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check_convergence()
Check convergence of REMA model
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.
compare_rema_models()
Plot REMA model comparisons and return AIC values when appropriate
extract_fixed()
Extract fixed effects Originally provided by https://github.com/kaskr/TMB_contrib_R/TMBhelper Internal function called by check_estimability.
fit_rema()
Fit REMA model
fit_tmb()
Fit TMB model using nlminb
get_osa_residuals()
Get one-step-head (OSA)
%>%
Pipe function
plot_extra_cv()
Plot the additional estimated observation error for biomass by strata and/or cpue by strata
plot_rema()
Plot survey data and model output
prepare_rema_input()
Prepare input data and parameters for REMA model
read_admb_re()
Convert ADMB version of the RE model data and output to REMA inputs
read_rep()
Read ADMB .rep file and return an R object of type 'list'
tidy_extra_cv()
Tidy estimates of extra biomass or CPUE index CV
tidy_rema()
Tidy REMA model output
