Summarize_Covariance: Explore spatio-temporal covariance

Description Usage Arguments

View source: R/Summarize_Covariance.R

Description

Summarize_Covariance plots and returns spatio-temporal covariance among categories

Usage

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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 = c(Omega1 =
  TRUE, Epsilon1 = TRUE, Omega2 = TRUE, Epsilon2 = TRUE), 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/VAST documentation built on Oct. 8, 2017, 1:15 a.m.