subspeciesDensityMap: Generate Subspecies Density Maps

In kaiyaprovost/subsppLabelR: Subspecies Labeled Occurences Generator

Generate Subspecies Density Maps

Description

This function uses 2D kernel density estimation to make a density raster of points for each subspecies. It then removes all but the most dense cells as definied by quant.

Usage

subspeciesDensityMap(
  localities,
  quant = 0.95,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  total_range,
  relative = T,
  raw_raster = T,
  subspp,
  spp,
  outputDir
)

Arguments

localities	Labeled localities as generated from labelSubspecies() or subspeciesOccQuery()
quant	quant for density, below which points are removed. E.g., if set to 0.95, removes 95 percent least dense squares.
xmin	Minimum longitude extent to clip to
xmax	Maximum longitude extent to clip to
ymin	Minimum latitute extent to clip to
ymax	Maximum latitude extent to clip to

Examples

listFromSubspeciesOcc = subspeciesOccQuery(spp="Cardinalis sinuatus",
   subsppList=c("sinuatus","peninsulae","fulvescens"),pointLimit=100,
   dbToQuery="gbif")
labeledLoc = labelSubspecies(subsppOccList=listFromSubspeciesOcc)
locs = labeledLoc[labeledLoc$subspecies=="sinuatus",]
dens = subspeciesDensityMap(localities=locs,quant=0.95,
   xmin=-125,xmax=-60,ymin=10,ymax=50)

kaiyaprovost/subsppLabelR documentation built on Feb. 28, 2025, 8 p.m.