This repository contains data and code for the novel extended multievent model presented in:
- Hollanders, M. and J. Andrew Royle. 2022. Know what you don't know: Embracing state uncertainty in disease-structured multistate models. Methods in Ecology and Evolution. 10.1111/2041-210X.13993
This repo was primarily created so that users would have direct access to the R code, given that the appendices in the Supporting Information of the manuscript are in PDF form. Appendices 1–4 are identical to those in the manuscript. Additionally, the repo contains the Mixophyes fleayi capture history used as a case study in the manuscript. For details on that dataset, see the README in the Dryad repository:
- Hollanders, M., and J. Andrew Royle. 2022. Know what you don't know: Embracing state uncertainty in disease-structured multistate models, Dataset. Dryad. https://doi.org/10.5061/dryad.s7h44j19h.
The Quarto document multievent-fleayi.qmd contains all the code to manipulate this capture history, analyse the data with the multievent model and a traditional Arnason-Schwarz model, and to create the figures. MCMC output is included in the folders mcmc-samples and mcmc-trace. Note that in addition to the MCMC draws and summaries for the multievent and Arnason-Schwarz models, there is also output for the multievent model without false-positives in the sampling process (MEdraws-del0), diagnostic process (MEdraws-lam0), and without any false-positives (MEdraws-dellam0).
The manuscript file is included as multievent-manuscript.qmd.