plot_recr_mcmc: Plot MCMC recruitments for iSCAM models
In pbs-assess/gfiscamutils: Provide functions for iSCAM models

plot_recr_mcmc

R Documentation

Plot MCMC recruitments for iSCAM models

Description

Plot the MCMC recruitment time series trajectories with credible intervals for iscam models.

Usage

plot_recr_mcmc(
  models,
  show_ro = TRUE,
  ro_color = base_color,
  legend_title = "Models",
  xlim = NULL,
  ylim = NULL,
  line_width = 1,
  point_size = 2,
  ro_ribbon = TRUE,
  ro_alpha = 0.3,
  palette = iscam_palette,
  base_color = "black",
  r_dodge = 0.1,
  x_space = 0.5,
  append_base_txt = NULL,
  leg_loc = c(1, 1),
  probs = c(0.025, 0.5, 0.975),
  text_title_size = 12,
  angle_x_labels = FALSE,
  ...
)

Arguments

`models`	A list of iscam model objects (class mdl_lst_cls)
`show_ro`	Show the initial recruitment, R0 median line and credible interval
`ro_color`	The color of the R0 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
`ro_ribbon`	See `refpts_ribbon` in `plot_biomass_mcmc()`
`ro_alpha`	See `refpts_alpha` in `plot_biomass_mcmc()`
`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
`r_dodge`	See `bo_dodge` in `plot_biomass_mcmc()`
`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
`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
`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
`text_title_size`	Size of text for the axis titles
`angle_x_labels`	If `TRUE` put 45 degree angle on x-axis tick labels
`...`	Absorbs arguments meant for other functions

Other Time series plotting functions: plot_biomass_grid_mcmc(), plot_biomass_mcmc(), plot_biomass_mpd(), 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_mpd(), plot_ts_mcmc(), plot_vuln_mcmc()