plot_biomass_index: Plot index of abundance

In James-Thorson/FishStatsUtils: Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox

Plot index of abundance

Description

plot_biomass_index plots an index proportional to population abundance

Usage

plot_biomass_index(
  fit,
  DirName = getwd(),
  PlotName = "Index",
  interval_width = 1,
  years_to_plot = NULL,
  category_names = NULL,
  year_labels = NULL,
  strata_names = NULL,
  use_biascorr = TRUE,
  plot_legend = TRUE,
  total_area_km2 = NULL,
  plot_log = FALSE,
  width = NULL,
  height = NULL,
  create_covariance_table = FALSE,
  Yrange = c(ifelse(plot_log == TRUE, NA, 0), NA),
  TmbData = fit$data_list,
  Sdreport = fit$parameter_estimates$SD,
  extrapolation_list = fit$extrapolation_list,
  ...
)

Arguments

DirName	Directory for saving plot and table
PlotName	Name for plot
interval_width	width for confidence intervals
years_to_plot	integer vector, specifying positions of year_labels for plotting (used to avoid plotting years with no data, etc.)
category_names	names for categories (if using package `VAST`)
year_labels	character vector specifying names for labeling times t_i
strata_names	names for spatial strata
use_biascorr	Boolean, whether to use bias-corrected estimates if available
plot_legend	Add legend for labelling colors
plot_log	Boolean, whether to plot y-axis in log-scale
width	plot width in inches
height	plot height in inches
TmbData	Formatted data inputs, from make_data
Sdreport	Standard deviation outputs from TMB model via sdreport(Obj)
...	Other inputs to 'par()'

Value

Return Tagged list of output

Table

table of index estimates by stratum and year, e.g., for including in an assessment model

References

For details regarding spatio-temporal index standardization see https://doi.org/10.1093/icesjms/fsu243

For details regarding fishing mortality and biomass reference points in models generating those, see https://doi.org/10.1111/faf.12398

James-Thorson/FishStatsUtils documentation built on Feb. 6, 2024, 4:26 a.m.