56 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>
scrogster/SLL_2016: Code and data for: Scroggie, M.P., Peterson, G.N.L., Rohr, D.H., Nicholson, E. & Heard, G.W. (2019) Disturbance has benefits as well as costs for fragmented populations of a cryptic grassland reptile.
No full textDisturbance has benefits as well as costs for fragmented populations of a cryptic grassland reptil
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).
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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>
Zonal hybridization in frogs of the Geocrinia laevis complex (Anura: Myobatrachidae) : population ecology and male acoustic behaviour
No full textTypescript (photocopy)Author's name on spine: M. ScroggieThesis (PhD) -- University of Melbourne, Faculty of Science, 2002Includes bibliographical references (leaves 193-214)Population ecology, life-history variation and the vocal behaviour of males were investigated in allopatric populations of two species of myobatrachid frogs (Geocrinia laevis and G. victoriana) and within a hybrid zone between the species.
The skeletochronological method was shown to be a reliable and accurate method for age- determination of frogs of the Geocrinia laevis complex. Population age-frequency data from four study populations obtained using skeletochronology allowed estimation of age at maturity, adult survival-rates and age-specific fecundity in populations of the two species, and in two hybrid zone populations. In all four study populations the age at maturity was 2 years post-zygote for both males and females. Estimated annual rates of survival among adults were less than 0.5 in all populations, with males having slightly lower rates of survival than females. The maximum observed longevity was 5 years post-zygote.
The measures of age-specific survival and fecundity for females from the four populations were used to construct matrix models of the populations. Elasticity analysis of these models revealed that rates-of-increase of the populations are expected to be particularly sensitive to perturbations in survival rates of juveniles and larvae.
Females of the G. laevis complex were found to invest heavily in reproductive output, with the level of reproductive effort (expressed as relative clutch mass) among the highest of any anuran for which comparable data are available. Maternal body-size was positively correlated with the numbers and sizes of eggs contained in clutches. Significant differences were detected among populations in the sizes of the eggs produced, independent of effects of maternal body-size.
Notwithstanding the differences which were observed between populations in egg-size, little evidence of differentiation in life-history traits was detected between the study populations of the two species and their hybrids. Hence it was concluded that interpopulational variation in life- history traits is of very limited significance to the dynamics and structure of the south-western Victorian hybrid zone between G. laevis and G. victoriana.
Measurements of the mating success of individual males from populations of both parental species, and from a hybrid zone population, did not reveal any consistent effects of male body-size on mating success. Within a hybrid-zone population, the attributes of advertisement-calls of males were not predictive of their mating success.
The territorial vocal behaviour of male hybrids was assessed. It was found that most hybrid males possess encounter calls functionally equivalent to those of G. victoriana, evoked by exposure to advertisement calls presented at high intensity. The responses to hybrid males during simulated territorial interactions were not related to a phenotypic index of hybridity, suggesting genetic and functional decoupling of the two components of the vocal repertoire (advertisement calls and encounter calls) among hybrid-zone males. This decoupling of the components of the vocal repertoire may be the result of selection on the vocal behaviour of males within hybrid populations.
It is concluded that sexual selection on the vocal behaviour of males within the hybrid zone is probably a crucial factor in determining the dynamics of hybridization in the G. laevis complex
Territorial vocal behavior in hybrid smooth froglets, Geocrinia laevis complex (Anura: Myobatrachidae)
No full textPrecision and accuracy of flyout counts of the common bent-wing bat (Miniopterus schreibersii)
No full textVisual flyout count data for the common bent-wing bat Miniopterus schreibersii, collected by a team of observers over two seasons at a disused mine in the Kinglake National Park, south-eastern Australia, was compared with infra-red video footage, collected simultaneously, in order to quantify the precision and accuracy of the observer counts. Bayesian statistical models were used to evaluate the relationship between observer counts and the actual number of bats emerging from the cave, as determined by analysis of the infra-red video footage of the flyout. The accuracy of flyout counts was found to decline with increasing flyout rates, with observers' counts becoming increasingly negatively biased as the rate of bat emergence from the mine increased. In addition, there was evidence of inter-observer variation in the accuracy of the counts. Although the bias in observer counts was relatively small, caution needs to be exercised in interpreting the results of visual flyout counts. We conclude that the use of infra-red video footage for determining numbers is preferable to visual observer counts. The major difficulty in using flyout counts for monitoring is the considerable night-to-night variation in numbers of bats emerging, which could be attributed to variation in the proportion of bats emerging to forage, or to the use of alternative roosting sites by individual bats on successive nights. Both observer error and short-term temporal variation in numbers of emerging bats have the potential to bias population estimates of bats, and need to be properly accounted for if flyout counts are to be used as a tool for population assessment and monitoring
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