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salmonMSE

Management Strategy Evaluation for Salmon Species

salmonMSE is a decision-support tool for Pacific salmon focusing on strategic trade-offs among harvest, hatchery and habitat management levers.

Funding for the development of salmonMSE is provided through the Pacific Salmon Strategy Initiative in collaboration with the Department of Fisheries and Oceans Canada.

Installation

salmonMSE can be downloaded from CRAN with:

install.packages("salmonMSE")

And the development version is available on GitHub with:

# install.packages("remotes")
remotes::install_github("Blue-Matter/salmonMSE")

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Version

Install

install.packages('salmonMSE')

Monthly Downloads

145

Version

0.1.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Quang Huynh

Last Published

September 23rd, 2025

Functions in salmonMSE (0.1.0)

calc_phi

Calculate equilibrium quantities with life history groups
calc_SRRpars

Convert density-dependent survival parameters
calc_Smsy_Ricker

Ricker reference points
calc_ref

Reference points
calc_SRR

Calculate abundance from density-dependent mortality
calc_pwild

Proportion wild spawners
SAR_fitness

Update natural mortality of juveniles
SMSE-class

Class "SMSE"
SHist-class

Class "SHist"
SOM-class

Class "SOM"
compare_spawners

Compare simulation runs
plot_LHG

Plot life history groups and release strategies
plot_statevar_ts

Plot core output from salmonMSE
calc_smolt

Smolt production
plot_decision_table

Decision table of performance metrics
get_F

Calculate F from harvest rate
fit_CM

Fit conditioning model to historical data
report_CM

Conditioning model markdown report
report

Generate markdown reports
check_SOM

Check inputs to SOM object
glossary

salmonMSE glossary
salmonMSE_env

Environment to store salmon specific variables, e.g, fitness, during the simulation
smolt_func

Predict smolt production
salmonMSE

Run salmonMSE
make_Harvest_MMP

Internal salmonMSE functions for converting operating model inputs and outputs
plot_tradeoff

Tradeoff figure
Bio-class

Class "Bio"
AHA

All-H Analyzer
CM2SOM

Convert conditioning model to operating model
PNI50

Example performance metrics
Harvest_MMP

Harvest component of operating model
Historical-class

Class "Historical"
Harvest-class

Class "Harvest"
CM_int

Estimation function for conditioning model
Hatchery-class

Class "Hatchery"
Habitat-class

Class "Habitat"