Data and code for 'Age truncation due to disease shrinks metapopulation viability for amphibians'

This repository provides all data and R code from the analysis for the following paper:

Heard, G.W., Scroggie, M.P., Hollanders, M., and Scheele, B.C. (in press). Age truncation due to disease shrinks metapopulation viability for amphibians. Journal of Applied Ecology.  

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:

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').

2. A script to generate the sample landscapes used for simulations of metapopulation dynamics for the pre- and post-Bd time periods ('Derive_landscape_rasters.R').

3. A script with functions for simulating metapopulation dynamics with the aid of the STEPS R package ('STEPS_model.R').

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'). 

5. A script to fit logistic regression models to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_GLM.R').

6. A script to fit multivariate normal hypervolumes to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_MVNH.R').

7. A script to generate each of the figures in the manuscript, plus Table 2 which requires post-hoc data compilation ('Generate_figures.R'). 

In combination, the data files and scripts allow all analyses from the paper to be reproduced.