In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Request 3 -- "Maximum age selectivity"

The SRG requests sensitivities on fishery selectivity parameterization (in the base model) by increasing the maximum age beyond which selectivity is held constant to ages 8, 10, and 12. Present the resulting fishery selectivity (2024 with uncertainty and MCMC traces and individual years with uncertainty), spawning biomass trajectories, fits to the acoustic survey index, and recruitment deviation estimates.

• Maximum age 6 (base) model: 262 parameters
• Maximum age 8 model: 333 parameters
• Maximum age 10 model: 403 parameters
• Maximum age 12 model: 473 parameters

Selectivity in 2024: maximum age of 6 (base model)

model_age_8 <- request_models[[1]][[1]]
model_age_10 <- request_models[[1]][[2]]
model_age_12 <- request_models[[1]][[3]]

plot_selex_posteriors(base_model,
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 13),
                      glow = TRUE)

Selectivity in 2024: maximum age of 8

plot_selex_posteriors(model_age_8,
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 13),
                      glow = TRUE)

Selectivity in 2024: maximum age of 10

plot_selex_posteriors(model_age_10,
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 13),
                      glow = TRUE)

Selectivity in 2024: maximum age of 12

plot_selex_posteriors(model_age_12,
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 13),
                      glow = TRUE)

Selectivity: maximum age of 6 (base model)

plot_selex_uncertainty(base_model,
                       n_col = 2,
                       ages = 1:13,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

Selectivity: maximum age of 8

plot_selex_uncertainty(model_age_8,
                       n_col = 2,
                       ages = 1:13,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

Selectivity: maximum age of 10

plot_selex_uncertainty(model_age_10,
                       n_col = 2,
                       ages = 1:13,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

Selectivity: maximum age of 12

plot_selex_uncertainty(model_age_12,
                       n_col = 2,
                       ages = 1:13,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

Spawning biomass: maximum age of 6 (base model), 8, 10, and 12

:::::: {.columns} ::: {.column width="50%"}

# Left
plot_biomass(list(base_model, model_age_8, model_age_10, model_age_12),
             c("base model", request_models_names[[1]]),
             ylim = c(0, 5),
             point_shape = ts_single_model_pointshape,
             leg_pos = c(0.75, 0.80))

:::

::: {.column width="50%"}

# Right
plot_rel_biomass(list(base_model, model_age_8, model_age_10, model_age_12),
             c("base model", request_models_names[[1]]),
                 ylim = c(0, 2.5),
                 alpha = 0.2,
                 leg_pos = c(0.75, 0.80)) |>
  suppressWarnings()

::: ::::::

Acoustic survey fit: maximum age of 6 (base model)

plot_survey_fit_mcmc(base_model,
                     type = "acoustic",
                     n_posts = 1000,
                     glow = TRUE,
                     glow_color = "black",
                     glow_offset = 0.5,
                     leg_ymax = 4.8,
                     leg_sep = 0.65,
                     x_lim = c(survey_start_yr, survey_end_yr),
                     y_lim = c(0, 6),
                     x_labs_mod = 5,
                     y_labs_by = 0.5,
                     tick_prop = 1,
                     vjust_x_labels = -2,
                     remove_yr_labels = NULL)

Acoustic survey fit: maximum age of 8

plot_survey_fit_mcmc(model_age_8,
                     type = "acoustic",
                     n_posts = 1000,
                     glow = TRUE,
                     glow_color = "black",
                     glow_offset = 0.5,
                     leg_ymax = 4.8,
                     leg_sep = 0.65,
                     x_lim = c(survey_start_yr, survey_end_yr),
                     y_lim = c(0, 6),
                     x_labs_mod = 5,
                     y_labs_by = 0.5,
                     tick_prop = 1,
                     vjust_x_labels = -2,
                     remove_yr_labels = NULL)

Acoustic survey fit: maximum age of 10

plot_survey_fit_mcmc(model_age_10,
                     type = "acoustic",
                     n_posts = 1000,
                     glow = TRUE,
                     glow_color = "black",
                     glow_offset = 0.5,
                     leg_ymax = 4.8,
                     leg_sep = 0.65,
                     x_lim = c(survey_start_yr, survey_end_yr),
                     y_lim = c(0, 6),
                     x_labs_mod = 5,
                     y_labs_by = 0.5,
                     tick_prop = 1,
                     vjust_x_labels = -2,
                     remove_yr_labels = NULL)

Acoustic survey fit: maximum age of 12

plot_survey_fit_mcmc(model_age_12,
                     type = "acoustic",
                     n_posts = 1000,
                     glow = TRUE,
                     glow_color = "black",
                     glow_offset = 0.5,
                     leg_ymax = 4.8,
                     leg_sep = 0.65,
                     x_lim = c(survey_start_yr, survey_end_yr),
                     y_lim = c(0, 6),
                     x_labs_mod = 5,
                     y_labs_by = 0.5,
                     tick_prop = 1,
                     vjust_x_labels = -2,
                     remove_yr_labels = NULL)

Rec devs: maximum age of 6 (base model), 8, 10, and 12

plot_recdevs(list(base_model, model_age_8, model_age_10, model_age_12),
             c("base model", request_models_names[[1]]),
             line_color = ts_single_line_color,
             leg_ncol = 2,
             leg_pos = c(0.30, 0.90))

pacific-hake/hake-assessment documentation built on Feb. 17, 2025, 1:58 p.m.