Package index • salmonMSE

S4 classes

Objects used to create stochastic operating models.

Run simulation of salmon operating model and view/compare results.

salmonMSE() ProjectSOM() simple_salmonMSE(): Run salmonMSE
compare(): Compare scenarios in markdown
compare_spawners() compare_fitness() compare_escapement(): Compare simulation runs
compare_statevar_ts() compare_statevar_hist(): Compare state variables from simulation runs
P_PNI50() P_PNI80() P_WILD50() P_SMSY85() P_SMSY80() P_Sgen100(): Example performance metrics
plot_LHG() plot_RS(): Plot life history groups and release strategies
plot_decision_table() plot_decision_table2(): Decision table of performance metrics
plot_statevar_ts() plot_statevar_hist() plot_spawners() plot_fitness() plot_escapement() plot_fishery() plot_Kobe(): Plot core output from salmonMSE
plot_tradeoff(): Tradeoff figure
report(<SMSE>): Generate markdown reports

Functions to estimate historical productivity and exploitation rates from coded wire tags and time series of hatchery releases and spawner abundance.

fit_CM() sample_CM(): Fit conditioning model to historical data
get_report() get_CMdata() CM_trace() CM_pairs() CM_fit_esc() CM_fit_pHOS() CM_fit_CWTesc() CM_fit_CWTcatch() CM_maturity() CM_vul() CM_SRR() CM_prod() CM_Srep() CM_M() CM_Megg() CM_Njuv() CM_recr() CM_esc() CM_F() CM_surv() CM_wt() CM_surv2() CM_wto() CM_ER() CM_CWT_ER() CM_covariate(): Figures for conditioning model results
CM_MSY() CM_Sgen(): Plot reference points from conditioning model
CM2SOM(): Convert conditioning model to operating model
report_CM(): Conditioning model markdown report

calc_SRR(): Calculate abundance from density-dependent mortality
calc_SRRpars(): Convert density-dependent survival parameters
calc_Smsy_Ricker() calc_Umsy_Ricker() calc_Sgen_Ricker(): Ricker reference points
calc_ref() calc_MSY() calc_Sgen(): Reference points
calc_smolt(): Smolt production
check_SOM(): Check inputs to SOM object
glossary: salmonMSE glossary
salmonMSE_env: Environment to store salmon specific variables, e.g, fitness, during the simulation
simple_SOM multi_SOM: Example objects from salmonMSE