dslramsey / RHDV_state_space

Data and code from Ramsey et al (2019) JAppEcol MS

Emerging RHDV2 suppresses the impact of endemic and novel strains of RHDV on wild rabbit populations

Notes

This repository contains data and code from:

Ramsey, D.S.L., Cox, T., Strive, T., Forsyth, D.M., Stuart, I., Hall, R., Elsworth, P., and Campbell, S. (2019). “Emerging RHDV2 suppresses the impact of endemic and novel strains of RHDV on wild rabbit populations” Journal of Applied Ecology

Getting started

File descriptions:

R/. – R code used to process the spotlight and seroprevalence data and fit Stan models.

Data/. – Contains csv files for the rabbit spotlight and serology datasets.

Stan/. – Stan code for the rabbit N-mixture state-space model as well as the MAR(1) and age-specific trend models fitted to the seroprevalence data for the three strains.

Prerequisites

The R scripts require packages tidyverse, lubridate, gridExtra, rstan and MCMCvis.