Code for similar population dynamics before and after a chytridiomycosis outbreak in a tropical riparian amphibian species.

This software release contains 4 files with R scripts organized according to the objective (e.g., format the data, model fitting, etc.). The overall objective of the project was to: analyzed ten years of capture-mark-recapture data spanning 2000−2014 for a population of Espadarana prosoblepon in El Copé, Panama, encompassing a period before and after a Batrachochytrium dendrobatidis (Bd) outbreak in 2004 using Jolly-Seber models.
We surveyed four 200-m permanent stream transects in Parque Nacional G. D. Omar Torríjos Herrera, El Copé, Coclé Province, Panama (8°39’57’’N, 80°35’33’’W) established as part of a long-term amphibian monitoring project. Between 2000 and 2004 [pre-Bd], we surveyed transects annually, and between 2010 and 2014 [post-Bd], we surveyed transects during the following months and years: July 2010, July 2011, June & July 2012, February & March 2013, June & July 2013, and March 2014. If two months were sampled consecutively in a year, we combined them into a single primary period (e.g., June and July 2012 combined) for a total of six primary periods post-Bd.
To analyze the data, we fit two Jolly Seber models that accounted for imperfect host detection. Using empirical demographic estimates (i.e., apparent survival, infection, and recovery probabilities, and abundance) in this amphibian species from the model, we explored whether animals infected with Bd have a lower survival probabilities than uninfected individuals, and whether survival probability of infected hosts was intensity-dependent.
The necessary data files to run all four scripts can be found in DiRenzo et al. (202Xa), whereas the accompanying research article can be found in DiRenzo et al. (202xb).