2024-03-28T12:05:36Zhttps://research-repository.st-andrews.ac.uk/oai/requestoai:research-repository.st-andrews.ac.uk:10023/6782019-04-01T08:35:17Zcom_10023_165com_10023_39com_10023_95com_10023_28col_10023_166col_10023_100
00925njm 22002777a 4500
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Thomas, Len
author
Buckland, Stephen T.
author
Newman, KB
author
Harwood, John
author
2005
This paper proposes a unified framework for defining and fitting stochastic, discrete-time, discrete-stage population dynamics models. The biological system is described by a state–space model, where the true but unknown state of the population is modelled by a state process, and this is linked to survey data by an observation process. All sources of uncertainty in the inputs, including uncertainty about model specification, are readily incorporated. The paper shows how the state process can be represented as a generalization of the standard Leslie or Lefkovitch matrix. By dividing the state process into subprocesses, complex models can be constructed from manageable building blocks. The paper illustrates the approach with a model of the British Grey Seal metapopulation, using sequential importance sampling with kernel smoothing to fit the model.
Australian and New Zealand Journal of Statistics 47(1): 19-34 March 2005
1369-1473
StAndrews.ResExp.Output.OutputID.8345
http://dx.doi.org/10.1111/j.1467-842x.2005.00369.x
http://hdl.handle.net/10023/678
auxiliary particle filter
ecology
Grey Seals
Halichoerus grypus
metapopulation
nonlinear stochastic matrix models
sequential importance sampling
state–space models
wildlife
conservation and management
A unified framework for modelling wildlife population dynamics
oai:research-repository.st-andrews.ac.uk:10023/6792019-04-01T08:35:18Zcom_10023_165com_10023_39com_10023_95com_10023_28col_10023_166col_10023_100
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Thomas, Len
author
1997
Many papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller & Benignus 1992; Taylor & Gerrodette 1993; Searcy-Bernal 1994; Thomas & Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.
Conservation Biology 11(1): 276-280 February 1997
0888-8892
StAndrews.ResExp.Output.OutputID.29914
http://dx.doi.org/10.1046/j.1523-1739.1997.96102.x
http://hdl.handle.net/10023/679
statistical power analysis
retrospective power analysis
confidence intervals
Retrospective power analysis
oai:research-repository.st-andrews.ac.uk:10023/6852019-04-01T08:35:19Zcom_10023_165com_10023_39com_10023_95com_10023_28col_10023_166col_10023_100
00925njm 22002777a 4500
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Thomas, Len
author
Martin, Kathy
author
1996
Population trends from the Breeding Bird Survey are widely used to focus conservation efforts on species thought to be in decline and to test preliminary hypotheses regarding the causes of these declines. A number of statistical methods have been used to estimate population trends, but there is no consensus us to which is the most reliable. We quantified differences in trend estimates or different analysis methods applied to the same subset of Breeding Bird Survey data. We estimated trends for 115 species in British Columbia using three analysis methods: U.S. National Biological Service route regression, Canadian Wildlife Service route regression, and nonparametric rank-trends analysis. Overall, the number of species estimated to be declining was similar among the three methods, but the number of statistically significant declines was not similar (15, 8, and 29 respectively). In addition, many differences existed among methods in the trend estimates assigned to individual species. Comparing the two route regression methods, Canadian Wildlife Service estimates had a greater absolute magnitude on average than those of the U.S. National Biological Service method. U.S. National Biological Service estimates were on average more positive than the Canadian Wildlife Service estimates when the respective agency's data selection criteria were applied separately. These results imply that our ability to detect population declines and to prioritize species of conservation concern depend strongly upon the analysis method used. This highlights the need for further research to determine how best to accurately estimate trends from the data. We suggest a method for evaluating the performance of the analysis methods by using simulated Breeding Bird Survey data.
Conservation Biology 10(2): 479-490 April 1996
0888-8892
StAndrews.ResExp.Output.OutputID.29915
http://dx.doi.org/10.1046/j.1523-1739.1996.10020479.x
http://hdl.handle.net/10023/685
analysis of biological population trends
North American Breeding Bird Survey
The importance of analysis method for breeding bird survey population trend estimates
oai:research-repository.st-andrews.ac.uk:10023/162532024-03-09T00:43:37Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_181com_10023_792com_10023_879com_10023_878col_10023_46col_10023_166col_10023_182col_10023_795col_10023_880
00925njm 22002777a 4500
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Schuert, Courtney
author
Pomeroy, Patrick
author
Twiss, Sean
author
2018-10-16
Background: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.
Schuert , C , Pomeroy , P & Twiss , S 2018 , ' Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal ' , Animal Biotelemetry , vol. 6 , 14 . https://doi.org/10.1186/s40317-018-0158-y
2050-3385
ORCID: /0000-0003-1603-5630/work/49580160
https://hdl.handle.net/10023/16253
10.1186/s40317-018-0158-y
Accelerometer
Grey seal
Maternal behaviour
Breeding behaviour
Machine learning
Classification
QH301 Biology
NDAS
NERC
Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal
oai:research-repository.st-andrews.ac.uk:10023/162602023-04-18T09:43:03Zcom_10023_165com_10023_39com_10023_28com_10023_792com_10023_95com_10023_879com_10023_878col_10023_166col_10023_859col_10023_795col_10023_100col_10023_880
00925njm 22002777a 4500
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Borkin, Kerry
author
Summers, Ron
author
Thomas, Len
author
2012-01-03
Red wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74-1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32-2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700-6,400) and 3,100 (95% CI 1,200-8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s-1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.
Borkin , K , Summers , R & Thomas , L 2012 , ' Surveying abundance and stand type associations of Formica aquilonia and F. lugubris (Hymenoptera: Formicidae) nest mounds over an extensive area : Trialing a novel method ' , European Journal of Entomology , vol. 109 , no. 1 , pp. 47-53 . https://doi.org/10.14411/eje.2012.007
PURE: 5285592
PURE UUID: aa10e06c-027d-482c-beef-a795410a9be5
Scopus: 84865189198
Scopus: 84865189198
ORCID: /0000-0002-7436-067X/work/54818839
http://hdl.handle.net/10023/16260
https://doi.org/10.14411/eje.2012.007
http://www.eje.cz/pdfarticles/1679/eje_109_1_047_Borkin.pdf
Distance sampling
Formica
Formicidae
Hymenoptera
Line transect
Old-growth
Pinus sylvestris
Scotland
QA Mathematics
QH301 Biology
Insect Science
Surveying abundance and stand type associations of Formica aquilonia and F. lugubris (Hymenoptera: Formicidae) nest mounds over an extensive area : Trialing a novel method
oai:research-repository.st-andrews.ac.uk:10023/19572022-04-14T09:30:16Zcom_10023_165com_10023_39com_10023_28com_10023_792com_10023_309com_10023_879com_10023_878col_10023_166col_10023_859col_10023_795col_10023_311col_10023_880
00925njm 22002777a 4500
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Summers, Ron W
author
Buckland, Stephen Terrence
author
2011-06
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.
Summers , R W & Buckland , S T 2011 , ' A first survey of the global population size and distribution of the Scottish Crossbill Loxia scotica ' , Bird Conservation International , vol. 21 , no. 2 , pp. 186-198 . https://doi.org/10.1017/S0959270909990323
0959-2709
PURE: 11461790
PURE UUID: b6d4376e-2518-4a62-991f-8bfb2b67317e
Scopus: 79958792770
ORCID: /0000-0002-9939-709X/work/73701083
http://hdl.handle.net/10023/1957
https://doi.org/10.1017/S0959270909990323
QL Zoology
A first survey of the global population size and distribution of the Scottish Crossbill Loxia scotica
oai:research-repository.st-andrews.ac.uk:10023/8172019-04-01T08:35:29Zcom_10023_165com_10023_39com_10023_95com_10023_28col_10023_166col_10023_100
00925njm 22002777a 4500
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Thomas, Len
author
Buckland, Stephen Terrence
author
Rexstad, Eric
author
Laake, J L
author
Strindberg, S
author
Hedley, S L
author
Bishop, J R B
author
Marques, Tiago A.
author
2010
1. Distance sampling is a widely used technique for estimating the size or density of biological populations. Many distance sampling designs and most analyses use the software Distance. 2. We briefly review distance sampling and its assumptions, outline the history, structure and capabilities of Distance, and provide hints on its use. 3. Good survey design is a crucial pre-requisite for obtaining reliable results. Distance has a survey design engine, with a built-in geographic information system, that allows properties of different proposed designs to be examined via simulation, and survey plans to be generated. 4. A first step in analysis of distance sampling data is modelling the probability of detection. Distance contains three increasingly sophisticated analysis engines for this: CDS (conventional distance sampling), which models detection probability as a function of distance from the transect and assumes all objects at zero distance are detected; MCDS (multiple covariate distance sampling), which allows covariates in addition to distance; and MRDS (mark-recapture distance sampling), which relaxes the assumption of certain detection at zero distance. 5. All three engines allow estimation of density or abundance, stratified if required, with associated measures of precision calculated either analytically or via the bootstrap. 6. Advanced analysis topics covered include the use of multipliers to allow analysis of indirect surveys (such as dung or nest surveys), the DSM (density surface modelling) analysis engine for spatial and habitat modelling, and information about accessing the analysis engines directly from other software. 7. Synthesis and applications. Distance sampling is a key method for producing abundance and density estimates in challenging field conditions. The theory underlying the methods continues to expand to cope with realistic estimation situations. In step with theoretical developments, state-of-the-art software that implements these methods is described that makes the methods accessible to practicing ecologists.
Journal of Applied Ecology 47 (1): 5-14 2010
0021-8901
StAndrews.ResExp.Output.OutputID.31422
http://dx.doi.org/10.1111/j.1365-2664.2009.01737.x
http://hdl.handle.net/10023/817
distance sampling
line transect sampling
point transect sampling
population density
population abundance
sighting surveys
survey design
wildlife surveys
Distance software: design and analysis of distance sampling surveys for estimating population size
oai:research-repository.st-andrews.ac.uk:10023/77722022-04-29T14:30:47Zcom_10023_165com_10023_39com_10023_28com_10023_792com_10023_309com_10023_879com_10023_878col_10023_166col_10023_859col_10023_795col_10023_311col_10023_880
00925njm 22002777a 4500
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Read, Andrew, J.
author
Barco, S.
author
Bell, J.
author
Borchers, David Louis
author
Burt, M Louise
author
Cummings, E.W.
author
Dunn, J.
author
Fougeres, J.
author
Hazen, L.
author
Williams-Hodge, L.E.
author
Laura, A-M.
author
McAlarney, R.J.
author
Nilsson, P.
author
Pabst, D.A.
author
Paxton, Charles G. M.
author
Schneider, S.Z.
author
Urian, Kim
author
Waples, D.M.
author
McLellan, W.A.
author
2014
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.
Read , A J , Barco , S , Bell , J , Borchers , D L , Burt , M L , Cummings , E W , Dunn , J , Fougeres , J , Hazen , L , Williams-Hodge , L E , Laura , A-M , McAlarney , R J , Nilsson , P , Pabst , D A , Paxton , C G M , Schneider , S Z , Urian , K , Waples , D M & McLellan , W A 2014 , ' Occurrence, distribution and abundance of cetaceans in Onslow Bay, North Carolina, USA ' , Journal of Cetacean Research and Management , vol. 14 , pp. 23-35 .
1561-0713
PURE: 191849725
PURE UUID: 91a71ad1-b549-4b58-8213-6217c9143031
Scopus: 84942418496
ORCID: /0000-0002-9350-3197/work/34033063
ORCID: /0000-0002-3944-0754/work/72842433
http://hdl.handle.net/10023/7772
https://archive.iwc.int/pages/preview.php?ref=3608&alternative=2475&k=&search=onslow%2C+bay%2C+year%3A2014&offset=0&order_by=relevance&sort=DESC&archive=0&
Abundance estimate
Monitoring
Survey-combined
Trends
Photo-ID
GB Physical geography
QA Mathematics
QH301 Biology
Occurrence, distribution and abundance of cetaceans in Onslow Bay, North Carolina, USA
oai:research-repository.st-andrews.ac.uk:10023/43562023-04-25T23:37:52Zcom_10023_165com_10023_39com_10023_28com_10023_879com_10023_878col_10023_166col_10023_859col_10023_880
00925njm 22002777a 4500
dc
Schick, Robert Schilling
author
Roberts, Jason
author
Eckert, Scott
author
Clark, James
author
Bailey, Helen
author
Chai, Fei
author
Shi, Li
author
Halpin, Patrick
author
2013-11-20
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.
Schick , R S , Roberts , J , Eckert , S , Clark , J , Bailey , H , Chai , F , Shi , L & Halpin , P 2013 , ' Pelagic movements of pacific leatherback turtles ( Dermochelys coriacea ) reveal the complex role of prey and ocean currents ' , Movement Ecology , vol. 1 , no. 11 , 11 . https://doi.org/10.1186/2051-3933-1-11
2051-3933
PURE: 84738893
PURE UUID: c1c6a7ce-1cb1-4133-a89a-b30d8f220202
Scopus: 84984915999
http://hdl.handle.net/10023/4356
https://doi.org/10.1186/2051-3933-1-11
Movement
Bayesian
Habitat suitability
Water column
Diving
Leatherback turtles
Marine predator
Dynamic covariates
Prey
Q Science
QL Zoology
SDG 14 - Life Below Water
Pelagic movements of pacific leatherback turtles (Dermochelys coriacea) reveal the complex role of prey and ocean currents
oai:research-repository.st-andrews.ac.uk:10023/40732023-04-18T09:46:34Zcom_10023_165com_10023_39com_10023_28com_10023_792com_10023_879com_10023_878col_10023_166col_10023_859col_10023_795col_10023_880
00925njm 22002777a 4500
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Langrock, Roland
author
King, Ruth
author
2013
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.
Langrock , R & King , R 2013 , ' Maximum likelihood estimation of mark-recapture-recovery models in the presence of continuous covariates ' , Annals of Applied Statistics , vol. 7 , no. 3 , pp. 1709-1732 . https://doi.org/10.1214/13-AOAS644
1932-6157
PURE: 28450207
PURE UUID: c92351bb-8671-4934-90fb-e19cffb4d445
Scopus: 84885046625
http://hdl.handle.net/10023/4073
https://doi.org/10.1214/13-AOAS644
http://www.e-publications.org/ims/submission/index.php/AOAS/user/submissionFile/14235?confirm=c4a65131
http://projecteuclid.org/euclid.aoas/1380804813
Arnason-Schwarz model
Hidden Markov model
Markov chain
Missing values
Soay sheep
State-space model
QA Mathematics
Maximum likelihood estimation of mark-recapture-recovery models in the presence of continuous covariates
oai:research-repository.st-andrews.ac.uk:10023/6772019-04-01T08:35:53Zcom_10023_165com_10023_39com_10023_95com_10023_28col_10023_166col_10023_100
00925njm 22002777a 4500
dc
Giminez, O
author
Bonner, S J
author
King, Ruth
author
Parker, R A
author
Brooks, S P
author
Jamieson, L E
author
Grosbois, V
author
Morgan, B J T
author
Thomas, Len
author
2008
The computer package WinBUGS is introduced. We first give a brief introduction to Bayesian theory and its implementation using Markov chain Monte Carlo (MCMC) algorithms. We then present three case studies showing how WinBUGS can be used when classical theory is difficult to implement. The first example uses data on white storks from Baden Württemberg, Germany, to demonstrate the use of mark-recapture models to estimate survival, and also how to cope with unexplained variance through random effects. Recent advances in methodology and also the WinBUGS software allow us to introduce (i) a flexible way of incorporating covariates using spline smoothing and (ii) a method to deal with missing values in covariates. The second example shows how to estimate population density while accounting for detectability, using distance sampling methods applied to a test dataset collected on a known population of wooden stakes. Finally, the third case study involves the use of state-space models of wildlife population dynamics to make inferences about density dependence in a North American duck species. Reversible Jump MCMC is used to calculate the probability of various candidate models. For all examples, data and WinBUGS code are provided.
Modeling Demographic Processes in Marked Populations 885-918 2008
978-0-387-78150-1
StAndrews.ResExp.Output.OutputID.16858
http://hdl.handle.net/10023/677
Bayesian statistics
density dependence
distance sampling
external covariates
hierarchical modelling
line transect
mark-recapture
random effects
reversible jump MCMC
spline smoothing
state-space model
survival estimation
WinBUGS for population ecologists: Bayesian modeling using Markov Chain Monte Carlo methods.
oai:research-repository.st-andrews.ac.uk:10023/77352023-04-25T23:42:21Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_181com_10023_792com_10023_879com_10023_878col_10023_46col_10023_166col_10023_182col_10023_795col_10023_880
00925njm 22002777a 4500
dc
Russell, Deborah Jill Fraser
author
Wanless, Sarah
author
Collingham, Yvonne C.
author
Huntley, Brian
author
Hamer, Keith C.
author
2015-11-02
Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.
Russell , D J F , Wanless , S , Collingham , Y C , Huntley , B & Hamer , K C 2015 , ' Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenarios ' , Diversity , vol. 7 , no. 4 , pp. 342-359 . https://doi.org/10.3390/d7040342
1424-2818
PURE: 209437567
PURE UUID: 6e2a05dd-523b-436f-b3f5-5929b6d0363d
Scopus: 84952908445
ORCID: /0000-0002-1969-102X/work/49052054
http://hdl.handle.net/10023/7735
https://doi.org/10.3390/d7040342
Agreement R8-H12-86
Climate envelope modelling
Climate response surface
Conservation
Ecological niche modelling
Extinction risk
Foraging ecology
Global warming
Marine spatial planning
Sea surface temperature
Species distribution model
QH301 Biology
SDG 13 - Climate Action
SDG 14 - Life Below Water
Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenarios