Management Strategy Evaluation for Salmon Species

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Documentation for package ‘salmonMSE’ version 0.1.0

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AHA All-H Analyzer
Bio-class Class '"Bio"'
calc_MSY Reference points
calc_ref Reference points
calc_Sgen Reference points
calc_Sgen_Ricker Ricker reference points
calc_smolt Smolt production
calc_Smsy_Ricker Ricker reference points
calc_SRR Calculate abundance from density-dependent mortality
calc_SRRpars Convert density-dependent survival parameters
calc_Umsy_Ricker Ricker reference points
check_SOM Check inputs to SOM object
CM2SOM Convert conditioning model to operating model
compare_escapement Compare simulation runs
compare_fitness Compare simulation runs
compare_spawners Compare simulation runs
fit_CM Fit conditioning model to historical data
glossary salmonMSE glossary
Habitat-class Class '"Habitat"'
Harvest-class Class '"Harvest"'
Hatchery-class Class '"Hatchery"'
Historical-class Class '"Historical"'
make_Fleet Internal salmonMSE functions for converting operating model inputs and outputs
make_Harvest_MMP Internal salmonMSE functions for converting operating model inputs and outputs
make_Stock Internal salmonMSE functions for converting operating model inputs and outputs
MMSE2SMSE Internal salmonMSE functions for converting operating model inputs and outputs
multiHist2SHist Internal salmonMSE functions for converting operating model inputs and outputs
plot_decision_table Decision table of performance metrics
plot_escapement Plot core output from salmonMSE
plot_fishery Plot core output from salmonMSE
plot_fitness Plot core output from salmonMSE
plot_Kobe Plot core output from salmonMSE
plot_LHG Plot life history groups and release strategies
plot_RS Plot life history groups and release strategies
plot_spawners Plot core output from salmonMSE
plot_statevar_hist Plot core output from salmonMSE
plot_statevar_ts Plot core output from salmonMSE
plot_tradeoff Tradeoff figure
PNI50 Example performance metrics
PNI80 Example performance metrics
report Generate markdown reports
report-method Generate markdown reports
report_CM Conditioning model markdown report
salmonMSE Run salmonMSE
salmonMSE-int Internal salmonMSE functions for converting operating model inputs and outputs
salmonMSE_env Environment to store salmon specific variables, e.g, fitness, during the simulation
sample_CM Fit conditioning model to historical data
Sgen100 Example performance metrics
SHist-class Class '"SHist"'
SMSE-class Class '"SMSE"'
SMSY85 Example performance metrics
SOM Class '"SOM"'
SOM-class Class '"SOM"'
SOM2MOM Internal salmonMSE functions for converting operating model inputs and outputs
WILD50 Example performance metrics