Function reference • wham

Exported functions that user can call directly
`check_convergence()`	Check convergence of WHAM model
`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_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_wham_input()`	Prepare input data and parameters for WHAM model
`prepare_projection()`	Prepare input data and parameters to project an already fit WHAM model
`project_wham()`	Project a fit WHAM model
`read_asap3_dat()`	Read an ASAP3 .dat file into R
`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 that user do not call
`check_estimability()`	Check for identifiability of fixed effects Originally provided by https://github.com/kaskr/TMB_contrib_R/TMBhelper Internal function called by `fit_tmb`.
`extract_fixed()`	Extract fixed effects Originally provided by https://github.com/kaskr/TMB_contrib_R/TMBhelper Internal function called by `check_estimability`.
`fit_tmb()`	Fit TMB model using nlminb
`fit_peel()`	Fit model peeling off i years of data
`read_asap3_fit()`	Read ASAP3 fit
`read_wham_fit()`	Read WHAM fit
`reduce_input()`	Reduce the years of the model
`wham_html()`	Create HTML file to view output plots in browser
`%>%`	Pipe function

Reference

Exported functions that user can call directly

Unexported functions that user do not call