plot_biomass_mpd: Plot the MCMC time series trajectories for iscam models,...
In pbs-assess/gfiscamutils: Provide functions for iSCAM models

plot_biomass_mpd

R Documentation

Plot the MCMC time series trajectories for iscam models, including spawning biomass and recruitment for both absolute and relative cases.

Description

Plot the MCMC time series trajectories for iscam models, including spawning biomass and recruitment for both absolute and relative cases.

Usage

plot_biomass_mpd(
  models,
  rel = FALSE,
  show_bo = TRUE,
  legend_title = "Models",
  xlim = NULL,
  ylim = NULL,
  line_width = 1,
  point_size = 2,
  alpha = 0.2,
  palette = iscam_palette,
  base_color = "black",
  bo_dodge = 0.1,
  x_space = 0.5,
  append_base_txt = NULL,
  show_bo_lines = FALSE,
  bo_refpts = c(0.2, 0.4),
  show_bmsy_lines = FALSE,
  bmsy_refpts = c(0.4, 0.8),
  bo_refpt_colors = c("red", "green"),
  bmsy_refpt_colors = c("salmon", "darkgreen"),
  leg_loc = NULL,
  text_title_size = 12,
  angle_x_labels = FALSE,
  ...
)

Arguments

`models`	A list of iscam model objects (class mdl_lst_cls)
`rel`	Logical. If `TRUE`, plot the relative biomass
`show_bo`	Logical. If `TRUE`, show the B0 point
`legend_title`	Title for legend
`xlim`	The x limits for the plot. If `NULL`, the limits of the data will be used
`ylim`	The y limits for the plot. If `NULL`, the limits of the data will be used
`line_width`	Width of all median lines on the plot
`point_size`	Point size for all median points on the plot
`alpha`	The transparency with values from 0 to 1 of the ribbon shading when `first_model_ribbon` is `TRUE`
`palette`	A palette value that is in RColorBrewer::brewer.pal.info
`base_color`	A color to prepend to the brewer colors which are set by `palette`. This is called `base_color` because it is likely to be a base model
`bo_dodge`	Value to offset the B0 point by on the x-axis (in years)
`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
`append_base_txt`	A vector of strings to append to the model names for display on the plot legend or title
`show_bo_lines`	Logical. If `TRUE`, show the B0 uncertainty
`bo_refpts`	A vector of 2 B0-based reference points
`show_bmsy_lines`	Logical. If `TRUE`, show the BMSY uncertainty
`bmsy_refpts`	A vector of 2 BMSY-based reference points
`bo_refpt_colors`	A vector of two colors, for the corresponding B0 values in `bo_refpts`
`bmsy_refpt_colors`	A vector of two colors, for the corresponding BMSY values in `bmsy_refpts`
`leg_loc`	A two-element vector describing the X-Y values between 0 and 1 to anchor the legend to. eg. c(1, 1) is the top right corner and c(0, 0) is the bottom left corner
`text_title_size`	Size of the axis label text
`angle_x_labels`	If `TRUE` put 45 degree angle on x-axis tick labels
`...`	Absorbs arguments meant for other functions

Value

A ggplot2::ggplot() object

Other Time series plotting functions: plot_biomass_grid_mcmc(), plot_biomass_mcmc(), plot_biomass_proj_mcmc(), 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()