This repo contains the analysis and manuscript for the paper "Limited impact of chytridiomycosis on juvenile frogs in a recovered species". The Quarto doc juveniles-analysis.qmd contains code for reading in data and covariates, the nimble code for the multievent model presented in Hollanders and Royle (2022) (https://doi.org/10.1111/2041-210X.13993), and the analysis to run the model comparing Bd infection patterns between juveniles and adults. The file further contains the code to recreate the plots. The juveniles-manuscript.qmd is the Quarto doc of the manuscript itself. The posterior MCMC sampes are read in at the top of the document, and called throughout the text to aid reproducibility and reduce errors.
The data folder contains all data called in juveniles-analysis.qmd. The mcmc-samples folder contains the posterior draws of both models, in addition to a ~summary.csv files that summarised posterior draws for different parameters. The mcmc-trace folder contains MCMC traceplots from the models.