2024-03-28T20:03:51Zhttps://research-repository.st-andrews.ac.uk/oai/requestoai:research-repository.st-andrews.ac.uk:10023/6672019-03-29T10:16:20Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_95com_10023_28col_10023_661col_10023_664col_10023_662
St Andrews Research Repository
advisor
Thomas, Len
advisor
Marques, Tiago Andre Lamas Oliveira
advisor
Silva, Monica Almeida
author
Faustino, ClΓ‘udia Estevinho Santos
2009-04-14T16:16:04Z
2009-04-14T16:16:04Z
2008
http://hdl.handle.net/10023/667
Management schemes dedicated to the conservation of wildlife populations rely on the effective monitoring of population size, and this requires the accurate and precise estimation of abundance. The accuracy and precision of estimates are determined to a large extent by the survey design. Line transect surveys are commonly applied to wildlife population assessments in which the primary purpose of a survey design is to ensure that the critical distance sampling assumptions are met.
Little information is available regarding cetacean abundance in the Archipelago of the Azores (Portugal). This study aims to design a line transect shipboard survey that allows the collection of data required to provide abundance estimates for such species. Several aspects must be taken into consideration when designing a survey to estimate cetacean abundance. This is an iterative process, and there is a constant trade off between the logistic constraints and the desired statistical robustness. Information on this process is provided to aid policy makers and environmental managers, such as the criteria used for the choices made when defining the elements of a survey design.
Three survey effort scenarios are provided to illustrate the range of possibilities between statistical robustness and logistic/ management restrictions. A survey is designed for the more economical scenario (L=5000Km), although the second scenario is the one recommended to be implemented (L=17,600Km) given it provides robust estimates of
abundance (CV<=0.2).
en
Atlantic ocean
Automated survey design
Cetacean density and abundance
Distance sampling
Distance 6.0
Statistical ecology
Designing a shipboard line transect survey to estimate cetacean abundance off the Azores Archipelago, Portugal
Thesis
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
URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/667/1/Faustino-MRes-dissertation-Revised-Nov08.pdf
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https://research-repository.st-andrews.ac.uk/bitstream/10023/667/2/Faustino_Azores_survey_2-2.zip
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Faustino_Azores_survey_2-2.zip
URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/667/4/Faustino-MRes-dissertation-Revised-Nov08.pdf.txt
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Faustino-MRes-dissertation-Revised-Nov08.pdf.txt
oai:research-repository.st-andrews.ac.uk:10023/6692019-03-29T10:16:21Zcom_10023_45com_10023_17com_10023_95com_10023_28col_10023_661col_10023_662
St Andrews Research Repository
advisor
Thomas, Len
author
Gangadharan, Aditya
2009-04-16T09:08:04Z
2009-04-16T09:08:04Z
2005
http://hdl.handle.net/10023/669
Density estimates for six large herbivore species were obtained through
analysis of line transect data from Nagarhole National Park, south-western India,
collected between 1989 and 2000. These species were Chital (Axis axis), Sambar
(Cervus unicolor), Gaur (Bos gaurus), Wild Pig (Sus scrofa), Muntjac (Muntiacus
muntjak) and Asian Elephant (Elephas maximus). Multiple Covariate Distance
Sampling (MCDS) models were used to derive these density estimates. The distance
histograms showed a relatively large spike at zero, which can lead to problems when
fitting MCDS models. The effects of this spike were investigated and remedied by
forward truncation. Density estimates from unmodified dataset were 10-15% higher
than estimates from the forward truncated data, with this going up to 37% for
Muntjac. These could possibly be over estimates. Empirical trend models were then
fit to the density estimates. Overall trends were stable, though there were intra-habitat
differences in trends for some species. The trends were similar both in cases where
forward truncation was done as well as in those where they were not.
en
Line transect
Distance sampling
Estimating density and abundance
Wildlife population size
Tiger prey
Large ungulates
Tropical forest
Forward truncation
Density estimation and time trend analysis of large herbivores in Nagarhole, India
Thesis
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
URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/669/1/GangadharanThesis.pdf
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URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/669/3/GangadharanThesis.pdf.txt
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GangadharanThesis.pdf.txt
oai:research-repository.st-andrews.ac.uk:10023/209472020-11-17T13:35:57Zcom_10023_95com_10023_28col_10023_662
St Andrews Research Repository
advisor
Donovan, Carl
author
Kang, Sujin
2020-11-11T09:53:17Z
2020-11-11T09:53:17Z
2008-11-27
http://hdl.handle.net/10023/20947
The Nonlinear Mixed Effect Viral Dynamic Model can easily handle unbalanced repeated and continuous measures data for individuals and is also popular in many other research areas such as biology and pharmacokinetics. Wu π¦π΅ π’π. (2004) described a Nonlinear Mixed Effects Biphasic Model to estimate short-term population and individual viral decay rates in their study. Perelson π¦π΅ π’π. (1999) and Ding π¦π΅ π’π. (1999) reported that initial viral decay estimated for viral decay models would be good markers of the potency of antiretroviral regimens. The aim of this study was to model viral decay rates, and check the validity of the model for the set of data provided and investigate whether the relationships found with baseline covariates and long-term response are consistent with Wu π¦π΅ π’π.βs (2004) findings.
The Nonlinear Mixed Effect Single and Biphasic Viral Dynamic Models were fitted, and their respective initial viral decay rates were derived. In this study, analyses and reports are focused on the first-phase viral decay rates of the models. The study found that the actual treatment groups were more potent than the control group. It was found that actual treatment effect and the number of multi-PI mutations at baseline had impacts on the initial viral decay rates for both models. Besides, baseline HIV-1 RNA levels had an impact on the initial viral decay rates for the biphasic model. There were no significant differences in the initial viral decay rates for different ages, ethnicities, and gender groups.
The study also shows that the initial viral decay rates were somewhat negatively correlated with the baseline HIV-1 RNA levels. A strong correlation between the initial viral decay rates and week 1 virus load reduction from baseline was observed. It was also observed that individuals with the higher initial viral decay rates were more likely to have suppressed virus load at week 24. Also, individuals with higher week 1 virus load reduction, i.e. early viral dynamics, were more likely to have suppressed virus load at week 24. These findings suggest that the antiviral potency or the initial viral decay rates are predictive of long-term viral load response.
en
HIV
Initial viral decay rates
Long-term response
Nonlinear mixed effect models
Single and biphasic viral dynamic models
Actual treatment effect
Number of multi-PI mutations
Baseline HIV-1 RNA levels
Nonlinear mixed effect models for modeling initial viral decay rates in an HIV study
Thesis
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URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/20947/2/SujinKangMscThesis.pdf
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SujinKangMscThesis.pdf.txt
oai:research-repository.st-andrews.ac.uk:10023/6682019-04-01T08:35:10Zcom_10023_95com_10023_28col_10023_662
St Andrews Research Repository
advisor
Thomas, Len
author
DiTraglia, Francis J.
2009-04-16T08:35:08Z
2009-04-16T08:35:08Z
2007
http://hdl.handle.net/10023/668
In this paper we present three models of random wildlife movement: a one dimensional model of wildlife-observer encounters on roads, an analogous two dimensional model, and an further two-dimensional model that borrows from the ideas of statistical mechanics. We then derive unbiased estimates of wildlife density in terms of encounters for each of these models. By extending these results to incorporate uncertain detection, we suggest three novel distance sampling methods and briefly consider possible field applications.
en
distance sampling
animal movement
population size
population density
wildlife population assessment
Models of random wildlife movement with an application to distance sampling
Thesis
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URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/668/1/DiTragliaMMathThesis.pdf
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URL
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oai:research-repository.st-andrews.ac.uk:10023/6652019-03-29T10:16:22Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_181com_10023_95com_10023_28col_10023_661col_10023_664col_10023_666col_10023_662
St Andrews Research Repository
advisor
Thomas, Len
advisor
Biuw, Martin
author
Photopoulos, Theoni
2009-04-14T15:24:46Z
2009-04-14T15:24:46Z
2007
http://hdl.handle.net/10023/665
The development of an animal-borne instrument that can record oceanographic measurements (CTD-SRDL) has enabled the collection of oceanographic data at a scale relevant to the counterpart behavioural data, both in time and 3-dimensional space. This has advanced the potential for studies of the behaviour of deep-diving marine animals and the way in which they respond to their environment, yet the nature of the data delivered by CTD-SRDLs presents substantial analytical challenges and places constraints on its biological interpretation. Behavioural and environmental data, collected using CTD-SRDLs deployed on southern elephant seals (Mirounga leonina) from the South Georgia subpopulation in 2004 and 2005, are analysed for 13 females and 4 males (21,015 dives). Compressed dive profiles are used to classify individual dives into six distinct types based on their 2-dimensional time-depth characteristics using random forest classification. The relationship between dive type and environmental variables, derived from oceanographic data recorded on board the animals, is investigated in the context of regression analysis, employing a multinomial model, as well as independently fitted Generalized Linear Models (GLM) and Generalized Additive Models (GAM) for each dive type. Regression is not found to be an appropriate method for analysing abstracted behavioural dive data, and other methods are suggested. We show that functional specializations can be manifested within a dive type, using square bottom dives (SQ) as an example. The usefulness of dive classification is discussed in the context of behavioural interpretation, and validity of the ecological functions attached to each class. Preliminary analyses are important drivers of further research into improving the interpretability of abstracted behavioural data, and developing efficient, standardized methods for widespread application to this type of data, which is obtained in abundance via satellite telemetry.
en
Elephant seal
Conductivity-temperature-depth satellite relay data logger
Behavioural study of deep-diving marine mammal
Behavioural changes of a long-ranging diver in response to oceanographic conditions
Thesis
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URL
https://research-repository.st-andrews.ac.uk/bitstream/10023/665/1/PhotopoulosMResThesis.pdf
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