plot_range_index: Plot shifts in distribution and area occupied

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

Plot shifts in distribution and area occupied

Description

plot_range_index plots center-of-gravity, kernel-area occupied, and effective-area occupied

Usage

plot_range_index(
  Sdreport,
  Report,
  TmbData,
  year_labels = NULL,
  years_to_plot = NULL,
  strata_names = NULL,
  PlotDir = getwd(),
  FileName_COG = "center_of_gravity.png",
  FileName_EffArea = "Effective_Area.png",
  Znames = rep("", ncol(TmbData$Z_gm)),
  use_biascorr = TRUE,
  category_names = NULL,
  interval_width = 1,
  ...
)

Arguments

Sdreport	TMB output from 'TMB::sdreport(Obj)'
Report	Reporting output from 'Obj$report()'
TmbData	Formatted data inputs, from 'VAST::Data_Fn(...)'
year_labels	character vector specifying names for labeling times t_i
years_to_plot	integer vector, specifying positions of year_labels for plotting (used to avoid plotting years with no data, etc.)
strata_names	names for spatial strata
PlotDir	Directory for plots
FileName_COG	Full filename (including directory) for center-of-gravity plot
FileName_EffArea	Full filename (including directory) for center-of-gravity plot
Znames	Names for center-of-gravity summary statistics
use_biascorr	Boolean, whether to use bias-corrected estimates if available
category_names	names for categories (if using package `VAST`)
interval_width	width for confidence intervals
...	Other inputs to 'par()'
FileName_Area	Full filename (including directory) for center-of-gravity plot

Value

Return Tagged list of output

COG_Table

table of center-of-gravity ("COG") estimates by year

KernelArea_Table

table of kernel-area approximation to area occupied, estimated by year

EffectiveArea_Table

table of effective-area approximation to area occupied, estimated by year, recommended over KernelArea_Table

References

For details regarding center of gravity see https://doi.org/10.1111/2041-210X.12567

For details regarding effective area occupied see https://doi.org/10.1098/rspb.2016.1853

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