Repository for corroboree frog (Pseudophryne pengilleyi) analysis

This repo contains four scripts for analyses contained in the manuscript. All analyses were conducted with nimble 0.13 in R 4.3.

1. corroboree-analysis-age.R fits negative binomial distributions to the age data from two extant and one museum population to estimate the mean age structure.
2. corroboree-analysis-prevalence.R fits a logistic regression to swab samples analysed for the presence of Bd. There are two intercept corresponding to the two sites and four random year effects (shared across sites; note that site Warogong-Cotterill just has one year of data). We then compute marginal means for each site and plot the predicted prevalence for each year.
3. corroboree-analysis-mortality.R estimated baseline annual mortality rates using the museum age structure which is then used to specify the intercept of a geometric survival model to estimate the effect of Bd infection on the mortality rates of laboratory-exposed frogs.
4. corroboree-analysis-elasticity.R contains the elasticity analysis populated with the survival estimates from (3) above to investigate the effect of a delayed age of maturation on the elasticity of adult survival.

Data for these files are contained within the data folder. MCMC output for the models in (1--3) above are contained in the mcmc folder. Figure output is in the figs folder.