Plot_factors: Plot factor-decomposition of covariance

Description Usage Arguments

View source: R/Plot_factors.R

Description

Plot_factors plots factor loadings, average spatial factors, and spatio-temporal factors

Usage

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Plot_factors(Report, ParHat, Data, SD, Year_Set = NULL,
  category_names = NULL, RotationMethod = "PCA", mapdetails_list = NULL,
  Dim_year = NULL, Dim_species = NULL, plotdir = paste0(getwd(), "/"),
  land_color = "grey")

Arguments

Report

output report, e.g., from Report <- obj$report()

ParHat

Tagged list of fitted data, e.g., from ParHat <- obj$env$parList()

Data

tagged list of input data

SD

standard deviation report, e.g., from SD <- sdreport( obj )

Year_Set

plotting-names for time dimension

category_names

character-vector listing name for each category

mapdetails_list

output from SpatialDeltaGLMM::MapDetails_Fn

Dim_year

Plotting dimension (row,column) for plot of years (default: square with sufficient size for number of years)

Dim_species

Plotting dimension (row,column) for plot of categories (default: square with sufficient size for number of categories)

plotdir

directory for saving plots

land_color

color for filling in land (use land_color=rgb(0,0,0,alpha=0) for transparent land)


James-Thorson/VAST documentation built on Oct. 8, 2017, 1:15 a.m.