plot_biomass_catch: Plot estimated biommass median and credible interval,...

In pbs-assess/herringutils: Provides Plotting, Table-making, and Utility Functions for the CSAS Herring Documents

Plot estimated biommass median and credible interval, projected biomass with credible interval, catch history, and LRP line with credible interval

Description

Plot estimated biommass median and credible interval, projected biomass with credible interval, catch history, and LRP line with credible interval

Usage

plot_biomass_catch(
  model,
  catch_df,
  point_size = 1,
  errorbar_size = 1,
  line_size = 0.75,
  ribbon_alpha = 0.5,
  lrp_ribbon_alpha = 0.35,
  show_lrp_ribbon = TRUE,
  show_catch = TRUE,
  between_bars = 0.75,
  refpt_show = "0.3sbo",
  show_prod_usr = TRUE,
  prod_yrs = 1990:1999,
  prop_prod = 1,
  show_prod_yrs = TRUE,
  show_sbo_usr = FALSE,
  prop_sbo = 0.5,
  show_blt_usr = FALSE,
  prop_blt = 1,
  col_catch = TRUE,
  xlim = NA,
  show_x_axis = TRUE,
  show_y_axis = TRUE,
  x_axis_label_size = 8,
  x_axis_tick_label_size = 8,
  y_axis_label_size = 8,
  y_axis_tick_label_size = 8,
  x_axis_label_newline_length = 50,
  y_axis_label_newline_length = 40,
  x_axis_position = "bottom",
  y_axis_position = "left",
  annot = "d",
  label_points = FALSE,
  label_round = 1,
  translate = FALSE
)

Arguments

model	an iscam model object
catch_df	a data frame of catch as constructed by [get_catch()]
point_size	size of point for projection year median biomass
errorbar_size	thickness of errorbar for projection year median biomass
line_size	thickness of the median and LRP lines
ribbon_alpha	transparency value for the biomass credibility interval ribbon
lrp_ribbon_alpha	transparency value for the LRP credibility interval ribbon
show_catch	Logical. Show catch bar plot.
between_bars	amount of space between catch bars
refpt_show	which reference point to show. See 'model$mcmccalcs$r.quants“ for choices
show_prod_usr	Logical. Show the productive period USR. Default TRUE.
prod_yrs	Numeric vector. Productive period to calculate the USR. Default 1990:1999.
prop_prod	Numeric. Proportion of productive period for USR. Default 1.0.
show_prod_yrs	Logical. Show vertical band for productive period. Default TRUE.
show_sbo_usr	Logical. Show SB_0. Default TRUE.
prop_sbo	Numeric. Proportion of SB_0 for USR. Default 0.6.
show_blt_usr	Logical. Show average long-term biomass USR. Default TRUE.
prop_blt	Numeric. Proportion of average long-term biomass for USR. Default 1.0.
col_catch	Logical. Colour catch bars, or just grey. Default TRUE.
xlim	x-limits for the plot. Implemented with [ggplot2::coord_cartesian()]
show_x_axis	see [modify_axes_labels()]
show_y_axis	see [modify_axes_labels()]
x_axis_label_size	see [modify_axes_labels()]
x_axis_tick_label_size	see [modify_axes_labels()]
y_axis_label_size	see [modify_axes_labels()]
y_axis_tick_label_size	see [modify_axes_labels()]
x_axis_label_newline_length	see [newline_format()]
y_axis_label_newline_length	see [newline_format()]
annot	a character to place in parentheses in the top left of the plot. If NA, nothing will appear
translate	Logical. If TRUE, translate to french

Value

A ggplot object

pbs-assess/herringutils documentation built on Jan. 10, 2025, 8:43 a.m.