This repository contains R code to extract data and replicate analyses in the manuscript titled Multi-species dependencies improve forecasts of population dynamics in a long-term monitoring study (currently in review; a preprint of a previous version is hosted on biorxiv at the following DOI: https://doi.org/10.32942/X2TS34)
portalcasting
tidyverse
forecast
cmdstanr (and Cmdstan)
mvgam
scoringRules
extraDistr
nleqslv
Raw rodent capture and covariate data have already been downloaded from the latest version of the portalr database and extracted to the data directory. Data can be prepared for analysis / modeling following instructions in the 1.prep_data.R script. Models are built using mvgam functionality in the 2.models.R script. A working version of cmdstanr is required to condition models on observed data. This script will produce large model objects (stored as class mvgam) that unfortunately cannot be uploaded to Github due to their size. Analysis of these models is completed in the 3.analysis.R script. Figures are produced throughout the workflow. All of these figures are stored in the Figures directory.