Many roads to reservoirs? How susceptibility and shedding shape host competence in amphibians

Host competence—the ability to acquire, harbor, and transmit infections—drives pathogen spread and persistence in multi-host communities. Evaluating species-specific competence is critical for predicting transmission, particularly for generalist fungal pathogens like Batrachochytrium dendrobatidis (Bd). Despite its central role in disease dynamics, we lack an epidemiologically grounded competence metric that rigorously accounts for how infection intensity affects a host's competence. This knowledge gap limits our ability to compare mechanisms across species and assess their roles in pathogen persistence. To address these challenges, we developed a novel, load-dependent competence metric using host-pathogen Integral Projection Models (IPMs) that integrates variation in susceptibility, within-host pathogen growth, and pathogen shedding dynamics.
We applied this metric to lab-based challenge experiments with three common North American amphibians (Notophthalmus viridescens, Rana clamitans,..., We conducted a controlled dose-response experiment to assess Bd susceptibility and shedding across species (details in Appendix S1). After confirming Bd-free status via qPCR following heat treatment, adult R. clamitans, N. viridescens, and R. catesbeianus were exposed to one of four Bd zoospore doses ($1\times104$ to $1\times107$) or a control. All exposures occurred at $21^\circ C$ in individual containers under standardized housing and feeding conditions.
We exposed individuals to a Tennessee Bd isolate (FMB003, GPL-1), with zoospore concentrations enumerated using a hemocytometer. Individuals were exposed for 24 hours, then monitored for infection and zoospore shedding repeatedly. Skin swabs to measure Bd infection load were taken every 6 days, followed by 24-hour water exposure in separate containers to quantify shedding. Experiment duration varied among species (56-79 days post-exposure). Swab and shedding samples were processed for Bd detection via qP..., This README describes various files:

1. The file \"comp_figures.Rmd\" provides the Bayesian hierarchical models used to construct the plots for the manuscript and appendix.
2. The files 'bull_comp_master.csv', 'newt_comp_master_data.csv', and 'comp_green_master.csv' are the data files from the each challenge experiment where bull = R. catesbeianus, newt = N. viridescens, and green = R. clamitans. The necessary columns are described below:

'ID': A unique identifier for individual hosts within a species.

'trt\": The dose (zoospores per mL) of Bd to which the hosts were exposed. This columns is given in scientific notation and will be read as a string. There were four unique doses: 1x10^4, 1x10^5, 1x10^6, and 1x10^7.

'temp': The temperature at which the hosts were held at for the duration of the experiment

'day & waterday': The day of the experiment at which the swab (day) and shedding sample (waterday) were taken.

'swabZE': The Bd load as measured by qPCR on the given individual at th...,