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salmonipm

Integrated population models for Pacific salmonids

https://github.com/ebuhle/salmonipm

Science Score: 67.0%

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Integrated population models for Pacific salmonids

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  • Stars: 6
  • Watchers: 8
  • Forks: 1
  • Open Issues: 7
  • Releases: 5
Created almost 9 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.md

salmonIPM

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

  1. Install and configure rstan (version 2.26 or higher) by following the instructions in the RStan Getting Started vignette.

  2. Install the current version of salmonIPM from GitHub using devtools.

r 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.

Citing salmonIPM

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, NMFSNWFSC14. http://doi.org/10.7289/V5/TM-NWFSC-140

Ohlberger, J., E. R. Buhle, T. W. Buehrens, N. W. Kendall, T. Harbison, A. M. Claiborne, J. P. Losee, J. Whitney, and M. D. Scheuerell. 2025. Declining marine survival of steelhead trout linked to climate and ecosystem change. Fish and Fisheries x:x-x. https://doi.org/10.1111/faf.12878

Buonanduci, M. S., E. R. Buhle, M. J. Case, E. R. Howe, J. C. Robertson, N. VanBuskirk, and A. K. Ettinger. 2025. Forest restoration can bolster salmon population persistence under climate change. Biological Conservation 305: 111099. https://doi.org/10.1016/j.biocon.2025.111099

DOI

Owner

  • Login: ebuhle
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Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "salmonIPM" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'salmonIPM: Integrated Population Models for Pacific Salmonids'
version: '[version]'
abstract: Fits integrated population models (IPMs) or run-reconstruction regressions
  for anadromous Pacific salmonid population dynamics using a hierarchical Bayesian
  framework implemented in Stan. Various models are available, representing alternative
  life-history structures and independent or hierarchically pooled populations. Users
  can specify stage-specific covariate effects and hyper-priors using formula syntax.
authors:
- family-names: Buhle
  given-names: Eric
  email: eric.buhle@noaa.gov
- family-names: Scheuerell
  given-names: Mark
  email: scheuerl@uw.edu
  orcid: https://orcid.org/0000-0002-8284-1254
url: https://ebuhle.github.io/salmonIPM/
doi: 10.5281/zenodo.14511463
contact:
- family-names: Buhle
  given-names: Eric
  email: eric.buhle@noaa.gov
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Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • Rcpp >= 0.12.0 depends
  • methods * depends
  • RcppParallel * imports
  • distributional * imports
  • dplyr >= 1.0.0 imports
  • ggdist * imports
  • ggplot2 * imports
  • gnorm * imports
  • loo * imports
  • mvtnorm * imports
  • parallel * imports
  • posterior * imports
  • rstan >= 2.32.0 imports
  • rstantools >= 2.4.0 imports
  • shinystan * imports
  • stats * imports
  • tidyr * imports
  • bayesplot * suggests
  • knitr * suggests
  • lifecycle * suggests
  • rmarkdown * suggests