occurrence is the flux rope ejection model. In this model, magnetic flux ropes form slowly over time periods of days to weeks. They then lose equilibrium and are ejected from the solar corona over a few hours. The contrasting time scales of formation and ejection pose a serious problem for numerical simulations. Aims. We simulate the whole life span of a flux rope from slow formation to rapid ejection and investigate whether magnetic flux ropes formed from a continuous magnetic field distribution, during a quasi-static evolution, can erupt to produce a CME. Methods. To model the full life span of magnetic flux ropes we couple two models. The global non-linear force-free field (GNLFFF) evolution model is used to follow the quasi-static formation of a flux rope. The MHD code ARMVAC is used to simulate the production of a CME through the loss of equilibrium and ejection of this flux rope. Results. We show that the two distinct models may be successfully coupled and that the flux rope is ejected out of our simulation box, where the outer boundary is placed at 2.5 R⊙. The plasma expelled during the flux rope ejection travels outward at a speed of 100 km s-1, which is consistent with the observed speed of CMEs in the low corona. Conclusions. Our work shows that flux ropes formed in the GNLFFF can lead to the ejection of a mass loaded magnetic flux rope in full MHD simulations. Coupling the two distinct models opens up a new avenue of research to investigate phenomena where different phases of their evolution occur on drastically different time scales.Blue whales respond to simulated mid-frequency military sonar
http://hdl.handle.net/10023/3837
Abstract: Mid-frequency military (1–10 kHz) sonars have been associated with lethal mass strandings of deep-diving toothed whales, but the effects on endangered baleen whale species are virtually unknown. Here, we used controlled exposure experiments with simulated military sonar and other mid-frequency sounds to measure behavioural responses of tagged blue whales (Balaenoptera musculus) in feeding areas within the Southern California Bight. Despite using source levels orders of magnitude below some operational military systems, our results demonstrate that mid-frequency sound can significantly affect blue whale behaviour, especially during deep feeding modes. When a response occurred, behavioural changes varied widely from cessation of deep feeding to increased swimming speed and directed travel away from the sound source. The variability of these behavioural responses was largely influenced by a complex interaction of behavioural state, the type of mid-frequency sound and received sound level. Sonar-induced disruption of feeding and displacement from high-quality prey patches could have significant and previously undocumented impacts on baleen whale foraging ecology, individual fitness and population health.2013-01-01T00:00:00ZGoldbogen, Jeremy A.Southall, Brandon L.De Ruiter, Stacy LynnCalambokidis, JohnFriedlaender, Ari S.Hazen, Elliott L.Falcone, Erin A.Schorr, Gregory S.Douglas, AnnieMoretti, David J.Kyburg, ChrisMcKenna, Megan F.Tyack, Peter LloydMid-frequency military (1–10 kHz) sonars have been associated with lethal mass strandings of deep-diving toothed whales, but the effects on endangered baleen whale species are virtually unknown. Here, we used controlled exposure experiments with simulated military sonar and other mid-frequency sounds to measure behavioural responses of tagged blue whales (Balaenoptera musculus) in feeding areas within the Southern California Bight. Despite using source levels orders of magnitude below some operational military systems, our results demonstrate that mid-frequency sound can significantly affect blue whale behaviour, especially during deep feeding modes. When a response occurred, behavioural changes varied widely from cessation of deep feeding to increased swimming speed and directed travel away from the sound source. The variability of these behavioural responses was largely influenced by a complex interaction of behavioural state, the type of mid-frequency sound and received sound level. Sonar-induced disruption of feeding and displacement from high-quality prey patches could have significant and previously undocumented impacts on baleen whale foraging ecology, individual fitness and population health.First direct measurements of behavioural responses by Cuvier's beaked whales to mid-frequency active sonar
http://hdl.handle.net/10023/3836
Abstract: Most marine mammal strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.2013-01-01T00:00:00ZDe Ruiter, Stacy LynnSouthall, Brandon L.Calambokidis, JohnZimmer, Walter M. X.Sadykova, DinaraFalcone, Erin A.Friedlaender, Ari S.Joseph, John E.Moretti, DavidSchorr, Gregory S.Thomas, LenTyack, Peter LloydMost marine mammal strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.Minimal and random generation of permutation and matrix groups
http://hdl.handle.net/10023/3823
Abstract: We prove explicit bounds on the numbers of elements needed to generate various types of finite permutation groups and finite completely reducible matrix groups, and present examples to show that they are sharp in all cases. The bounds are linear in the degree of the permutation or matrix group in general, and logarithmic when the group is primitive. They can be combined with results of Lubotzky to produce explicit bounds on the number of random elements required to generate these groups with a specified probability. These results have important applications to computational group theory. Our proofs are inductive and largely theoretical, but we use computer calculations to establish the bounds in a number of specific small cases.2013-08-01T00:00:00ZHolt, DerekRoney-Dougal, Colva MaryWe prove explicit bounds on the numbers of elements needed to generate various types of finite permutation groups and finite completely reducible matrix groups, and present examples to show that they are sharp in all cases. The bounds are linear in the degree of the permutation or matrix group in general, and logarithmic when the group is primitive. They can be combined with results of Lubotzky to produce explicit bounds on the number of random elements required to generate these groups with a specified probability. These results have important applications to computational group theory. Our proofs are inductive and largely theoretical, but we use computer calculations to establish the bounds in a number of specific small cases.Estimating animal population density using passive acoustics
http://hdl.handle.net/10023/3496
Abstract: Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here2013-05-01T00:00:00ZMarques, Tiago A.Thomas, LenMartin, StephenMellinger, DavidWard, JessicaMoretti, DavidHarris, Danielle VeronicaTyack, Peter LloydReliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented hereEstimating prevalence of injecting drug users and associated heroin-related death rates in England by using regional data and incorporating prior information
http://hdl.handle.net/10023/3494
Abstract: Injecting drug users (IDUs) have a direct social and economic effect yet can typically be regarded as a hidden population within a community. We estimate the size of the IDU population across the nine different Government Office regions of England in 2005–2006 by using capture–recapture methods with age (ranging from 15 to 64 years) and gender as covariate information. We consider a Bayesian model averaging approach using log-linear models, where we can include explicit prior information within the analysis in relation to the total IDU population (elicited from the number of drug-related deaths and injectors’ drug-related death rates). Estimation at the regional level allows for regional heterogeneity with these regional estimates aggregated to obtain a posterior mean estimate for the number of England's IDUs of 195840 with 95% credible interval (181700, 210480). There is significant variation in the estimated regional prevalence of current IDUs per million of population aged 15–64 years, and in injecting drug-related death rates across the gender × age cross-classifications. The propensity of an IDU to be seen by at least one source also exhibits strong regional variability with London having the lowest propensity of being observed (posterior mean probability 0.21) and the South West the highest propensity (posterior mean 0.46).2014-01-01T00:00:00ZKing, RuthBird, SheilaOverstall, AntonyHay, GordonHutchinson, SharonInjecting drug users (IDUs) have a direct social and economic effect yet can typically be regarded as a hidden population within a community. We estimate the size of the IDU population across the nine different Government Office regions of England in 2005–2006 by using capture–recapture methods with age (ranging from 15 to 64 years) and gender as covariate information. We consider a Bayesian model averaging approach using log-linear models, where we can include explicit prior information within the analysis in relation to the total IDU population (elicited from the number of drug-related deaths and injectors’ drug-related death rates). Estimation at the regional level allows for regional heterogeneity with these regional estimates aggregated to obtain a posterior mean estimate for the number of England's IDUs of 195840 with 95% credible interval (181700, 210480). There is significant variation in the estimated regional prevalence of current IDUs per million of population aged 15–64 years, and in injecting drug-related death rates across the gender × age cross-classifications. The propensity of an IDU to be seen by at least one source also exhibits strong regional variability with London having the lowest propensity of being observed (posterior mean probability 0.21) and the South West the highest propensity (posterior mean 0.46).Estimating seasonal abundance of a central place forager using counts and telemetry data
http://hdl.handle.net/10023/3454
Abstract: Obtaining population estimates of species that are not easily observed directly can be problematic. However, central place foragers can often be observed some of the time, e.g. when seals are hauled out. In these instances, population estimates can be derived from counts, combined with information on the proportion of time that animals can be observed. We present a modelling framework to estimate seasonal absolute abundance using counts and information from satellite telemetry data. The method was tested on a harbour seal population in an area of southeast Scotland. Counts were made monthly, between November 2001 and June 2003, when seals were hauled out on land and were corrected for the proportion of time the seals were at sea using satellite telemetry. Harbour seals (n=25) were tagged with satellite relay data loggers between November 2001 and March 2003. To estimate the proportion of time spent hauled out, time at sea on foraging trips was modelled separately from haul-out behaviour close to haul-out sites because of the different factors affecting these processes. A generalised linear mixed model framework was developed to capture the longitudinal nature of the data and the repeated measures across individuals. Despite seasonal variability in the number of seals counted at haul-out sites, the model generated estimates of abundance, with an overall mean of 846 (95% CI: 767 to 979). The methodology shows the value of using count and telemetry data collected concurrently for estimating absolute abundance, information that is essential to assess interactions between predators, fish stocks and fisheries.
Description: R.J.S. was supported by a Natural Environment Research Council studentship.2009-01-01T00:00:00ZSharples, RJMacKenzie, Monique LeaHammond, Philip StevenObtaining population estimates of species that are not easily observed directly can be problematic. However, central place foragers can often be observed some of the time, e.g. when seals are hauled out. In these instances, population estimates can be derived from counts, combined with information on the proportion of time that animals can be observed. We present a modelling framework to estimate seasonal absolute abundance using counts and information from satellite telemetry data. The method was tested on a harbour seal population in an area of southeast Scotland. Counts were made monthly, between November 2001 and June 2003, when seals were hauled out on land and were corrected for the proportion of time the seals were at sea using satellite telemetry. Harbour seals (n=25) were tagged with satellite relay data loggers between November 2001 and March 2003. To estimate the proportion of time spent hauled out, time at sea on foraging trips was modelled separately from haul-out behaviour close to haul-out sites because of the different factors affecting these processes. A generalised linear mixed model framework was developed to capture the longitudinal nature of the data and the repeated measures across individuals. Despite seasonal variability in the number of seals counted at haul-out sites, the model generated estimates of abundance, with an overall mean of 846 (95% CI: 767 to 979). The methodology shows the value of using count and telemetry data collected concurrently for estimating absolute abundance, information that is essential to assess interactions between predators, fish stocks and fisheries.Generating transformation semigroups using endomorphisms of preorders, graphs, and tolerances
http://hdl.handle.net/10023/3383
Abstract: Let ΩΩ be the semigroup of all mappings of a countably infinite set Ω. If U and V are subsemigroups of ΩΩ, then we write U≈V if there exists a finite subset F of ΩΩ such that the subsemigroup generated by U and F equals that generated by V and F. The relative rank of U in ΩΩ is the least cardinality of a subset A of ΩΩ such that the union of U and A generates ΩΩ. In this paper we study the notions of relative rank and the equivalence ≈ for semigroups of endomorphisms of binary relations on Ω. The semigroups of endomorphisms of preorders, bipartite graphs, and tolerances on Ω are shown to lie in two equivalence classes under ≈. Moreover such semigroups have relative rank 0, 1, 2, or d in ΩΩ where d is the minimum cardinality of a dominating family for NN. We give examples of preorders, bipartite graphs, and tolerances on Ω where the relative ranks of their endomorphism semigroups in ΩΩ are 0, 1, 2, and d. We show that the endomorphism semigroups of graphs, in general, fall into at least four classes under ≈ and that there exist graphs where the relative rank of the endomorphism semigroup is 2ℵ0.2010-09-01T00:00:00ZMitchell, James DavidMorayne, MichalPeresse, Yann HamonQuick, MartynLet ΩΩ be the semigroup of all mappings of a countably infinite set Ω. If U and V are subsemigroups of ΩΩ, then we write U≈V if there exists a finite subset F of ΩΩ such that the subsemigroup generated by U and F equals that generated by V and F. The relative rank of U in ΩΩ is the least cardinality of a subset A of ΩΩ such that the union of U and A generates ΩΩ. In this paper we study the notions of relative rank and the equivalence ≈ for semigroups of endomorphisms of binary relations on Ω. The semigroups of endomorphisms of preorders, bipartite graphs, and tolerances on Ω are shown to lie in two equivalence classes under ≈. Moreover such semigroups have relative rank 0, 1, 2, or d in ΩΩ where d is the minimum cardinality of a dominating family for NN. We give examples of preorders, bipartite graphs, and tolerances on Ω where the relative ranks of their endomorphism semigroups in ΩΩ are 0, 1, 2, and d. We show that the endomorphism semigroups of graphs, in general, fall into at least four classes under ≈ and that there exist graphs where the relative rank of the endomorphism semigroup is 2ℵ0.Fitting complex ecological point process models with integrated nested Laplace approximation
http://hdl.handle.net/10023/3364
Abstract: Summary 1. We highlight an emerging statistical method, integrated nested Laplace approximation (INLA), which is ideally suited for fitting complex models to many of the rich spatial data sets that ecologists wish to analyse. 2. INLA is an approximation method that nevertheless provides very exact estimates. In this article, we describe the INLA methodology highlighting where it offers opportunities for drawing inference from (spatial) ecological data that would previously have been too complex to make practical model fitting feasible. 3. We use INLA to fit a complex joint model to the spatial pattern formed by a plant species, Thymus carnosus, as well as to the health status of each individual. 4. The key ecological result revealed by our spatial analysis of these data, relates to the distance-to-water covariate. We find that T. carnosus plants are generally healthier when they are further away from the water. 5. We suggest that this may be the result of a combination of (1) plants having alternative rooting strategies depending on how close to water they grow and (2) the rooting strategy determining how well the plants were able to tolerate an unusually dry summer. 6. We anticipate INLA becoming widely used within spatial ecological analysis over the next decade and suggest that both ecologists and statisticians will benefit greatly from working collaboratively to further develop and apply these emerging statistical methods.2013-04-01T00:00:00ZIllian, Janine BaerbelMartino, SaraSørbye, Sigrunn H.Gallego-Fernández, Juan B.Zunzunegui, MariaEsquivias, M. PazTravis, Justin M.Summary 1. We highlight an emerging statistical method, integrated nested Laplace approximation (INLA), which is ideally suited for fitting complex models to many of the rich spatial data sets that ecologists wish to analyse. 2. INLA is an approximation method that nevertheless provides very exact estimates. In this article, we describe the INLA methodology highlighting where it offers opportunities for drawing inference from (spatial) ecological data that would previously have been too complex to make practical model fitting feasible. 3. We use INLA to fit a complex joint model to the spatial pattern formed by a plant species, Thymus carnosus, as well as to the health status of each individual. 4. The key ecological result revealed by our spatial analysis of these data, relates to the distance-to-water covariate. We find that T. carnosus plants are generally healthier when they are further away from the water. 5. We suggest that this may be the result of a combination of (1) plants having alternative rooting strategies depending on how close to water they grow and (2) the rooting strategy determining how well the plants were able to tolerate an unusually dry summer. 6. We anticipate INLA becoming widely used within spatial ecological analysis over the next decade and suggest that both ecologists and statisticians will benefit greatly from working collaboratively to further develop and apply these emerging statistical methods.A family of spatial biodiversity measures based on graphs
http://hdl.handle.net/10023/3350
Abstract: While much research in ecology has focused on spatially explicit modelling as well as on measures of biodiversity, the concept of spatial (or local) biodiversity has been discussed very little. This paper generalises existing measures of spatial biodiversity and introduces a family of spatial biodiversity measures by flexibly defining the notion of the individuals’ neighbourhood within the framework of graphs associated to a spatial point pattern. We consider two non-independent aspects of spatial biodiversity, scattering, i.e. the spatial arrangement of the individuals in the study area and exposure, the local diversity in an individual’s neighbourhood. A simulation study reveals that measures based on the most commonly used neigh-bourhood defined by the geometric graph do not distinguish well between scattering and exposure. This problem is much less pronounced when other graphs are used. In an analysis of the spatial diversity in a rainforest, the results based on the geometric graph have been shown to spuriously indicate a decrease in spatial biodiversity when no such trend was detected by the other types of neighbourhoods. We also show that the choice neighbourhood markedly impacts on the classification of species according to how strongly and in what way different species spatially structure species diversity. Clearly, in an analysis of spatial or local diversity an appropriate choice of local neighbourhood is crucial in particular in terms of the biological interpretation of the results. Due to its general definition, the approach discussed here offers the necessary flexibility that allows suitable and varying neighbourhood structures to be chosen.2012-12-01T00:00:00ZRajala, TIllian, Janine BaerbelWhile much research in ecology has focused on spatially explicit modelling as well as on measures of biodiversity, the concept of spatial (or local) biodiversity has been discussed very little. This paper generalises existing measures of spatial biodiversity and introduces a family of spatial biodiversity measures by flexibly defining the notion of the individuals’ neighbourhood within the framework of graphs associated to a spatial point pattern. We consider two non-independent aspects of spatial biodiversity, scattering, i.e. the spatial arrangement of the individuals in the study area and exposure, the local diversity in an individual’s neighbourhood. A simulation study reveals that measures based on the most commonly used neigh-bourhood defined by the geometric graph do not distinguish well between scattering and exposure. This problem is much less pronounced when other graphs are used. In an analysis of the spatial diversity in a rainforest, the results based on the geometric graph have been shown to spuriously indicate a decrease in spatial biodiversity when no such trend was detected by the other types of neighbourhoods. We also show that the choice neighbourhood markedly impacts on the classification of species according to how strongly and in what way different species spatially structure species diversity. Clearly, in an analysis of spatial or local diversity an appropriate choice of local neighbourhood is crucial in particular in terms of the biological interpretation of the results. Due to its general definition, the approach discussed here offers the necessary flexibility that allows suitable and varying neighbourhood structures to be chosen.Multispecies functional response of the minke whale Balaenoptera acutorostrata based on small-scale foraging studies
http://hdl.handle.net/10023/3345
Abstract: Atlantic minke whales are important predators in the Barents Sea ecosystem; capelin Mallotus villosus, krill Thysanoessa sp. and Meganyctephanes norvegica and herring Clupea harengus are their major prey. Their consumption of commercial species may present an economic problem for the local fishery. In order to estimate this consumption and understand the potential consequences for prey dynamics, it is essential to determine the multispecies functional response of the whales. The parameterisation of a functional response requires measurements of consumption rates and prey availability. In this localised study, undigested stomach contents were used to assess the amount of each prey that had been consumed immediately prior to capture. To determine the availability of prey to the whales, standard acoustic surveys were run in the same area within 2 d of the capture of the whales. The spatial distribution of prey was modelled using generalised additive models (GAMs). In order to generate a measure of prey availability and the uncertainty in this value, a simple model was assumed for whale movement, and prey abundance was sampled over space according to a Gaussian kernel. A multispecies functional response (MSFR) model was then fitted to the consumption and prey availability data using Bayesian methods. Simple simulations, based on the fitted MSFR, indicate that minke whales may deplete local capelin aggregations at small spatial scales. This is the first time that a multispecies functional response has been fitted for a cetacean predator, and the methods outlined here may prove useful for modelling marine mammal-fish interactions in other systems.2007-07-01T00:00:00ZSmout, Sophie CarolineLindstrom, UlfAtlantic minke whales are important predators in the Barents Sea ecosystem; capelin Mallotus villosus, krill Thysanoessa sp. and Meganyctephanes norvegica and herring Clupea harengus are their major prey. Their consumption of commercial species may present an economic problem for the local fishery. In order to estimate this consumption and understand the potential consequences for prey dynamics, it is essential to determine the multispecies functional response of the whales. The parameterisation of a functional response requires measurements of consumption rates and prey availability. In this localised study, undigested stomach contents were used to assess the amount of each prey that had been consumed immediately prior to capture. To determine the availability of prey to the whales, standard acoustic surveys were run in the same area within 2 d of the capture of the whales. The spatial distribution of prey was modelled using generalised additive models (GAMs). In order to generate a measure of prey availability and the uncertainty in this value, a simple model was assumed for whale movement, and prey abundance was sampled over space according to a Gaussian kernel. A multispecies functional response (MSFR) model was then fitted to the consumption and prey availability data using Bayesian methods. Simple simulations, based on the fitted MSFR, indicate that minke whales may deplete local capelin aggregations at small spatial scales. This is the first time that a multispecies functional response has been fitted for a cetacean predator, and the methods outlined here may prove useful for modelling marine mammal-fish interactions in other systems.Estimating demographic parameters for capture-recapture data in the presence of multiple mark types
http://hdl.handle.net/10023/3344
Abstract: In mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage.2011-06-01T00:00:00ZSmout, Sophie CarolineKing, RuthPomeroy, PatrickIn mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage.Every group is a maximal subgroup of the free idempotent generated semigroup over a band
http://hdl.handle.net/10023/3342
Abstract: Given an arbitrary group G we construct a semigroup of idempotents (band) BG with the property that the free idempotent generated semigroup over BG has a maximal subgroup isomorphic to G. If G is finitely presented then BG is finite. This answers several questions from recent papers in the area.2013-05-01T00:00:00ZDolinka, IRuskuc, NikGiven an arbitrary group G we construct a semigroup of idempotents (band) BG with the property that the free idempotent generated semigroup over BG has a maximal subgroup isomorphic to G. If G is finitely presented then BG is finite. This answers several questions from recent papers in the area.On disjoint unions of finitely many copies of the free monogenic semigroup
http://hdl.handle.net/10023/3341
Abstract: Every semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite.2013-08-01T00:00:00ZAbughazalah, NabilahRuskuc, NikEvery semigroup which is a finite disjoint union of copies of the free monogenic semigroup (natural numbers under addition) is finitely presented and residually finite.Ideals and finiteness conditions for subsemigroups
http://hdl.handle.net/10023/3335
Abstract: In this paper we consider a number of finiteness conditions for semigroups related to their ideal structure, and ask whether such conditions are preserved by sub- or supersemigroups with finite Rees or Green index. Specific properties under consideration include stability, D=J and minimal conditions on ideals.2014-01-01T00:00:00ZGray, Robert DuncanMaltcev, VictorMitchell, James DavidRuskuc, N.In this paper we consider a number of finiteness conditions for semigroups related to their ideal structure, and ask whether such conditions are preserved by sub- or supersemigroups with finite Rees or Green index. Specific properties under consideration include stability, D=J and minimal conditions on ideals.The geometric mean of relative abundance indices : a biodiversity measure with a difference
http://hdl.handle.net/10023/3310
Abstract: The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1
Description: This work is partly supported by the European Research Council2011-09-02T00:00:00ZBuckland, Stephen TerrenceStudeny, Angelika CarolineMagurran, AnneIllian, Janine BaerbelNewson, StuartThe 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1Using INLA to fit a complex point process model with temporally varying effects – a case study
http://hdl.handle.net/10023/3306
Abstract: Integrated nested Laplace approximation (INLA) provides a fast and yet quite exact approach to fitting complex latent Gaussian models which comprise many statistical models in a Bayesian context, including log Gaussian Cox processes. This paper discusses how a joint log Gaussian Cox process model may be fitted to independent replicated point patterns. We illustrate the approach by fitting a model to data on the locations of muskoxen (Ovibos moschatus) herds in Zackenberg valley, Northeast Greenland and by detailing how this model is specified within the R-interface R-INLA. The paper strongly focuses on practical problems involved in the modelling process, including issues of spatial scale, edge effects and prior choices, and finishes with a discussion on models with varying boundary conditions.2012-07-01T00:00:00ZIllian, Janine BaerbelSoerbye, SRue, HHendrichsen, DIntegrated nested Laplace approximation (INLA) provides a fast and yet quite exact approach to fitting complex latent Gaussian models which comprise many statistical models in a Bayesian context, including log Gaussian Cox processes. This paper discusses how a joint log Gaussian Cox process model may be fitted to independent replicated point patterns. We illustrate the approach by fitting a model to data on the locations of muskoxen (Ovibos moschatus) herds in Zackenberg valley, Northeast Greenland and by detailing how this model is specified within the R-interface R-INLA. The paper strongly focuses on practical problems involved in the modelling process, including issues of spatial scale, edge effects and prior choices, and finishes with a discussion on models with varying boundary conditions.A Bayesian approach to fitting Gibbs processes with temporal random effects
http://hdl.handle.net/10023/3305
Abstract: We consider spatial point pattern data that have been observed repeatedly over a period of time in an inhomogeneous environment. Each spatial point pattern can be regarded as a “snapshot” of the underlying point process at a series of times. Thus, the number of points and corresponding locations of points differ for each snapshot. Each snapshot can be analyzed independently, but in many cases there may be little information in the data relating to model parameters, particularly parameters relating to the interaction between points. Thus, we develop an integrated approach, simultaneously analyzing all snapshots within a single robust and consistent analysis. We assume that sufficient time has passed between observation dates so that the spatial point patterns can be regarded as independent replicates, given spatial covariates. We develop a joint mixed effects Gibbs point process model for the replicates of spatial point patterns by considering environmental covariates in the analysis as fixed effects, to model the heterogeneous environment, with a random effects (or hierarchical) component to account for the different observation days for the intensity function. We demonstrate how the model can be fitted within a Bayesian framework using an auxiliary variable approach to deal with the issue of the random effects component. We apply the methods to a data set of musk oxen herds and demonstrate the increased precision of the parameter estimates when considering all available data within a single integrated analysis.
Description: This work is partially supported by Research Councils UK2012-12-01T00:00:00ZKing, RuthIllian, Janine BaerbelKing, Stuart EdwardNightingale, Glenna FaithHendrichsen, DitteWe consider spatial point pattern data that have been observed repeatedly over a period of time in an inhomogeneous environment. Each spatial point pattern can be regarded as a “snapshot” of the underlying point process at a series of times. Thus, the number of points and corresponding locations of points differ for each snapshot. Each snapshot can be analyzed independently, but in many cases there may be little information in the data relating to model parameters, particularly parameters relating to the interaction between points. Thus, we develop an integrated approach, simultaneously analyzing all snapshots within a single robust and consistent analysis. We assume that sufficient time has passed between observation dates so that the spatial point patterns can be regarded as independent replicates, given spatial covariates. We develop a joint mixed effects Gibbs point process model for the replicates of spatial point patterns by considering environmental covariates in the analysis as fixed effects, to model the heterogeneous environment, with a random effects (or hierarchical) component to account for the different observation days for the intensity function. We demonstrate how the model can be fitted within a Bayesian framework using an auxiliary variable approach to deal with the issue of the random effects component. We apply the methods to a data set of musk oxen herds and demonstrate the increased precision of the parameter estimates when considering all available data within a single integrated analysis.Quantifying temporal change in biodiversity : challenges and opportunities
http://hdl.handle.net/10023/3284
Abstract: Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.2013-01-07T00:00:00ZDornelas, MariaMagurran, AnneBuckland, Stephen TerrenceChao, AnneChazdon, Robin LColwell, Robert KCurtis, TomGaston, Kevin JGotelli, Nicolas JKosnik, Matthew AMcGill, BrianMcCune, Jenny LMorlon, HélèneMumby, Peter JØvreås, LiseStudeny, AngelikaVellend, MarkGrowing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.The functional response of a generalist predator
http://hdl.handle.net/10023/3269
Abstract: Background: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.2010-05-27T00:00:00ZSmout, Sophie CarolineAsseburg, CMatthiopoulos, JasonFernández, CarmenRedpath, SThirgood, SHarwood, JohnBackground: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.A non-technical overview of spatially explicit capture-recapture models
http://hdl.handle.net/10023/3259
Abstract: Most capture-recapture studies are inherently spatial in nature, with capture probabilities depending on the location of traps relative to animals. The spatial component of the studies has until recently, however, not been incorporated in statistical capture-recapture models. This paper reviews capture-recapture models that do include an explicit spatial component. This is done in a non-technical way, omitting much of the algebraic detail and focussing on the model formulation rather than on the estimation methods (which include inverse prediction, maximum likelihood and Bayesian methods). One can view spatially explicit capture-recapture (SECR) models as an endpoint of a series of spatial sampling models, starting with circular plot survey models and moving through conventional distance sampling models, with and without measurement errors, through mark-recapture distance sampling (MRDS) models. This paper attempts a synthesis of these models in what I hope is a style accessible to non-specialists, placing SECR models in the context of other spatial sampling models.2012-02-01T00:00:00ZBorchers, DavidMost capture-recapture studies are inherently spatial in nature, with capture probabilities depending on the location of traps relative to animals. The spatial component of the studies has until recently, however, not been incorporated in statistical capture-recapture models. This paper reviews capture-recapture models that do include an explicit spatial component. This is done in a non-technical way, omitting much of the algebraic detail and focussing on the model formulation rather than on the estimation methods (which include inverse prediction, maximum likelihood and Bayesian methods). One can view spatially explicit capture-recapture (SECR) models as an endpoint of a series of spatial sampling models, starting with circular plot survey models and moving through conventional distance sampling models, with and without measurement errors, through mark-recapture distance sampling (MRDS) models. This paper attempts a synthesis of these models in what I hope is a style accessible to non-specialists, placing SECR models in the context of other spatial sampling models.Workshop on new developments in cetacean survey methods
http://hdl.handle.net/10023/3216
Abstract: This report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.2011-01-01T00:00:00ZBorchers, David LouisThomas, LenBuckland, Stephen TerrenceSkaug, HansBarlow, JayThis report contains the slides from a workshop on New Developments in Cetacean Survey Methods held on 27th November 2011 at the 19th Biennial Conference on the Biology of Marine Mammals, Tampa, Florida. Review talks were given on Passive Acoustic Density Estimation (Len Thomas); Dealing with g(0)<1: Perception Bias (Stephen Buckland); Dealing with g(0)<1: Availability Bias (Hans Skaug); Dealing with Measurement Error (David Borchers); and Density Surface Modelling (Jay Barlow). The sessions were followed by a discussion, and this is summarized at the end of the report.A detailed investigation of the properties of a Vlasov-Maxwell equilibrium for the force-free Harris sheet
http://hdl.handle.net/10023/3153
Abstract: A detailed discussion is presented of the Vlasov-Maxwell equilibrium for the force-free Harris sheet recently found by Harrison and Neukirch [Phys. Rev. Lett. 102, 135003 (2009)]. The derivation of the distribution function and a discussion of its general properties and their dependence on the distribution function parameters will be given. In particular, the distribution function can be single-peaked or multipeaked in two of the velocity components, with possible implications for stability. The dependence of the shape of the distribution function on the values of its parameters will be investigated and the relation to macroscopic quantities such as the current sheet thickness will be discussed.2009-12-01T00:00:00ZNeukirch, ThomasWilson, F.Harrison, M. G.A detailed discussion is presented of the Vlasov-Maxwell equilibrium for the force-free Harris sheet recently found by Harrison and Neukirch [Phys. Rev. Lett. 102, 135003 (2009)]. The derivation of the distribution function and a discussion of its general properties and their dependence on the distribution function parameters will be given. In particular, the distribution function can be single-peaked or multipeaked in two of the velocity components, with possible implications for stability. The dependence of the shape of the distribution function on the values of its parameters will be investigated and the relation to macroscopic quantities such as the current sheet thickness will be discussed.Growth of generating sets for direct powers of classical algebraic structures
http://hdl.handle.net/10023/3058
Abstract: For an algebraic structure A denote by d(A) the smallest size of a generating set for A, and let d(A)=(d(A),d(A2),d(A3),…), where An denotes a direct power of A. In this paper we investigate the asymptotic behaviour of the sequence d(A) when A is one of the classical structures—a group, ring, module, algebra or Lie algebra. We show that if A is finite then d(A) grows either linearly or logarithmically. In the infinite case constant growth becomes another possibility; in particular, if A is an infinite simple structure belonging to one of the above classes then d(A) is eventually constant. Where appropriate we frame our exposition within the general theory of congruence permutable varieties.2010-08-01T00:00:00ZQuick, MartynRuskuc, NikFor an algebraic structure A denote by d(A) the smallest size of a generating set for A, and let d(A)=(d(A),d(A2),d(A3),…), where An denotes a direct power of A. In this paper we investigate the asymptotic behaviour of the sequence d(A) when A is one of the classical structures—a group, ring, module, algebra or Lie algebra. We show that if A is finite then d(A) grows either linearly or logarithmically. In the infinite case constant growth becomes another possibility; in particular, if A is an infinite simple structure belonging to one of the above classes then d(A) is eventually constant. Where appropriate we frame our exposition within the general theory of congruence permutable varieties.A general discrete-time modeling framework for animal movement using multistate random walks
http://hdl.handle.net/10023/2605
Abstract: Recent developments in animal tracking technology have permitted the collection of detailed data on the movement paths of individuals from many species. However, analysis methods for these data have not developed at a similar pace, largely due to a lack of suitable candidate models, coupled with the technical difficulties of fitting such models to data. To facilitate a general modeling framework, we propose that complex movement paths can be conceived as a series of movement strategies among which animals transition as they are affected by changes in their internal and external environment. We synthesize previously existing and novel methodologies to develop a general suite of mechanistic models based on biased and correlated random walks that allow different behavioral states for directed (e.g., migration), exploratory (e.g., dispersal), area-restricted (e.g., foraging), and other types of movement. Using this “tool-box” of nested model components, multi-state movement models may be custom-built for a wide variety of species and applications. As a unified state-space modeling framework, it allows the simultaneous investigation of numerous hypotheses about animal movement from imperfectly observed data, including time allocations to different movement behavior states, transitions between states, the use of memory or navigation, and strengths of attraction (or repulsion) to specific locations. The inclusion of covariate information permits further investigation of specific hypotheses related to factors driving different types of movement behavior. Using reversible jump Markov chain Monte Carlo methods to facilitate Bayesian model selection and multi-model inference, we apply the proposed methodology to real data by adapting it to the natural history of the grey seal (Halichoerus grypus) in the North Sea. Although previous grey seal studies tended to focus on correlated movements, we found overwhelming evidence that bias towards haul-out or foraging locations better explained seal movement than simple or correlated random walks. Posterior model probabilities also provided evidence that seals transition among directed, area-restricted, and exploratory movements associated with haul-out, foraging, and other behaviors. With this intuitive framework for modeling and interpreting animal movement, we believe the development and application of bespoke movement models will become more accessible to ecologists and non-statisticians.2012-08-01T00:00:00ZMcClintock, Brett ThomasKing, RuthThomas, LenMatthiopoulos, JasonMcConnell, Bernie JMorales, JuanRecent developments in animal tracking technology have permitted the collection of detailed data on the movement paths of individuals from many species. However, analysis methods for these data have not developed at a similar pace, largely due to a lack of suitable candidate models, coupled with the technical difficulties of fitting such models to data. To facilitate a general modeling framework, we propose that complex movement paths can be conceived as a series of movement strategies among which animals transition as they are affected by changes in their internal and external environment. We synthesize previously existing and novel methodologies to develop a general suite of mechanistic models based on biased and correlated random walks that allow different behavioral states for directed (e.g., migration), exploratory (e.g., dispersal), area-restricted (e.g., foraging), and other types of movement. Using this “tool-box” of nested model components, multi-state movement models may be custom-built for a wide variety of species and applications. As a unified state-space modeling framework, it allows the simultaneous investigation of numerous hypotheses about animal movement from imperfectly observed data, including time allocations to different movement behavior states, transitions between states, the use of memory or navigation, and strengths of attraction (or repulsion) to specific locations. The inclusion of covariate information permits further investigation of specific hypotheses related to factors driving different types of movement behavior. Using reversible jump Markov chain Monte Carlo methods to facilitate Bayesian model selection and multi-model inference, we apply the proposed methodology to real data by adapting it to the natural history of the grey seal (Halichoerus grypus) in the North Sea. Although previous grey seal studies tended to focus on correlated movements, we found overwhelming evidence that bias towards haul-out or foraging locations better explained seal movement than simple or correlated random walks. Posterior model probabilities also provided evidence that seals transition among directed, area-restricted, and exploratory movements associated with haul-out, foraging, and other behaviors. With this intuitive framework for modeling and interpreting animal movement, we believe the development and application of bespoke movement models will become more accessible to ecologists and non-statisticians.Status assessment of the Critically Endangered Azores Bullfinch Pyrrhula murina
http://hdl.handle.net/10023/2552
Abstract: The Azores Bullfinch is endemic to the island of São Miguel (Azores, Portugal). Its status was uplisted to Critically Endangered in 2005 on the basis of an extremely small and declining population that was considered to be restricted to a very small mountain range (43 km2), in a single location, within which the spread of invasive plants constituted a threat to habitat quality. Nevertheless, information was mostly inferred, or the product of, non-systematic studies. In order to carry out a complete assessment of the conservation status we analysed: (i) population trend, calculated from annual monitoring 1991–2008, (ii) population size, and (iii) range size, obtaining estimates in a single morning study in 2008 involving the simultaneous participation of 48 observers. Contrary to previous inferences, the population is no longer decreasing, although quality of laurel forest habitat continues to decline due to the persistent threat of invasive species. Population size (mean ± SE) was estimated at 1,064 ± 304 individuals using distance sampling methods, although the estimate was very sensitive to the survey method used. Range size estimates (extent of occurrence and area of occupancy) were 144 km2 and 83 km2 respectively. Given the present information, we propose the downlisting of Azores Bullfinch to Endangered on the IUCN Red List.
Description: 'This work was part of the Azores Bullﬁnch monitoring programme included in the project LIFE NAT/P/000013 “Recovery of Azores Bullﬁnch’s habitat in the Special Protection Area of Pico da Vara / Ribeira do Guilherme”'2011-01-01T00:00:00ZCeia, Ricardo S.Ramos, Jaime A.Heleno, Ruben H.Hilton, Geoff M.Marques, Tiago A.The Azores Bullfinch is endemic to the island of São Miguel (Azores, Portugal). Its status was uplisted to Critically Endangered in 2005 on the basis of an extremely small and declining population that was considered to be restricted to a very small mountain range (43 km2), in a single location, within which the spread of invasive plants constituted a threat to habitat quality. Nevertheless, information was mostly inferred, or the product of, non-systematic studies. In order to carry out a complete assessment of the conservation status we analysed: (i) population trend, calculated from annual monitoring 1991–2008, (ii) population size, and (iii) range size, obtaining estimates in a single morning study in 2008 involving the simultaneous participation of 48 observers. Contrary to previous inferences, the population is no longer decreasing, although quality of laurel forest habitat continues to decline due to the persistent threat of invasive species. Population size (mean ± SE) was estimated at 1,064 ± 304 individuals using distance sampling methods, although the estimate was very sensitive to the survey method used. Range size estimates (extent of occurrence and area of occupancy) were 144 km2 and 83 km2 respectively. Given the present information, we propose the downlisting of Azores Bullfinch to Endangered on the IUCN Red List.Geometric grid classes of permutations
http://hdl.handle.net/10023/2450
Abstract: A geometric grid class consists of those permutations that can be drawn on a specified set of line segments of slope ±1 arranged in a rectangular pattern governed by a matrix. Using a mixture of geometric and language theoretic methods, we prove that such classes are specified by finite sets of forbidden permutations, are partially well ordered, and have rational generating functions. Furthermore, we show that these properties are inherited by the subclasses (under permutation involvement) of such classes, and establish the basic lattice theoretic properties of the collection of all such subclasses.2013-11-01T00:00:00ZAlbert, M.H.Atkinson, M.D.Bouvel, M.Ruskuc, NikVatter, V.A geometric grid class consists of those permutations that can be drawn on a specified set of line segments of slope ±1 arranged in a rectangular pattern governed by a matrix. Using a mixture of geometric and language theoretic methods, we prove that such classes are specified by finite sets of forbidden permutations, are partially well ordered, and have rational generating functions. Furthermore, we show that these properties are inherited by the subclasses (under permutation involvement) of such classes, and establish the basic lattice theoretic properties of the collection of all such subclasses.Unary FA-presentable semigroups
http://hdl.handle.net/10023/2375
Abstract: Automatic presentations, also called FA-presentations, were introduced to extend nite model theory to innite structures whilst retaining the solubility of interesting decision problems. A particular focus of research has been the classication of those structures of some species that admit automatic presentations. Whilst some successes have been obtained, this appears to be a dicult problem in general. A restricted problem, also of signicant interest, is to ask this question for unary automatic presentations: auto-matic presentations over a one-letter alphabet. This paper studies unary FA-presentable semigroups. We prove the following: Every unary FA-presentable structure admits an injective unary automatic presentation where the language of representatives consists of every word over a one-letter alphabet. Unary FA-presentable semigroups are locally nite, but non-nitely generated unary FA-presentable semigroups may be innite. Every unary FA-presentable semigroup satises some Burnside identity.We describe the Green's relations in unary FA-presentable semigroups. We investigate the relationship between the class of unary FA-presentable semigroups and various semigroup constructions. A classication is given of the unary FA-presentable completely simple semigroups.2012-06-08T00:00:00ZCain, Alan JamesRuskuc, NikThomas, R.M.Automatic presentations, also called FA-presentations, were introduced to extend nite model theory to innite structures whilst retaining the solubility of interesting decision problems. A particular focus of research has been the classication of those structures of some species that admit automatic presentations. Whilst some successes have been obtained, this appears to be a dicult problem in general. A restricted problem, also of signicant interest, is to ask this question for unary automatic presentations: auto-matic presentations over a one-letter alphabet. This paper studies unary FA-presentable semigroups. We prove the following: Every unary FA-presentable structure admits an injective unary automatic presentation where the language of representatives consists of every word over a one-letter alphabet. Unary FA-presentable semigroups are locally nite, but non-nitely generated unary FA-presentable semigroups may be innite. Every unary FA-presentable semigroup satises some Burnside identity.We describe the Green's relations in unary FA-presentable semigroups. We investigate the relationship between the class of unary FA-presentable semigroups and various semigroup constructions. A classication is given of the unary FA-presentable completely simple semigroups.Three-dimensional solutions of the magnetohydrostatic equations : rigidly rotating magnetized coronae in spherical geometry
http://hdl.handle.net/10023/2269
Abstract: Context. Magnetohydrostatic (MHS) equilibria are often used to model astrophysical plasmas, for example, planetary magnetospheres or coronae of magnetized stars. However, finding realistic three-dimensional solutions to the MHS equations is difficult, with only a few known analytical solutions and even finding numerical solution is far from easy. Aims. We extend the results of a previous paper on three-dimensional solutions of the MHS equations around rigidly rotating massive cylinders to the much more realistic case of rigidly rotating massive spheres. An obvious application is to model the closed field line regions of the coronae of rapidly rotating stars. Methods. We used a number of simplifying assumptions to reduce the MHS equations to a single elliptic partial differential equation for a pseudo-potential U, from which all physical quantities, such as the magnetic field, the plasma pressure, and the density, can be derived by differentiation. The most important assumptions made are stationarity in the co-rotating frame of reference, a particular form for the current density, and neglect of outflows. Results. In this paper we demonstrate that standard methods can be used to find numerical solutions to the fundamental equation of the theory. We present three simple different cases of magnetic field boundary conditions on the surface of the central sphere, corresponding to an aligned dipole field, a non-aligned dipole field, and a displaced dipole field. Our results show that it should be possible in the future to use this method without dramatically increasing the demands on computational resources to improve upon potential field models of rotating magnetospheres and coronae.2010-10-01T00:00:00ZAl-Salti, NasserNeukirch, ThomasContext. Magnetohydrostatic (MHS) equilibria are often used to model astrophysical plasmas, for example, planetary magnetospheres or coronae of magnetized stars. However, finding realistic three-dimensional solutions to the MHS equations is difficult, with only a few known analytical solutions and even finding numerical solution is far from easy. Aims. We extend the results of a previous paper on three-dimensional solutions of the MHS equations around rigidly rotating massive cylinders to the much more realistic case of rigidly rotating massive spheres. An obvious application is to model the closed field line regions of the coronae of rapidly rotating stars. Methods. We used a number of simplifying assumptions to reduce the MHS equations to a single elliptic partial differential equation for a pseudo-potential U, from which all physical quantities, such as the magnetic field, the plasma pressure, and the density, can be derived by differentiation. The most important assumptions made are stationarity in the co-rotating frame of reference, a particular form for the current density, and neglect of outflows. Results. In this paper we demonstrate that standard methods can be used to find numerical solutions to the fundamental equation of the theory. We present three simple different cases of magnetic field boundary conditions on the surface of the central sphere, corresponding to an aligned dipole field, a non-aligned dipole field, and a displaced dipole field. Our results show that it should be possible in the future to use this method without dramatically increasing the demands on computational resources to improve upon potential field models of rotating magnetospheres and coronae.Three-dimensional solutions of the magnetohydrostatic equations : rigidly rotating magnetized coronae in cylindrical geometry
http://hdl.handle.net/10023/2267
Abstract: Context. Solutions of the magnetohydrostatic (MHS) equations are very important for modelling astrophysical plasmas, such as the coronae of magnetized stars. Realistic models should be three-dimensional, i.e., should not have any spatial symmetries, but finding three-dimensional solutions of the MHS equations is a formidable task. Aims. We present a general theoretical framework for calculating three-dimensional MHS solutions outside massive rigidly rotating central bodies, together with example solutions. A possible future application is to model the closed field region of the coronae of fast-rotating stars. Methods. As a first step, we present in this paper the theory and solutions for the case of a massive rigidly rotating magnetized cylinder, but the theory can easily be extended to other geometries, We assume that the solutions are stationary in the co-rotating frame of reference. To simplify the MHS equations, we use a special form for the current density, which leads to a single linear partial differential equation for a pseudo-potential U. The magnetic field can be derived from U by differentiation. The plasma density, pressure, and temperature are also part of the solution. Results. We derive the fundamental equation for the pseudo-potential both in coordinate independent form and in cylindrical coordinates. We present numerical example solutions for the case of cylindrical coordinates.2010-05-01T00:00:00ZAl-Salti, NasserNeukirch, ThomasRyan, Richard DanielContext. Solutions of the magnetohydrostatic (MHS) equations are very important for modelling astrophysical plasmas, such as the coronae of magnetized stars. Realistic models should be three-dimensional, i.e., should not have any spatial symmetries, but finding three-dimensional solutions of the MHS equations is a formidable task. Aims. We present a general theoretical framework for calculating three-dimensional MHS solutions outside massive rigidly rotating central bodies, together with example solutions. A possible future application is to model the closed field region of the coronae of fast-rotating stars. Methods. As a first step, we present in this paper the theory and solutions for the case of a massive rigidly rotating magnetized cylinder, but the theory can easily be extended to other geometries, We assume that the solutions are stationary in the co-rotating frame of reference. To simplify the MHS equations, we use a special form for the current density, which leads to a single linear partial differential equation for a pseudo-potential U. The magnetic field can be derived from U by differentiation. The plasma density, pressure, and temperature are also part of the solution. Results. We derive the fundamental equation for the pseudo-potential both in coordinate independent form and in cylindrical coordinates. We present numerical example solutions for the case of cylindrical coordinates.Universal scaling rules predict evolutionary patterns of myogenesis in species with indeterminate growth
http://hdl.handle.net/10023/2170
Abstract: Intraspecific phenotypic variation is ubiquitous and often associated with resource exploitation in emerging habitats. For example, reduced body size has evolved repeatedly in Arctic charr (Salvelinus alpinus L.) and threespine stickleback (Gasterosteus aculeatus L.) across post-glacial habitats of the Northern Hemisphere. Exploiting these models, we examined how body size and myogenesis evolve with respect to the 'optimum fibre size hypothesis', which predicts that selection acts to minimize energetic costs associated with ionic homeostasis by optimizing muscle fibre production during development. In eight dwarf Icelandic Arctic charr populations, the ultimate production of fast-twitch muscle fibres (FN(max)) was only 39.5 and 15.5 per cent of that in large-bodied natural and aquaculture populations, respectively. Consequently, average fibre diameter (FD) scaled with a mass exponent of 0.19, paralleling the relaxation of diffusional constraints associated with mass-specific metabolic rate scaling. Similar reductions in FN(max) were observed for stickleback, including a small-bodied Alaskan population derived from a larger-bodied oceanic stock over a decadal timescale. The results suggest that in species showing indeterminate growth, body size evolution is accompanied by strong selection for fibre size optimization, theoretically allowing resources saved from ionic homeostasis to be allocated to other traits affecting fitness, including reproduction. Gene flow between small- and large-bodied populations residing in sympatry may counteract the evolution of this trait.2012-06-07T00:00:00ZJohnston, Ian AlistairKristjansson, Bjarni K.Paxton, Charles G. M.Vieira-Johnston, Vera Lucia AlmeidaMacQueen, Daniel JohnBell, Michael A.Intraspecific phenotypic variation is ubiquitous and often associated with resource exploitation in emerging habitats. For example, reduced body size has evolved repeatedly in Arctic charr (Salvelinus alpinus L.) and threespine stickleback (Gasterosteus aculeatus L.) across post-glacial habitats of the Northern Hemisphere. Exploiting these models, we examined how body size and myogenesis evolve with respect to the 'optimum fibre size hypothesis', which predicts that selection acts to minimize energetic costs associated with ionic homeostasis by optimizing muscle fibre production during development. In eight dwarf Icelandic Arctic charr populations, the ultimate production of fast-twitch muscle fibres (FN(max)) was only 39.5 and 15.5 per cent of that in large-bodied natural and aquaculture populations, respectively. Consequently, average fibre diameter (FD) scaled with a mass exponent of 0.19, paralleling the relaxation of diffusional constraints associated with mass-specific metabolic rate scaling. Similar reductions in FN(max) were observed for stickleback, including a small-bodied Alaskan population derived from a larger-bodied oceanic stock over a decadal timescale. The results suggest that in species showing indeterminate growth, body size evolution is accompanied by strong selection for fibre size optimization, theoretically allowing resources saved from ionic homeostasis to be allocated to other traits affecting fitness, including reproduction. Gene flow between small- and large-bodied populations residing in sympatry may counteract the evolution of this trait.An update to the methods in Endangered Species Research 2011 paper "Estimating North Pacific right whale Eubalaena japonica density using passive acoustic cue counting"
http://hdl.handle.net/10023/2158
2012-01-01T00:00:00ZMarques, Tiago A.Munger, LisaThomas, LenWiggins, SeanHildebrand, JohnOn residual finiteness of direct products of algebraic systems
http://hdl.handle.net/10023/2146
Abstract: It is well known that if two algebraic structures A and B are residually finite then so is their direct product. Here we discuss the converse of this statement. It is of course true if A and B contain idempotents, which covers the case of groups, rings, etc. We prove that the converse also holds for semigroups even though they need not have idempotents. We also exhibit three examples which show that the converse does not hold in general.2009-09-01T00:00:00ZGray, R.Ruskuc, NikIt is well known that if two algebraic structures A and B are residually finite then so is their direct product. Here we discuss the converse of this statement. It is of course true if A and B contain idempotents, which covers the case of groups, rings, etc. We prove that the converse also holds for semigroups even though they need not have idempotents. We also exhibit three examples which show that the converse does not hold in general.Properties of the subsemigroups of the bicyclic monoid
http://hdl.handle.net/10023/2142
Abstract: In this paper we study some properties of the subsemigroups of the bicyclic monoid B, by using a recent description of its subsemigroups. We start by giving necessary and sufficient conditions for a subsemigroup to be finitely generated. Then we show that all finitely generated subsemigroups are automatic and finitely presented. Finally we prove that a subsemigroup of B is residually finite if and only if it does not contain a copy of B.2008-06-01T00:00:00ZDescalco, L.Ruskuc, NikIn this paper we study some properties of the subsemigroups of the bicyclic monoid B, by using a recent description of its subsemigroups. We start by giving necessary and sufficient conditions for a subsemigroup to be finitely generated. Then we show that all finitely generated subsemigroups are automatic and finitely presented. Finally we prove that a subsemigroup of B is residually finite if and only if it does not contain a copy of B.On generators and presentations of semidirect products in inverse semigroups
http://hdl.handle.net/10023/2136
Abstract: In this paper we prove two main results. The first is a necessary and sufficient condition for a semidirect product of a semilattice by a group to be finitely generated. The second result is a necessary and sufficient condition for such a semidirect product to be finitely presented.2009-06-01T00:00:00ZDombi, Erzsebet RitaRuskuc, NikIn this paper we prove two main results. The first is a necessary and sufficient condition for a semidirect product of a semilattice by a group to be finitely generated. The second result is a necessary and sufficient condition for such a semidirect product to be finitely presented.Maximal subgroups of free idempotent-generated semigroups over the full transformation monoid
http://hdl.handle.net/10023/2134
Abstract: Let Tn be the full transformation semigroup of all mappings from the set {1, . . . , n} to itself under composition. Let E = E(Tn) denote the set of idempotents of Tn and let e ∈ E be an arbitrary idempotent satisfying |im (e)| = r ≤ n − 2. We prove that the maximal subgroup of the free idempotent generated semigroup over E containing e is isomorphic to the symmetric group Sr.2012-05-01T00:00:00ZGray, RRuskuc, NikLet Tn be the full transformation semigroup of all mappings from the set {1, . . . , n} to itself under composition. Let E = E(Tn) denote the set of idempotents of Tn and let e ∈ E be an arbitrary idempotent satisfying |im (e)| = r ≤ n − 2. We prove that the maximal subgroup of the free idempotent generated semigroup over E containing e is isomorphic to the symmetric group Sr.On the growth of generating sets for direct powers of semigroups
http://hdl.handle.net/10023/2129
Abstract: For a semigroup S its d-sequence is d(S) = (d1, d2, d3, . . .), where di is the smallest number of elements needed to generate the ith direct power of S. In this paper we present a number of facts concerning the type of growth d(S) can have when S is an infinite semigroup, comparing them with the corresponding known facts for infinite groups, and also for finite groups and semigroups.2012-01-01T00:00:00ZHyde, James ThomasLoughlin, NicholasQuick, MartynRuskuc, NikWallis, AlistairFor a semigroup S its d-sequence is d(S) = (d1, d2, d3, . . .), where di is the smallest number of elements needed to generate the ith direct power of S. In this paper we present a number of facts concerning the type of growth d(S) can have when S is an infinite semigroup, comparing them with the corresponding known facts for infinite groups, and also for finite groups and semigroups.A toolbox for fitting complex spatial point process models using integrated nested Laplace approximation (INLA)
http://hdl.handle.net/10023/2120
Abstract: This paper develops methodology that provides a toolbox for routinely fitting complex models to realistic spatial point pattern data. We consider models that are based on log-Gaussian Cox processes and include local interaction in these by considering constructed covariates. This enables us to use integrated nested Laplace approximation and to considerably speed up the inferential task. In addition, methods for model comparison and model assessment facilitate the modelling process. The performance of the approach is assessed in a simulation study. To demonstrate the versatility of the approach, models are tted to two rather dierent examples, a large rainforest data set with covariates and a point pattern with multiple marks.
Description: "The authors also gratefully acknowledge the financial support of Research Councils UK for Illian"2012-12-01T00:00:00ZIllian, Janine BaerbelSorbye, S HRue, HThis paper develops methodology that provides a toolbox for routinely fitting complex models to realistic spatial point pattern data. We consider models that are based on log-Gaussian Cox processes and include local interaction in these by considering constructed covariates. This enables us to use integrated nested Laplace approximation and to considerably speed up the inferential task. In addition, methods for model comparison and model assessment facilitate the modelling process. The performance of the approach is assessed in a simulation study. To demonstrate the versatility of the approach, models are tted to two rather dierent examples, a large rainforest data set with covariates and a point pattern with multiple marks.The steady-state form of large-amplitude internal solitary waves
http://hdl.handle.net/10023/2084
Abstract: A new numerical scheme for obtaining the steady-state form of an internal solitary wave of large amplitude is presented. A stratified inviscid two-dimensional fluid under the Boussinesq approximation flowing between horizontal rigid boundaries is considered. The stratification is stable, and buoyancy is continuously differentiable throughout the domain of the flow. Solutions are obtained by tracing the buoyancy frequency along streamlines from the undisturbed far field. From this the vorticity field can be constructed and the streamfunction may then be obtained by inversion of Laplace's operator. The scheme is presented as an iterative solver, where the inversion of Laplace's operator is performed spectrally. The solutions agree well with previous results for stratification in which the buoyancy frequency is a discontinuous function. The new numerical scheme allows significantly larger amplitude waves to be computed than have been presented before and it is shown that waves with Richardson numbers as low as 0.062 can be computed straightforwardly. The method is also extended to deal in a novel way with closed streamlines when they occur in the domain. The new solutions are tested in independent fully nonlinear time-dependent simulations and are verified to be steady. Waves with regions of recirculation are also discussed.2011-01-10T00:00:00ZKing, Stuart EdwardCarr, MagdaDritschel, David GerardA new numerical scheme for obtaining the steady-state form of an internal solitary wave of large amplitude is presented. A stratified inviscid two-dimensional fluid under the Boussinesq approximation flowing between horizontal rigid boundaries is considered. The stratification is stable, and buoyancy is continuously differentiable throughout the domain of the flow. Solutions are obtained by tracing the buoyancy frequency along streamlines from the undisturbed far field. From this the vorticity field can be constructed and the streamfunction may then be obtained by inversion of Laplace's operator. The scheme is presented as an iterative solver, where the inversion of Laplace's operator is performed spectrally. The solutions agree well with previous results for stratification in which the buoyancy frequency is a discontinuous function. The new numerical scheme allows significantly larger amplitude waves to be computed than have been presented before and it is shown that waves with Richardson numbers as low as 0.062 can be computed straightforwardly. The method is also extended to deal in a novel way with closed streamlines when they occur in the domain. The new solutions are tested in independent fully nonlinear time-dependent simulations and are verified to be steady. Waves with regions of recirculation are also discussed.Complex Region Spatial Smoother (CReSS)
http://hdl.handle.net/10023/2048
Abstract: Conventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.
Description: This work is supported with funding from NERC UK2011-01-01T00:00:00ZScott Hayward, Lindesay Alexandra SarahMacKenzie, Monique LeaDonovan, Carl RobertWalker, CameronAshe, ErinConventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.The primitive permutation groups of degree less than 4096
http://hdl.handle.net/10023/2045
Abstract: In this paper we use the Classification of the Finite Simple Groups, the O’Nan– Scott Theorem and Aschbacher’s theorem to classify the primitive permutation groups of degree less than 4096. The results will be added to the primitive groups databases of GAP and Magma.
Description: The first author is supported by an EPSRC doctoral training grant. The second and third authors acknowledge the support of EPSRC grant number EP/C523229/1.2011-10-14T00:00:00ZCoutts, Hannah JaneQuick, MartynRoney-Dougal, Colva MaryIn this paper we use the Classification of the Finite Simple Groups, the O’Nan– Scott Theorem and Aschbacher’s theorem to classify the primitive permutation groups of degree less than 4096. The results will be added to the primitive groups databases of GAP and Magma.Groups with the basis property
http://hdl.handle.net/10023/2044
Abstract: We study finite groups for which every minimal generating set has the same cardinality. A group has the basis property if it and every subgroup satisfies this condition on minimal generating sets. We classify all finite groups with the basis property.
Description: "The ﬁrst author is supported by an EPSRC Doctoral Training Grant"2011-11-15T00:00:00ZMcDougall-Bagnall, Jonathan M.Quick, MartynWe study finite groups for which every minimal generating set has the same cardinality. A group has the basis property if it and every subgroup satisfies this condition on minimal generating sets. We classify all finite groups with the basis property.Comparing pre- and post-construction distributions of long-tailed ducks Clangula hyemalis in and around the Nysted offshore wind farm, Denmark : a quasi-designed experiment accounting for imperfect detection, local surface features and autocorrelation
http://hdl.handle.net/10023/2008
Abstract: We report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post-construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on organisms over a gradient in space and time that offers an alternative to Before-After/Control-Impact designs in environmental impact assessment.2011-01-01T00:00:00ZPetersen, Ib KragMacKenzie, Monique LeaRexstad, EricWisz, Mary S.Fox, Anthony D.We report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post-construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on organisms over a gradient in space and time that offers an alternative to Before-After/Control-Impact designs in environmental impact assessment.Finite groups are big as semigroups
http://hdl.handle.net/10023/2004
Abstract: We prove that a finite group G occurs as a maximal proper subsemigroup of an infinite semigroup (in the terminology of Freese, Ježek, and Nation, G is a big semigroup) if and only if |G| ≥ 3. In fact, any finite semigroup whose minimal ideal contains a subgroup with at least three elements is big.2011-09-01T00:00:00ZDolinka, IgorRuskuc, NikWe prove that a finite group G occurs as a maximal proper subsemigroup of an infinite semigroup (in the terminology of Freese, Ježek, and Nation, G is a big semigroup) if and only if |G| ≥ 3. In fact, any finite semigroup whose minimal ideal contains a subgroup with at least three elements is big.A first survey of the global population size and distribution of the Scottish Crossbill Loxia scotica
http://hdl.handle.net/10023/1957
Abstract: A survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.
Description: "The survey was part-financed by Scottish Natural Heritage"2011-06-01T00:00:00ZSummers, Ron WBuckland, Stephen TerrenceA survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.Estimating bird abundance : making methods work
http://hdl.handle.net/10023/1930
Abstract: In many bird monitoring Surveys, no attempt is made to estimate bird densities or abundance. instead, counts of one form or another are made, and these are assumed to correlate with bird density. Unless complete Counts Oil Sample plots are feasible, this approach can easily lead to false conclusions, because detectability of birds varies by species, habitat, observer and many other factors. Trends in time of counts often reflect trends in detectability, rather than trends in abundance. Conclusions are further compromised when surveys are conducted at unrepresentative sites. We consider how to avoid these problems. We give a brief description of distance sampling methods, which allow detectability to be estimated. We consider strategies to ease their implementation, to enhance their reliability, to adapt the methods for difficult species, and to deal with circumstances in which representative sampling is problematic. We also consider some of the common problems encountered, and suggest solutions.2008-09-01T00:00:00ZBuckland, Stephen T.Marsden, Stuart J.Green, Rhys E.In many bird monitoring Surveys, no attempt is made to estimate bird densities or abundance. instead, counts of one form or another are made, and these are assumed to correlate with bird density. Unless complete Counts Oil Sample plots are feasible, this approach can easily lead to false conclusions, because detectability of birds varies by species, habitat, observer and many other factors. Trends in time of counts often reflect trends in detectability, rather than trends in abundance. Conclusions are further compromised when surveys are conducted at unrepresentative sites. We consider how to avoid these problems. We give a brief description of distance sampling methods, which allow detectability to be estimated. We consider strategies to ease their implementation, to enhance their reliability, to adapt the methods for difficult species, and to deal with circumstances in which representative sampling is problematic. We also consider some of the common problems encountered, and suggest solutions.Double-observer line transect methods : levels of independence
http://hdl.handle.net/10023/1928
Abstract: Double-observer line transect methods are becoming increasingly widespread, especially for the estimation of marine mammal abundance from aerial and shipboard surveys when detection of animals on the line is uncertain. The resulting data supplement conventional distance sampling data with two-sample mark–recapture data. Like conventional mark–recapture data, these have inherent problems for estimating abundance in the presence of heterogeneity. Unlike conventional mark–recapture methods, line transect methods use knowledge of the distribution of a covariate, which affects detection probability (namely, distance from the transect line) in inference. This knowledge can be used to diagnose unmodeled heterogeneity in the mark–recapture component of the data. By modeling the covariance in detection probabilities with distance, we show how the estimation problem can be formulated in terms of different levels of independence. At one extreme, full independence is assumed, as in the Petersen estimator (which does not use distance data); at the other extreme, independence only occurs in the limit as detection probability tends to one. Between the two extremes, there is a range of models, including those currently in common use, which have intermediate levels of independence. We show how this framework can be used to provide more reliable analysis of double-observer line transect data. We test the methods by simulation, and by analysis of a dataset for which true abundance is known. We illustrate the approach through analysis of minke whale sightings data from the North Sea and adjacent waters.2010-03-01T00:00:00ZBuckland, Stephen TerrenceLaake, Jeffrey L.Borchers, David LouisDouble-observer line transect methods are becoming increasingly widespread, especially for the estimation of marine mammal abundance from aerial and shipboard surveys when detection of animals on the line is uncertain. The resulting data supplement conventional distance sampling data with two-sample mark–recapture data. Like conventional mark–recapture data, these have inherent problems for estimating abundance in the presence of heterogeneity. Unlike conventional mark–recapture methods, line transect methods use knowledge of the distribution of a covariate, which affects detection probability (namely, distance from the transect line) in inference. This knowledge can be used to diagnose unmodeled heterogeneity in the mark–recapture component of the data. By modeling the covariance in detection probabilities with distance, we show how the estimation problem can be formulated in terms of different levels of independence. At one extreme, full independence is assumed, as in the Petersen estimator (which does not use distance data); at the other extreme, independence only occurs in the limit as detection probability tends to one. Between the two extremes, there is a range of models, including those currently in common use, which have intermediate levels of independence. We show how this framework can be used to provide more reliable analysis of double-observer line transect data. We test the methods by simulation, and by analysis of a dataset for which true abundance is known. We illustrate the approach through analysis of minke whale sightings data from the North Sea and adjacent waters.Design and analysis of line transect surveys for primates
http://hdl.handle.net/10023/1927
Abstract: Line transect surveys are widely used for estimating abundance of primate populations. The method relies on a small number of key assumptions, and if these are not met, substantial bias may occur. For a variety of reasons, primate surveys often do not follow what is generally considered to be best practice, either in survey design or in analysis. The design often comprises too few lines (sometimes just one), subjectively placed or placed along trails, so lacks both randomization and adequate replication. Analysis often involves flawed or inefficient models, and often uses biased estimates of the locations of primate groups relative to the line. We outline the standard method, emphasizing the assumptions underlying the approach. We then consider options for when it is difficult or impossible to meet key assumptions. We explore the performance of these options by simulation, focusing particularly on the analysis of primate group sizes, where many of the variations in survey methods have been developed. We also discuss design issues, field methods, analysis, and potential alternative methodologies for when standard line transect sampling cannot deliver reliable abundance estimates.
Description: An erratum to this article can be found at http://dx.doi.org/10.1007/s10764-010-9470-y2010-10-01T00:00:00ZBuckland, Stephen TerrencePlumptre, A JThomas, LenRexstad, Eric ALine transect surveys are widely used for estimating abundance of primate populations. The method relies on a small number of key assumptions, and if these are not met, substantial bias may occur. For a variety of reasons, primate surveys often do not follow what is generally considered to be best practice, either in survey design or in analysis. The design often comprises too few lines (sometimes just one), subjectively placed or placed along trails, so lacks both randomization and adequate replication. Analysis often involves flawed or inefficient models, and often uses biased estimates of the locations of primate groups relative to the line. We outline the standard method, emphasizing the assumptions underlying the approach. We then consider options for when it is difficult or impossible to meet key assumptions. We explore the performance of these options by simulation, focusing particularly on the analysis of primate group sizes, where many of the variations in survey methods have been developed. We also discuss design issues, field methods, analysis, and potential alternative methodologies for when standard line transect sampling cannot deliver reliable abundance estimates.Line transect sampling of primates : can animal-to-observer distance methods work?
http://hdl.handle.net/10023/1926
Abstract: Line transect sampling is widely used for estimating abundance of primate populations. Animal-to-observer distances (AODs) are commonly used in analysis, in preference to perpendicular distances from the line. This is in marked contrast with standard practice for other applications of line transect sampling. We formalize the mathematical shortcomings of approaches based on AODs, and show that they are likely to give strongly biased estimates of density. We review papers that claim good performance for the method, and explore this performance through simulations. These confirm strong bias in estimates of density using AODs. We conclude that AOD methods are conceptually flawed, and that they cannot in general provide valid estimates of density.
Description: An erratum to this article can be found at http://dx.doi.org/10.1007/s10764-010-9469-42010-06-01T00:00:00ZBuckland, Stephen TerrencePlumptre, A JThomas, LenRexstad, EricLine transect sampling is widely used for estimating abundance of primate populations. Animal-to-observer distances (AODs) are commonly used in analysis, in preference to perpendicular distances from the line. This is in marked contrast with standard practice for other applications of line transect sampling. We formalize the mathematical shortcomings of approaches based on AODs, and show that they are likely to give strongly biased estimates of density. We review papers that claim good performance for the method, and explore this performance through simulations. These confirm strong bias in estimates of density using AODs. We conclude that AOD methods are conceptually flawed, and that they cannot in general provide valid estimates of density.Estimating the Barents Sea polar bear subpopulation size
http://hdl.handle.net/10023/1879
Abstract: A large scale survey was conducted in August 2004 to estimate the size of the Barents Sea polar bear subpopulation. We combined helicopter line transect distance sampling surveys in most of the survey area with total counts in small areas not suitable for distance sampling. Due to weather constraints we failed to survey some of the areas originally planned to be covered by distance sampling. For those, abundance was estimated using a ratio estimator, in which the auxiliary variable was the number of satellite telemetry fixes (in previous years). We estimated that the Barents Sea subpopulation had approximately 2650 (95% CI approx 1900 to 3600) bears. Given current intense interest in polar bear management due to the potentially disastrous effects of climate change, it is surprising that many subpopulation sizes are still unknown. We show here that line transect sampling is a promising method for addressing the need for abundance estimates.2009-01-01T00:00:00ZAars, JMarques, Tiago Andre Lamas OliveiraAndersen, MBelikov, SBoltunov, ABuckland, Stephen TerrenceWiig, OA large scale survey was conducted in August 2004 to estimate the size of the Barents Sea polar bear subpopulation. We combined helicopter line transect distance sampling surveys in most of the survey area with total counts in small areas not suitable for distance sampling. Due to weather constraints we failed to survey some of the areas originally planned to be covered by distance sampling. For those, abundance was estimated using a ratio estimator, in which the auxiliary variable was the number of satellite telemetry fixes (in previous years). We estimated that the Barents Sea subpopulation had approximately 2650 (95% CI approx 1900 to 3600) bears. Given current intense interest in polar bear management due to the potentially disastrous effects of climate change, it is surprising that many subpopulation sizes are still unknown. We show here that line transect sampling is a promising method for addressing the need for abundance estimates.The effect of sea-ice loss on beluga whales (Delphinapterus leucas) in West Greenland
http://hdl.handle.net/10023/1856
Abstract: An aerial survey was conducted to estimate the abundance of belugas (Delphinapterus leucas) on their wintering ground in West Greenland in March–April 2006 and 2008. The survey was conducted as a double platform aerial line transect survey, and sampled approximately 17% of the total survey area of ca. 125 000 km2. The abundance of belugas was 10 595 (95% confidence interval 4904–24 650). The largest abundance was found at the northern part of Store Hellefiske Bank, at the eastern edge of the Baffin Bay pack ice, a pattern similar to that found in eight systematic surveys conducted since 1981. A clear relationship between decreasing sea-ice cover and increasing offshore distance of beluga sightings was established from all previous surveys, suggesting that belugas expand their distribution westward as new areas on the banks of West Greenland open up earlier in spring with reduced sea-ice coverage or early annual ice recession. This is in contrast to the relatively confined distribution of belugas near the coast in limited open areas in the early 1980s, when sea-ice cover was greater. However, the effects of the changes in coastal availability of belugas can also be observed with the correlation between catches from the local Inuit hunt and sea-ice cover, where the catches increased significantly with increasing sea-ice coverage during the period 1954–2006. These results, based on nearly 30 years of dedicated survey effort, are among the first available evidence showing a shift in distribution of an Arctic cetacean in response to changes in sea-ice coverage.2010-01-01T00:00:00ZHeide-Jørgensen, M. P.Laidre, K. L.Borchers, David LouisMarques, Tiago A.Stern, H.Simon, M.An aerial survey was conducted to estimate the abundance of belugas (Delphinapterus leucas) on their wintering ground in West Greenland in March–April 2006 and 2008. The survey was conducted as a double platform aerial line transect survey, and sampled approximately 17% of the total survey area of ca. 125 000 km2. The abundance of belugas was 10 595 (95% confidence interval 4904–24 650). The largest abundance was found at the northern part of Store Hellefiske Bank, at the eastern edge of the Baffin Bay pack ice, a pattern similar to that found in eight systematic surveys conducted since 1981. A clear relationship between decreasing sea-ice cover and increasing offshore distance of beluga sightings was established from all previous surveys, suggesting that belugas expand their distribution westward as new areas on the banks of West Greenland open up earlier in spring with reduced sea-ice coverage or early annual ice recession. This is in contrast to the relatively confined distribution of belugas near the coast in limited open areas in the early 1980s, when sea-ice cover was greater. However, the effects of the changes in coastal availability of belugas can also be observed with the correlation between catches from the local Inuit hunt and sea-ice cover, where the catches increased significantly with increasing sea-ice coverage during the period 1954–2006. These results, based on nearly 30 years of dedicated survey effort, are among the first available evidence showing a shift in distribution of an Arctic cetacean in response to changes in sea-ice coverage.Density estimation implications of increasing ambient noise on beaked whale click detection and classification
http://hdl.handle.net/10023/1652
Abstract: Acoustic based density estimates are being increasingly used. Usually density estimation methods require one to evaluate the eﬀective survey area of the acoustic sensors, or equivalently estimate the mean detection probability of detecting the animals or cues of interest. This is often done based on an estimated detection function, the probability of detecting an object of interest as a function of covariates, usually distance and additional covariates. If the actual survey data and the data used to estimate a detection function are not collected simultaneously, as in Marques et al. (2009), the estimated detection function might not correspond to the detection process that generated the survey data. This would lead to biaseddensity estimates. Here we evaluate the inﬂuence of ambient noise in the detection and classiﬁcation of beaked whale clicks at the Atlantic Undersea Test and Evaluation Center (AUTEC) hydrophones, to assess if the density estimates reported in Marques et al. (2009) might have been biased. To do so we contaminated a data set with increasing levels of ambient noise, and then estimated the detection function accounting for the noise level as an additional covariate. The results obtained suggest that for the particular results obtained at AUTEC’s deep water hydrophones the inﬂuence of ambient noise on the beaked whale’s click detection probability might have been minor, and hence unlikely to have had an impact on density estimates. However, we do not exclude the possibility that the results could be diﬀerent under other scenarios.2010-01-01T00:00:00ZMarques, Tiago Andre Lamas OliveiraWard, JessicaJarvis, SusanMoretti, DavidMorrissey, RonaldDiMarzio, NancyThomas, LenAcoustic based density estimates are being increasingly used. Usually density estimation methods require one to evaluate the eﬀective survey area of the acoustic sensors, or equivalently estimate the mean detection probability of detecting the animals or cues of interest. This is often done based on an estimated detection function, the probability of detecting an object of interest as a function of covariates, usually distance and additional covariates. If the actual survey data and the data used to estimate a detection function are not collected simultaneously, as in Marques et al. (2009), the estimated detection function might not correspond to the detection process that generated the survey data. This would lead to biaseddensity estimates. Here we evaluate the inﬂuence of ambient noise in the detection and classiﬁcation of beaked whale clicks at the Atlantic Undersea Test and Evaluation Center (AUTEC) hydrophones, to assess if the density estimates reported in Marques et al. (2009) might have been biased. To do so we contaminated a data set with increasing levels of ambient noise, and then estimated the detection function accounting for the noise level as an additional covariate. The results obtained suggest that for the particular results obtained at AUTEC’s deep water hydrophones the inﬂuence of ambient noise on the beaked whale’s click detection probability might have been minor, and hence unlikely to have had an impact on density estimates. However, we do not exclude the possibility that the results could be diﬀerent under other scenarios.Generating continuous mappings with Lipschitz mappings
http://hdl.handle.net/10023/1616
Abstract: If X is a metric space, then C-X and L-X denote the semigroups of continuous and Lipschitz mappings, respectively, from X to itself. The relative rank of C-X modulo L-X is the least cardinality of any set U\L-X where U generates C-X. For a large class of separable metric spaces X we prove that the relative rank of C-X modulo L-X is uncountable. When X is the Baire space N-N, this rank is N-1. A large part of the paper emerged from discussions about the necessity of the assumptions imposed on the class of spaces from the aforementioned results.2007-05-01T00:00:00ZCichon, JMitchell, James DavidMorayne, MIf X is a metric space, then C-X and L-X denote the semigroups of continuous and Lipschitz mappings, respectively, from X to itself. The relative rank of C-X modulo L-X is the least cardinality of any set U\L-X where U generates C-X. For a large class of separable metric spaces X we prove that the relative rank of C-X modulo L-X is uncountable. When X is the Baire space N-N, this rank is N-1. A large part of the paper emerged from discussions about the necessity of the assumptions imposed on the class of spaces from the aforementioned results.Generating the full transformation semigroup using order preserving mappings
http://hdl.handle.net/10023/1553
Abstract: For a linearly ordered set X we consider the relative rank of the semigroup of all order preserving mappings O-X on X modulo the full transformation semigroup Ex. In other words, we ask what is the smallest cardinality of a set A of mappings such that <O-X boolean OR A> = T-X. When X is countably infinite or well-ordered (of arbitrary cardinality) we show that this number is one, while when X = R (the set of real numbers) it is uncountable.2003-09-01T00:00:00ZHiggins, PMMitchell, James DavidRuskuc, NikolaFor a linearly ordered set X we consider the relative rank of the semigroup of all order preserving mappings O-X on X modulo the full transformation semigroup Ex. In other words, we ask what is the smallest cardinality of a set A of mappings such that <O-X boolean OR A> = T-X. When X is countably infinite or well-ordered (of arbitrary cardinality) we show that this number is one, while when X = R (the set of real numbers) it is uncountable.On defining groups efficiently without using inverses
http://hdl.handle.net/10023/1442
Abstract: Let G be a group, and let <A \ R> be a finite group presentation for G with \R\ greater than or equal to \A\. Then there exists a, finite semigroup, presentation <B \ Q> for G such that \Q\ - \B\ = \R\ - \A\. Moreover, B is either the same generating set or else it contains one additional generator.2002-07-01T00:00:00ZCampbell, Colin MatthewMitchell, James DavidRuskuc, NikolaLet G be a group, and let <A \ R> be a finite group presentation for G with \R\ greater than or equal to \A\. Then there exists a, finite semigroup, presentation <B \ Q> for G such that \Q\ - \B\ = \R\ - \A\. Moreover, B is either the same generating set or else it contains one additional generator.