plot_range_edge: Plot shifts in range edges

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

Plot shifts in range edges

Description

plot_range_edge plots range edges

Usage

plot_range_edge(
  Sdreport,
  Obj,
  year_labels = NULL,
  years_to_plot = NULL,
  strata_names = NULL,
  category_names = NULL,
  working_dir = getwd(),
  quantiles = c(0.05, 0.95),
  n_samples = 100,
  interval_width = 1,
  width = NULL,
  height = NULL,
  calculate_relative_to_average = FALSE,
  seed = 123456,
  ...
)

Arguments

Sdreport	Standard deviation outputs from TMB model via sdreport(Obj)
Obj	Fitted TMB object from package 'VAST', i.e., output from 'fit_model(...)$tmb_list$Obj'
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
category_names	names for categories (if using package `VAST`)
working_dir	Directory for plots
quantiles	vector specifying quantiles to use for calculating range edges
n_samples	number of samples from the joint predictive distribution for fixed and random effects. Default is 100, which is slow.
interval_width	width for confidence intervals
width	plot width in inches
height	plot height in inches
calculate_relative_to_average	Boolean, whether to calculate edge in UTM coordinates (default), or instead calculate relative to median across all years. The latter reduces standard errors, and is appropriate when checking significance for comparison across years for a single species. The former (default) is appropriate for checking significance for comparison across species.
seed	integer used to set random-number seed when sampling variables, as passed to set.seed(.)
...	Other inputs to 'par()'

References

For details regarding multivariate index standardization and expansion see https://doi.org/10.22541/au.160331933.33155622/v1

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