createPcaToCompare: Generating a pca for comparison across niches.

In kaiyaprovost/subsppLabelR: Subspecies Labeled Occurences Generator

Generating a pca for comparison across niches.

Description

This function uses ecospat to create PCA across Environments to compare niches. Requires some custom ecospat functions which are given below.

Usage

createPcaToCompare(loc_thin_bgstuff, perspecies_bgstuff, species, verbose = T)

Arguments

loc_thin_bgstuff	Background points for all species.
perspecies_bgstuff	Background points for each species.
species	Species name, for plotting

Examples

loc_good_clean = cleanByEnvironment(Env, loc)
locs_thinned = spThinBySubspecies(loc_good_clean,thin.par=10,reps=1,lat.col="latitude",long.col="longitude",spec.col="assigned")
loc_thin_bgstuff = backgroundForPCA(localities=loc_good[,c("Longitude","Latitude")],r=200000,num=(100*nrow(localities)),e=Env)
perspecies_bgstuff = backgroundPerSpecies(loc_thin)
pcaOutput = createPcaToCompare(loc_thin_bgstuff,perspecies_bgstuffspecies)
pca_grid_clim = pcaOutput$grid_clim

kaiyaprovost/subsppLabelR documentation built on March 17, 2024, 5:09 p.m.