This is the development repo for salmonIPM, an R package that fits integrated population models to data from anadromous Pacific salmonid populations using a hierarchical Bayesian framework implemented in Stan. Various models are available, representing alternative life histories and data structures as well as independent or hierarchically pooled populations. Users can specify stage-specific covariate effects and hyper-priors using formula syntax.
Installation
Install and configure rstan (version 2.26 or higher) by following the instructions in the RStan Getting Started vignette.
Install the current version of salmonIPM from GitHub using devtools. Because the repo is private for the time being, it is necessary to generate a personal access token (PAT) and pass it to
install_github()as discussed here.
if(!require("devtools")) install.packages("devtools")
devtools::install_github("ebuhle/salmonIPM", auth_token = "my_PAT")We recommend using multiple cores if available when installing salmonIPM to reduce compilation time. You can do this by setting the R environment variable MAKEFLAGS to -jX, where X is the number of cores. This can be done interactively using Sys.setenv(MAKEFLAGS = "-jX") or it can be specified in .Renviron.