Management Strategy Evaluation for Salmon Species

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Documentation for package ‘salmonMSE’ version 2.1.0

• DESCRIPTION file
• Package NEWS
• Package README

Help Pages

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
CMfigures	Figures for conditioning model results
CM_covariate	Figures for conditioning model results
CM_CWT_ER	Figures for conditioning model results
CM_ER	Figures for conditioning model results
CM_esc	Figures for conditioning model results
CM_F	Figures for conditioning model results
CM_fit_CWTcatch	Figures for conditioning model results
CM_fit_CWTesc	Figures for conditioning model results
CM_fit_esc	Figures for conditioning model results
CM_fit_pHOS	Figures for conditioning model results
CM_M	Figures for conditioning model results
CM_maturity	Figures for conditioning model results
CM_Megg	Figures for conditioning model results
CM_Njuv	Figures for conditioning model results
CM_pairs	Figures for conditioning model results
CM_prod	Figures for conditioning model results
CM_recr	Figures for conditioning model results
CM_Srep	Figures for conditioning model results
CM_SRR	Figures for conditioning model results
CM_surv	Figures for conditioning model results
CM_surv2	Figures for conditioning model results
CM_trace	Figures for conditioning model results
CM_vul	Figures for conditioning model results
CM_wt	Figures for conditioning model results
CM_wto	Figures for conditioning model results
compare	Compare scenarios in markdown
compare_escapement	Compare simulation runs
compare_fitness	Compare simulation runs
compare_spawners	Compare simulation runs
compare_statevar_hist	Compare state variables from simulation runs
compare_statevar_ts	Compare state variables from simulation runs
fit_CM	Fit conditioning model to historical data
get_CMdata	Figures for conditioning model results
get_report	Figures for conditioning model results
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
multi_SOM	Example objects from salmonMSE
plot_decision_table	Decision table of performance metrics
plot_decision_table2	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"'
simple_SOM	Example objects from salmonMSE
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