summarize_covariance: Explore spatio-temporal covariance

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

Explore spatio-temporal covariance

Description

summarize_covariance plots and returns spatio-temporal covariance among categories

Usage

summarize_covariance(
  Report,
  Data,
  ParHat,
  SD = NULL,
  category_order = 1:Data$n_c,
  category_names = 1:Data$n_c,
  plotdir = paste0(getwd(), "/"),
  figname = "Cov",
  plotTF = NULL,
  plot_cor = TRUE,
  mgp = c(2, 0.5, 0),
  tck = -0.02,
  oma = c(0, 5, 2, 0),
  ...
)

Arguments

Report	output report, e.g., from Report <- obj$report()
Data	tagged list of input data
ParHat	Tagged list of fitted data, e.g., from ParHat <- obj$env$parList()
SD	standard deviation report, e.g., from SD <- sdreport( obj )
category_order	integer-vector to re-order categories while plotting
category_names	character-vector listing name for each category
plotdir	directory (absolute path) for plots
figname	character for first-part of figure names
plotTF	integer-vector (length 4) specifying which covariances to plot (recommended: use plotTF=FieldConfig)
plot_cor	Boolean, whether to plot correlation or covariance
mgp	passed to par
tck	passed to par
oma	passed to par
...	passed to ThorsonUtilities::save_fig

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