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.
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Install and configure rstan (version 2.26 or higher) by following the instructions in the RStan Getting Started vignette.
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Install the current version of salmonIPM from GitHub using devtools.
if(!require("devtools")) install.packages("devtools")
devtools::install_github("ebuhle/salmonIPM")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.
Buhle, E. R. and M. D. Scheuerell. 2024. salmonIPM: Integrated population models for Pacific salmonids (version x.x.x). https://doi.org/10.5281/zenodo.14511463
Buhle, E. R., M. D. Scheuerell, T. D. Cooney, M. J. Ford, R. W. Zabel, and J. T. Thorson. 2018. Using integrated population models to evaluate fishery and environmental impacts on Pacific salmon viability. U.S. Department of Commerce, NOAA Technical Memorandum, NMFS‐NWFSC‐14. http://doi.org/10.7289/V5/TM-NWFSC-140
