plot_biomass_phase: Plot production using a phase plot with a path through time....

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

Plot production using a phase plot with a path through time. Includes the reference point and its credible interval

Description

Plot production using a phase plot with a path through time. Includes the reference point and its credible interval

Usage

plot_biomass_phase(
  model,
  catch_df,
  new_surv_yr = NA,
  point_size = 2.5,
  line_size = 0.5,
  path_line_size = 0.4,
  text_size = 2,
  zeroline_size = 0.5,
  zeroline_type = "dashed",
  lrp_ribbon_alpha = 0.35,
  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 = 0.6,
  show_blt_usr = FALSE,
  prop_blt = 1,
  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 = "f",
  translate = FALSE
)

Arguments

model	an iscam model object
catch_df	a data frame of catch as constructed by [get_catch()]
new_surv_yr	year in which the survey changed from surface to dive
point_size	size for points for years
line_size	thickness of the straight lines on the plot
path_line_size	thickness of the path line between points
text_size	size for year marker text labels
zeroline_size	thickness of the line across zero
zeroline_type	type of the line across zero
lrp_ribbon_alpha	transparency of the reference point credible interval ribbon
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 USR. Default FALSE.
prop_sbo	Numeric. Proportion of SB_0 for USR. Default 0.6.
show_blt_usr	Logical. Show average long-term biomass USR. Default FALSE.
prop_blt	Numeric. Proportion of average long-term biomass for USR. Default 1.0.
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.