Code and data

A0215_L_raniformis_tweakedHere you can find statistical code and data from papers that I’ve published, or co-authored. I’ll update this page as new papers come out, and attempt to post code and data from past papers as well. Most code will be of the R variety, with a smattering of BUGS and JAGS code for good measure. Given the restrictions on the file types that can be uploaded on WordPress sites, some code and data are provided in .docx format.

I discuss my motivations for uploading my code and data on this website here.

Drop me a line if you have any queries. And just one request – if you use the code or data presented here, please cite the relevant paper.

Enjoy!

10.  Scroggie, M.P., Peterson, G.N.L, Rohr, D.H., Nicholson, E. and Heard, G.W. (in press). Disturbance has benefits as well as costs for fragmented populations of a cryptic grassland reptileLandscape Ecology.

  • R code and data for the analysis are available from a Zenodo archive found here.

9. Scroggie, M.P., Preece, K., Nicholson, E., McCarthy, M.A., Parris, K.M. and Heard, G.W. (2019). Optimizing habitat management for amphibians: from simple models to complex decisionsBiological Conservation 236, 60-69.

  • R code and data for the optimisation are available from a Zenodo archive found here.

8.  Heard, G.W., Scroggie, M.P., Ramsey, D.S.L, Clemann, N., Hodgson, J.A. and Thomas, C.D. (2018) Can habitat management mitigate disease impacts on threatened amphibians? Conservation Letters 11 e12375.

  • R code for running simulations of wetland water temperature regimes, pathogen prevalence and frog metapopulation viability for each management scenario. Download here.
  • Data required to run the simulations. Download here.

7. Heard, G.W., Canessa, S., and Parris, K.M. (2015). Interspecific variation in the phenology of advertisement calling in a temperate Australian frog community. Ecology and Evolution 5, 3927–3938.

6. Heard, G.W., Thomas, C.D., Hodgson, J.A., Scroggie, M.P., Ramsey, D.S.L and Clemann, N. (2015). Refugia and connectivity sustain amphibian metapopulations afflicted by disease. Ecology Letters 18, 853-863.

  • R code and data for water temperature modelling. Download here (Appendix S4).
  • R code and data for modelling chytrid prevalence. Download here (Appendix S5).
  • R code and data for modelling GGF occupancy dynamics. Download here (Appendix S6).
  • R code for simulating metapopulation viability. Download here (Appendix S7).

5. Canessa, S., Heard, G.W., Robertson, P. and Sluiter, I.R.K. (2015). Dealing with trade-offs in destructive sampling designs for occupancy surveysPLoS ONE 10(3): e0120340.

  • JAGS code for the detection model for Hemiergis millewae. Download here.
  • Data for the detection model. Download here.
  • Spreadsheet for optimisation of search strategies. Download here.

4. Heard, G.W., Scroggie, M.P., Clemann, N. and Ramsey, D.S.L. (2014). Wetland characteristics influence disease risk for a threatened amphibianEcological Applications 24, 650–662.

  • OpenBUGS code for the hierarchical model of the probability of infection, including data. Download here.
  • OpenBUGS code for the hierarchical linear model of zoospore load, including data. Download here.
  • OpenBUGS code for the Cormack-Jolly-Seber model, incorporating the hierarchical model of the probability of infection (and the data). Download here.
  • R code for simulating the effect of chytridiomycosis on survival rates. Download here.

3. Heard, G.W., McCarthy, M.A., Scroggie, M.P., Baumgartner, J.B., and Parris, K.M. (2013). A Bayesian model of metapopulation viability, with application to an endangered amphibianDiversity and Distributions 19, 555-566.

  • R code for fitting the multi-season occupancy model (using OpenBUGS) and extracting the parameter estimates. Download here, or email me for this in ‘.r’ format.
  • R code for simulating the dynamics of the Donnybrook metapopulation. Download here, or email me for this in ‘.r’ format.
  • Excel spreadsheet with 5000 estimates of the parameters of the model. Download here, or email for this in ‘.txt’ format (as per the code).
  • Summaries of the parameters and plots of the fitted relationships. Download here.

2. Heard, G.W., Scroggie, M.P., and Malone, B.S. (2012). The life history and decline of the threatened Australian frog, Litoria raniformisAustral Ecology 37, 276-284.

  • OpenBUGS code for fitting a von Bertalanffy model to growth increment data for  Growling Grass Frogs (growth data included). For Males download here and for Females download here.
  • OpenBUGS code for estimating survival and recapture probabilities of Growling Grass Frogs using a Cormack-Jolly-Seber model (mark-recap data included). Download here.

1. Heard, G.W., Scroggie, M.P., and Malone, B.S. (2008). Visible Implant Alphanumeric tags as an alternative to toe-clipping for marking amphibians – a case studyWildlife Research 35, 747-759.

  • OpenBUGS code for assessing variation in the incidence of tag loss (includes data). Download here.
  • OpenBUGS code for assessing the effect of observer experience on the probability of correctly reading tags, with random effects of frogs and observers (includes data). Download here.
  • OpenBUGS code for modelling the growth trajectories of tagged and control frogs (includes data). Download here.
  • Full raw data (growth trajectories and tag loss). Download here.

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