R: Management Strategy Evaluation for Salmon Species

# Management Strategy Evaluation for Salmon Species

## 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