Gets index fits results

Gets index fits results

Usage

get_idx_fits(data, rep, year_labs)

Arguments

data

Data list fed into RTMB

rep

Report list output from RTMB

year_labs

Year labels to use (vector)

Value

Fits to indices as a dataframe

See also

Other Model Diagnostics: do_jitter(), do_likelihood_profile(), do_retrospective(), do_runs_test(), get_catch_fits_plot(), get_comp_prop(), get_idx_fits_plot(), get_model_rep_from_mcmc(), get_nLL_plot(), get_osa(), get_retrospective_plot(), get_retrospective_relative_difference(), plot_resids()

Examples

if (FALSE) { # \dontrun{
idx_fits <- get_idx_fits(data = data, rep = rep, year_labs = seq(1960, 2024, 1))

idx_fits <- idx_fits %>%
  mutate(
    Idx = case_when(
      Type == "Fishery" & Year < 1995 ~ "Japanese Fishery CPUE Index",
      Type == "Fishery" & Year >= 1995 ~ "Domestic Fishery CPUE Index",
      Type == 'Survey' & Fleet == 1 ~ "Domestic LL Survey Relative Population Numbers",
      Type == 'Survey' & Fleet == 2 ~ "GOA Trawl Survey Biomass (kt)",
      Type == 'Survey' & Fleet == 3 ~ 'Japanese LL Survey Relative Population Numbers'
    )
  )
ggplot() +
  geom_line(idx_fits, mapping = aes(x = Year, y = value), lwd = 1.3, col = 'red') +
  geom_pointrange(idx_fits, mapping = aes(x = Year, y = obs, ymin = lci, ymax = uci), color = 'blue', pch = 1) +
  labs(x = "Year", y = 'Index') +
  theme_bw(base_size = 20) +
  facet_wrap(~Idx, scales = 'free', ncol = 2)

} # }