Management Strategy Evaluation for Salmon Species

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Documentation for package ‘salmonMSE’ version 3.0.0

• 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_MSY	Plot reference points from conditioning model
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_Sgen	Plot reference points from conditioning model
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"'
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
ProjectSOM	Run salmonMSE
P_PNI50	Example performance metrics
P_PNI80	Example performance metrics
P_Sgen100	Example performance metrics
P_SMSY80	Example performance metrics
P_SMSY85	Example performance metrics
P_WILD50	Example performance metrics
report	Generate markdown reports
report-method	Generate markdown reports
report_CM	Conditioning model markdown report
salmonMSE	Run salmonMSE
salmonMSE_env	Environment to store salmon specific variables, e.g, fitness, during the simulation
sample_CM	Fit conditioning model to historical data
simpleSOM	Class '"simpleSOM"'
simpleSOM-class	Class '"simpleSOM"'
simple_salmonMSE	Run salmonMSE
simple_SOM	Example objects from salmonMSE
SMSE-class	Class '"SMSE"'
SOM	Class '"SOM"'
SOM-class	Class '"SOM"'