VredfoxIPM: an integrated population modelling workflow for supporting mesopredator management
This repository contains code for a reproducible, modular workflow for Bayesian integrated population analysis (using Nimble, https://github.com/nimble-dev/nimble) for hunted red foxes on the Varanger penninsula, Norway.
The workflow is available as both a manual implementation ("RedFox_IPM_Analysis.R") and as a semi-automated "targets" pipeline (see https://books.ropensci.org/targets/) and contains the following parts:
- Download of raw data from COAT data portal (https://data.coat.no/)
- Wrangling, formatting, and preparation of observational data and prior information
- Definition and setup of integrated population model (IPM)
- Complete simulation of initial values
- Running of IPM using MCMC
- Extraction and visualization of primary results
- Follow-up analyses (incl. vizualizations)
A schematic overview of the workflow and its parts is shown below:
The workflow is fully function-based, and each function is documented in its respective script within the folder "R". The folder "vignettes" contains a richly documented "walkthrough" of the manual workflow ("workflow_walkthrough.Rmd"), including instructions for installing necessary dependencies and accessing all requisite data.
Auxiliary data, computed results, and finished plots and other visualizations can be found on OSF: https://osf.io/756re/
The scientific article associated with this repository and presenting the workflow and results on Varanger red foxes will shortly be made available as a pre-print.