plot_ts_mcmc: Plot MCMC time series plots for iSCAM models

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

Plot MCMC time series plots for iSCAM models

Description

Plot time series plots for MCMC output with credible intervals for single or multiple models

Usage

plot_ts_mcmc(
  models,
  quant_df = "sbt_quants",
  facet_wrap_var = c("none", "sex", "gear"),
  palette = iscam_palette,
  all_one_color = NULL,
  base_color = "black",
  legend_title = tr("Models"),
  x_label = tr("Year"),
  y_label = tr("Spawning Biomass (thousand t)"),
  append_base_txt = NULL,
  x_space = 0.5,
  y_space = 0,
  xlim = NULL,
  ylim = NULL,
  line_width = 1,
  point_size = 2,
  first_model_ribbon = TRUE,
  alpha = 0.2,
  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)
quant_df	A name of a value which can be found in the model$mcmccalcs list for each iscam model in the models list
facet_wrap_var	A column in the quant_df data frame which will be used to split the output into separate panel plots. If "none", no faceting will be done
palette	A palette value that is in RColorBrewer::brewer.pal.info
all_one_color	If not NULL, overrides palette and the color that this is defined as will be used for all lines on the plot (all models)
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
legend_title	Title for legend
x_label	The x-axis title label
y_label	The y-axis title label
append_base_txt	A vector of strings to append to the model names for display on the plot legend or title
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
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
first_model_ribbon	Logical. If TRUE, give the first model a shaded credible interval instead of dotted lines
alpha	The transparency with values from 0 to 1 of the ribbon shading when first_model_ribbon is TRUE
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	Add the model description as a title with this font size. The text comes from the model_desc attribute of model. If this is NULL, don't show a title
angle_x_labels	If TRUE put 45 degree angle on x-axis tick labels
...	Absorbs arguments meant for other functions

Details

Plot a single model or multiple models overlaid for comparison. If a single model, it must have a class attribute of mdl_cls. A list of multiple models must have a class attribute of mdl_lst_cls and each model in the list must have a class attribute of mdl_cls.

The model description text will appear in a legend if models length is greater than 1, and as a title if there is only one model. The description text is found in the model_desc attribute of a mdl_cls class ("iscam_model") object. The attribute is set in the model_setup() function, from either the bridge_model_text or sens_model_text arguments.

Value

A ggplot2::ggplot() object

See Also

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_mcmc(), plot_recr_mpd(), plot_vuln_mcmc()

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