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

Request 3 -- "Selectivity for age-1 index"

Provide plots of selectivity in 2024 as well as mountain plots for sensitivities to removing age-1 index, to the alternative values of phi (deviations for selectivity), and for adding in the eDNA index

Two time-varying selectivity figures and posterior selectivity for the survey and the fishery, each showing just 1000 draws, for the requested sensitivities are shown in the subsequent slides.

Remove age-1 index: time-varying selectivity

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

tv_selex_start_yr <- 1990

# Left
plot_selex_mountains(sens_models[[2]][[2]],
                     yrs = tv_selex_start_yr:last_data_yr,
                     ages = 1:8,
                     fill_num_colors = 50,
                     scale = 20)

:::

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

# Right
plot_selex_uncertainty(sens_models[[2]][[2]],
                       n_col = 2,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

::: ::::::

Remove age-1 index: survey (left) and fishery (right)

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

# Left
plot_selex_posteriors(sens_models[[2]][[2]],
                      type = "survey",
                      age_range = c(1, 8),
                      n_posts = 1000,
                      post_med_line_color = "red3",
                      unc_line_color = "red3",
                      glow = TRUE)

:::

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

# Right
plot_selex_posteriors(sens_models[[2]][[2]],
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 8),
                      glow = TRUE)

::: ::::::

Phi 0.21: time-varying selectivity

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

tv_selex_start_yr <- 1990

# Left
plot_selex_mountains(sens_models[[3]][[2]],
                     yrs = tv_selex_start_yr:last_data_yr,
                     ages = 1:8,
                     fill_num_colors = 50,
                     scale = 20)

:::

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

# Right
plot_selex_uncertainty(sens_models[[3]][[2]],
                       n_col = 2,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

::: ::::::

Phi 0.21: survey (left) and fishery (right)

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

# Left
plot_selex_posteriors(sens_models[[3]][[2]],
                      type = "survey",
                      age_range = c(1, 8),
                      n_posts = 1000,
                      post_med_line_color = "red3",
                      unc_line_color = "red3",
                      glow = TRUE)

:::

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

# Right
plot_selex_posteriors(sens_models[[3]][[2]],
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 8),
                      glow = TRUE)

::: ::::::

Phi 0.70: time-varying selectivity

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

tv_selex_start_yr <- 1990

# Left
plot_selex_mountains(sens_models[[3]][[3]],
                     yrs = tv_selex_start_yr:last_data_yr,
                     ages = 1:8,
                     fill_num_colors = 50,
                     scale = 20)

:::

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

# Right
plot_selex_uncertainty(sens_models[[3]][[3]],
                       n_col = 2,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

::: ::::::

Phi 0.70: survey (left) and fishery (right)

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

# Left
plot_selex_posteriors(sens_models[[3]][[3]],
                      type = "survey",
                      age_range = c(1, 8),
                      n_posts = 1000,
                      post_med_line_color = "red3",
                      unc_line_color = "red3",
                      glow = TRUE)

:::

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

# Right
plot_selex_posteriors(sens_models[[3]][[3]],
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 8),
                      glow = TRUE)

::: ::::::

Phi 2.10: time-varying selectivity

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

tv_selex_start_yr <- 1990

# Left
plot_selex_mountains(sens_models[[3]][[4]],
                     yrs = tv_selex_start_yr:last_data_yr,
                     ages = 1:8,
                     fill_num_colors = 50,
                     scale = 20)

:::

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

# Right
plot_selex_uncertainty(sens_models[[3]][[4]],
                       n_col = 2,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

::: ::::::

Phi 2.10: survey (left) and fishery (right)

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

# Left
plot_selex_posteriors(sens_models[[3]][[4]],
                      type = "survey",
                      age_range = c(1, 8),
                      n_posts = 1000,
                      post_med_line_color = "red3",
                      unc_line_color = "red3",
                      glow = TRUE)

:::

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

# Right
plot_selex_posteriors(sens_models[[3]][[4]],
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 8),
                      glow = TRUE)

::: ::::::

eDNA: time-varying selectivity

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

tv_selex_start_yr <- 1990

# Left
plot_selex_mountains(sens_models[[2]][[4]],
                     yrs = tv_selex_start_yr:last_data_yr,
                     ages = 1:8,
                     fill_num_colors = 50,
                     scale = 20)

:::

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

# Right
plot_selex_uncertainty(sens_models[[2]][[4]],
                       n_col = 2,
                       pad_top = TRUE,
                       pad_bottom = TRUE,
                       label_loc = c(1, 0.65),
                       label_font_size = 3)

::: ::::::

eDNA: survey (left) and fishery (right)

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

# Left
plot_selex_posteriors(sens_models[[2]][[4]],
                      type = "survey",
                      age_range = c(1, 8),
                      n_posts = 1000,
                      post_med_line_color = "red3",
                      unc_line_color = "red3",
                      glow = TRUE)

:::

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

# Right
plot_selex_posteriors(sens_models[[2]][[4]],
                      type = "fishery",
                      n_posts = 1000,
                      age_range = c(1, 8),
                      glow = TRUE)