R scripts, input and output data for: Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs

An important part of infectious disease management is predicting factors that influence disease outbreaks, such as R, the number of secondary infections arising from an infected individual. Estimating R is particularly challenging for environmentally transmitted pathogens given time lags between cases and subsequent infections. Here, we calculated R for Bacillus anthracis infections arising from anthrax carcass sites in Etosha National Park, Namibia. Combining host behavioural data, pathogen concentrations, and simulation models, we show that R is spatially and temporally variable, driven by spore concentrations at death, host visitation rates and early preference for foraging at infectious sites. While spores were detected up to a decade after death, most secondary infections occurred within two years. Transmission simulations under scenarios combining site infectiousness and host exposure risk under different environmental conditions led to dramatically different outbreak dynamics, fr..., Camera trap data were collected from 13 sites between 2010–2013 in Etosha National Park, Namibia. Soil samples were collected to analyse the concentration of Bacillus anthracis spores between 2010–2022 in Etosha National Park.
Statistical analysis was used to analyse camera trap data, and a simulation model was built to estimate the reproduction number of anthrax in Etosha National Park., , # Reproduction Number analysis and model

Files to run the model from the manuscript \"Season of death, pathogen persistence and wildlife behavior alter number of anthrax secondary infections from environmental reservoirs'.

Six CSV data files and one R code are used to run the analysis and modeling.

Eleven CSV files represent the output of the model (Rscript 'R_estimation_Code.R, using the input data CSV files). Those outputs are used in the R code 'Plots_R_estimation_Code.R' to plot the figures in the MS and the SI.

## Description of the data and file structure

Input files :

* Camera_all_individuals.csv : Records each individual zebra and wildebeest observed on the camera. The columns are :
* Date = Date of recording;
* ID = Camera ID;
* Treatment = Carcass or Control site;
* Tini = Time at which the individual entered the zone;
* Tend = Time at which the individual exited the zone;
* Individual = When herd visiting the site at the same time, t...