plot_biomass_proj_mcmc: Plot a model's time series (either spawning biomass or...

In pbs-assess/gfiscamutils: Provide functions for iSCAM models

Plot a model's time series (either spawning biomass or relaive spawning biomass) and its projections

Description

Plot a model's time series (either spawning biomass or relaive spawning biomass) and its projections

Usage

plot_biomass_proj_mcmc(
  model,
  model_name = "Base model",
  rel = FALSE,
  probs = c(0.025, 0.5, 0.975),
  x_space = 0.5,
  y_space = ifelse(rel, 0.05, 0.5),
  show_bo_lines = FALSE,
  bo_refpts = c(0.2, 0.4),
  bo_refpt_colors = c("red", "green"),
  line_width = 1,
  point_size = 2,
  angle_x_labels = FALSE,
  ylim = NULL,
  xlim = NULL,
  nudge_catch_labels = c(x = 0.3, y = 0),
  proj_catch_vals = NULL,
  append_to_catch_level_names = "kt",
  ...
)

Arguments

model	An ISCAM model object (class mdl_cls)
model_name	Name of the input model
rel	Logical. Make plot relative to initial estimate (B0), also known as depletion
probs	A 3-element vector of probabilities that appear in the output data frames. This is provided in case the data frames have more than three different quantile levels
x_space	The amount of x-interval space to pad the left and right of the plot with. To remove all padding, make this 0
y_space	The amount of y-interval space to pad the top and bottom of the plot with. To remove all padding, make this 0
show_bo_lines	Logical. If TRUE, show the B0 uncertainty
bo_refpts	A vector of 2 B0-based reference points
bo_refpt_colors	A vector of two colors, for the corresponding
line_width	Width of all median lines on the plot
point_size	Point size for all median points on the plot
angle_x_labels	If TRUE put 45 degree angle on x-axis tick labels
ylim	The y limits for the plot. If NULL, the limits of the data will be used
xlim	The x limits for the plot. If NULL, the limits of the data will be used
nudge_catch_labels	Position to nudge the catch labels by on the right of the ending of the lines
proj_catch_vals	The catch values to include in the plot. If NULL, include all values present in the list from the output (model$mcmccalcs$proj_sbt_quants). If non-null, is a vector of values of catch to filter the projection biomass table on. Only show those values in the plot
append_to_catch_level_names	Text to append to the catch levels in the plot
...	Arguments passed to plot_ts_mcmc()

Value

An ggplot2::ggplot() object

See Also

Other Time series plotting functions: plot_biomass_grid_mcmc(), plot_biomass_mcmc(), plot_biomass_mpd(), plot_catch_fit_mcmc(), plot_f_mcmc(), plot_index_mcmc(), plot_index_mpd(), plot_q_mcmc(), plot_rdevs_mcmc(), plot_recr_grid_mcmc(), plot_recr_mcmc(), plot_recr_mpd(), plot_ts_mcmc(), plot_vuln_mcmc()

pbs-assess/gfiscamutils documentation built on Oct. 24, 2024, 1:37 p.m.