Gets composition data proportions normalized according to the assessment specifications from RTMB
get_comp_prop.Rd
Gets composition data proportions normalized according to the assessment specifications from RTMB
Value
List of fishery age, lengths, survey age, lengths dataframe as well as in matrix form (dimensioned by region, year, bin, sex, fleet)
Examples
if (FALSE) { # \dontrun{
comp_props <- get_comp_prop(data = data, rep = rep, age_labels = 2:31, len_labels = seq(41, 99, 2), year_labels = 1960:2024)
comp_props$Fishery_Ages %>%
filter(Fleet == 1, Sex == 1) %>%
ggplot() +
geom_col(aes(x = Age, y = obs)) +
geom_line(aes(x = Age, y = pred)) +
facet_wrap(~Year, ncol = 3)
comp_props$Survey_Ages %>%
group_by(Region, Age, Sex, Fleet) %>%
summarize(lwr_obs = quantile(obs, 0.1),
upr_obs = quantile(obs, 0.9),
lwr_pred = quantile(pred, 0.1),
upr_pred = quantile(pred, 0.9),
obs = mean(obs),
pred = mean(pred)) %>%
ggplot() +
geom_line(mapping = aes(x = Age, y = obs, color = 'Obs', lty = 'Obs'), lwd = 1.3) +
geom_ribbon(mapping = aes(x = Age, y = obs, ymin = lwr_obs, ymax = upr_obs, fill = 'Obs'), alpha = 0.3) +
geom_line(mapping = aes(x = Age, y = pred, color = 'Pred', lty = 'Pred'), lwd = 1.3) +
geom_ribbon(mapping = aes(x = Age, y = pred, ymin = lwr_pred, ymax = upr_pred, fill = 'Pred'), alpha = 0.3) +
facet_grid(Region~Fleet, labeller = labeller(
Region = c('1' = "Region 1"),
Fleet = c('1' = 'Domestic LL Survey', '3' = 'JP LL Survey')
)) +
labs(x = 'Age', y = 'Proportion', color = '', linetype = '', fill = '') +
theme_bw(base_size = 20) +
theme(legend.position = 'top')
} # }