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

eDNA

Adding an eDNA relative index of abundance

leg_font_size <- 5
leg_locs <- c(0.7, 0.85)
ribbon_line_type <- 0

plot_biomass(model_lst = list(base_model,
                              sens_models[[2]][[4]]),
             model_names = c(base_model_name,
                             sens_models_desc[[2]][3]),
             x_expansion = 4,
             ylim = c(0, 5),
             y_breaks = seq(0, 5, 1),
             tick_prop = 1.5,
             vjust_x_labels = -0.25,
             leg_font_size = leg_font_size,
             leg_pos = leg_locs,
             rev_colors = TRUE,
             ribbon_line_type = ribbon_line_type) +
  theme(axis.title.x = element_text(size = 12),
        axis.title.y = element_text(size = 12),
        legend.key.size = unit(0.5, units = "cm"),
        legend.text = element_text(size = 10))

Adding an eDNA relative index of abundance

plot_rel_biomass(model_lst = list(base_model,
                                  sens_models[[2]][[4]]),
                 model_names = c(base_model_name,
                                 sens_models_desc[[2]][3]),
                 x_expansion = 4,
                 ylim = c(0, 2.5),
                 y_breaks = seq(0, 2.5, 0.5),
                 tick_prop = 1.25,
                 vjust_x_labels = -1.5,
                 hjust_y_labels = 1,
                 leg_font_size = 5,
                 leg_pos = c(0.7, 0.85),
                 rev_colors = TRUE,
                 ribbon_line_type = 0) +
  theme(legend.key.size = unit(0.5, units = "cm"),
        legend.text = element_text(size = 10))

Adding an eDNA relative index of abundance

plot_survey_index_fits(sens_models[[2]][[4]],
                       list(sens_models[[2]][[4]]),
                       model_names = "",
                       survey_type = "edna",
                       tick_prop = 1,
                       vjust_x_labels = -2,
                       leg_pos = "none",
                       ylim = c(0, 0.5),
                       y_breaks = seq(0, 0.5, 0.1),
                       xlim = c(2019, 2023),
                       x_breaks = seq(2019, 2023, 1),
                       x_labs_mod = 1,
                       x_expansion = 0.5,
                       obs_upper_bar_width = 0.05) +
  theme(legend.key.size = unit(0.5, units = "cm"),
        legend.text = element_text(size = 10))

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