45 research outputs found
scrogster/Fox_Model: Invasive prey controlling invasive predators? European rabbit abundance does not determine red fox population dynamics.
No full text<p>Scroggie, M.P., Forsyth, D.F., McPhee, S., Matthews, J., Stuart, I.G., Stamation, K.A., Lindeman, M. & Ramsey, D.S.L. (2018) Invasive prey controlling invasive predators? European rabbit abundance does not determine red fox population dynamics.</p>
Data and code for 'Disease shrinks metapopulation viability for amphibians'
No full text<p>This repository provides all data and R code from the analysis presented in the following paper:</p>
<p>Heard, G.W., Scroggie, M.P., Hollanders, M., and Scheele, B.C. (in review). Disease-induced mortality shrinks metapopulation viability for amphibians. </p>
<p>The data are provided as a series of .csv files. A GRD file is provided for the landscape rasters. R code is provided separately for each of the following components:</p>
<p>1. A script to complete regression modelling of age structure data for populations of the focal species pre- and post-Bd, plus estimation of adult survival rates from the age structure data using the 'catch curve' approach ('Age_structure_analysis.R').</p>
<p>2. A script to generate the sample landscapes used for simulations of metapopulation dynamics for the pre- and post-Bd epochs ('Derive_landscape_rasters.R').</p>
<p>3. A script with functions for simulating metapopulation dynamics with the aid of the STEPS R package ('STEPS_model.R').</p>
<p>4. A script to run the metapopulation simulations across all the demographic and connectivity scenarios, where connectivity scenarios are defined by the sample landscapes ('Run_STEPS_simulations.R'). </p>
<p>5. A script to fit logistic regression models to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_GLM.R').</p>
<p>6. A script to fit multivariate normal hypervolumes to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_MVNH.R').</p>
<p>In combination, the data files and scripts allow all analyses from the paper to be reproduced. </p>
Code and data for "Optimising habitat management for amphibians: from simple models to complex decisions"
No full textThe zip archive contains code and data to reproduce the analysis contained in the following manuscript:
Scroggie, M.P., Preece, K., Nicholson, E., McCarthy, M.A., Parris, K.M. and Heard, G.W. Optimising habitat management for amphibians: from simple models to complex decisions.
Included in the archive is the source code of two R packages (METAPOP, and METAPOPPLAN), which must first be installed, along with their various dependencies which include Rcpp, RcppArmadillo, sp, spdep and rgeos. As package METAPOPPLAN contains C++ code, installation requires the presence of the appropriate C++ compilers and other software development tools. These should be available or easily installable on Linux or other Unix based systems, but Microsoft Windows users must first install the appropriate version of Rtools, which can be downloaded from https://cran.r-project.org/bin/windows/Rtools/.
With all appropriate packages installed, the analysis can be replicated by running the included Makefile.
Total execution time will be quite long, due to the large number of simulations that must be run. On my Windows system, with 12 cores and 4GB of RAM, execution took approximately 10 days. The code will run much faster if the various management scenarios included in the analysis are executed in parallel. This can be done by executing make with a -j argument specifying the number of cores to utilise. For example, if your system has 12 cores, invoke *make* as follows:
make -j 12
Overall execution time will scale roughly with the number of available cores, up to a maximum of 24 (the total number of management scenarios).
</p
scrogster/Fox_Model: minor bug fix
No full text<p>This version implements a minor bugfix: an error in the indexing of covariate values related to season and warren ripping has been corrected, leading to some minor changes in some parameter estimates, but no change to the overall conclusions of the analysis. Thanks to Nick Golding for detecting this error.</p>
Territorial vocal behavior in hybrid smooth froglets, Geocrinia laevis complex (Anura: Myobatrachidae)
No full textA Bayesian model of metapopulation viability, with application to an endangered amphibian
No full textAim: Population viability analysis (PVA) is used to quantify the risks faced by species under alternative management regimes. Bayesian PVAs allow uncertainty in the parameters of the underlying population model to be easily propagated through to the predictions. We developed a Bayesian stochastic patch occupancy model (SPOM) and used this model to assess the viability of a metapopulation of the growling grass frog (Litoria raniformis) under different urbanization scenarios. Location: Melbourne, Victoria, Australia. Methods: We fitted a Bayesian model that accounted for imperfect detection to a multiseason occupancy dataset for L. raniformis collected across northern Melbourne. The probability of extinction was modelled as a function of effective wetland area, aquatic vegetation cover and connectivity, using logistic regression. The probability of colonization was modelled as a function of connectivity alone. We then simulated the dynamics of a metapopulation of L. raniformis subject to differing levels of urbanization and compensatory wetland creation. Uncertainty was propagated by conducting simulations for 5000 estimates of the parameters of the models for extinction and colonization. Results: There was considerable uncertainty in both the probability of quasi-extinction and the minimum number of occupied wetlands under most urbanization scenarios. Uncertainty around the change in quasi-extinction risk and minimum metapopulation size increased with increasing habitat loss. For our focal metapopulation, the analysis revealed that significant investment in new wetlands may be required to offset the impacts of urbanization. Main conclusions: Bayesian approaches to PVA allow parametric uncertainty to be propagated and considered in management decisions. They also provide means of identifying parameters that represent critical uncertainties, and, through the use of informative priors, can easily assimilate new data to reduce parametric uncertainty. These advantages, and the ready availability of software to run Bayesian analyses, will ensure that Bayesian approaches are used increasingly for PVAs.12 page(s
Analyses of Victorian hog deer (axis porcinus) checking station data: demographics, body condition and time of harvest
No full textThis report looks into the sustainability and health of deer within Victoria\u27s regional areas. Hog Deer (Axis porcinus) are a popular and highly valued game species in Victoria, with licensed hunters permitted to harvest one male and one female during an annual hunting season during the month of April. All harvested deer must be tagged and presented at a checking station within 24 hours of harvest. A variety of morphological and biological data are recorded for each harvested animal during inspection at the checking stations.
The objectives of this study were to (i) summarise biological data collected for all Hog Deer inspected at the four mainland checking stations during 1997–2011 (i.e. excluding Sunday Island, which is owned and managed by the Para Park Co-operative Game Reserve Limited), and (ii) provide recommendations for improving the usefulness of future data collection. A total of 1122 deer were presented at the mainland checking stations (70.4% male; 29.6% female) during 1997–2011, with annual totals ranging from 38 in 1999 to 111 in 2011.
There was little evidence that the number or sex ratio of deer harvested annually changed substantially over the course of the study period. The overall percentages of deer harvested on public (52%) and private (48%) land also did not show any discernable trend during the study period. The ages of deer (estimated by molar eruption and tooth wear) ranged from 1 to 12 years for females and males. Although the age structures differed slightly for females and males, there was no evidence that this changed over the study period, although inconsistent recording of ages limited the opportunity for quantitative analyses of these data
Experimental Examination of the Potential for Three Introduced Fish Species to Prey on Tadpoles of the Endangered Booroolong Frog, Litoria booroolongensis
No full text
