Package index • wham

Exported functions that user can call directly

check_convergence(): Check convergence of WHAM model
check_estimability(): Check for identifiability of fixed effects Originally provided by the TMBhelper package. Internal function called by fit_tmb.
compare_wham_models(): Compare multiple WHAM (or ASAP) models
do_reference_points(): Add reporting of biological reference points to WHAM model
do_retro_peels(): Fit retrospective peels and add them to the fitted model object
do_sdreport(): Add TMB sdreport object to WHAM model
fit_peel(): Fit model peeling off i years of data
fit_tmb(): Fit TMB model using nlminb
fit_wham(): Fit WHAM model
jitter_wham(): Jitter starting values of a fitted WHAM model
make_osa_residuals(): Calculate one-step-ahead residuals
mohns_rho(): Calculate Mohn's rho for a WHAM model with peels
plot_wham_output(): Plot WHAM output
prepare_projection(): Prepare input data and parameters to project an already fit WHAM model
prepare_wham_input(): Prepare input data and parameters for WHAM model
project_wham(): Project a fit WHAM model
read_asap3_dat(): Read an ASAP3 .dat file into R
read_asap3_fit(): Read ASAP3 fit
read_wham_fit(): Read WHAM fit
retro(): Run retrospective analysis
self_test(): Perform self-test simulation and estimation of a fitted WHAM model
set_age_comp(): Specify the age composition models for fleet(s) and indices.
set_catch(): Specify catch selectivity blocks and aggregate and age composition observations for catch
set_ecov(): Specify configuration for environmental covariates, effects on the population, and parameter values
set_F(): Specify configuration for fully-selected fishing mortality
set_indices(): Specify index selectivity blocks and aggregate and age composition observations for indices
set_L(): Specify model and parameter configuration for "extra" mortality not directly attributed to natural mortality
set_M(): Specify model and parameter configuration for natural mortality
set_move(): Specify model and parameter configuration for movement when input$data$n_regions > 1
set_NAA(): Specify model and parameter configuration for numbers at age
set_osa_obs(): Set up observation vector that is used by the model for likelihood calculations and one-step-ahead residuals.
set_q(): Specify model and parameter configuration for catchability
set_selectivity(): Specify model and parameter configuration for selectivity

Unexported functions

extract_fixed(): Extract fixed effects Originally provided by the TMBhelper package. Internal function called by check_estimability.
reduce_input(): Reduce the years of the model
wham_html(): Create HTML file to view output plots in browser