subspeciesMatchChecker: Check Subspecies Matches and Labels

In kaiyaprovost/subsppLabelR: Subspecies Labeled Occurences Generator

Check Subspecies Matches and Labels

Description

This function takes the locations of points relative to polygons from locatePolygonPoints() or similar and checks where points are assigned. Points that are in 1) no polygons, 2) multiple polygons, or 3) have a subspecies label that does not match their assignment are flagged as "suspect". Any points that are in single polygons and either 1) were originally unlabeled or 2) have a subspecies label that matches their assignment are flagged as "good".

Usage

subspeciesMatchChecker(locfile, subsppNames)

Arguments

locfile

Points with subspecies assignments and boolean locations with respect to polygons.

Examples

listFromSubspeciesOcc = subspeciesOccQuery(spp="Cardinalis sinuatus",subsppList=c("sinuatus","peninsulae","fulvescens"),pointLimit=100,dbToQuery="gbif")
labeledLoc = labelSubspecies(subsppOccList=listFromSubspeciesOcc)
locs = labeledLoc[labeledLoc$subspecies=="sinuatus",]
locs_sin = labeledLoc[labeledLoc$subspecies=="sinuatus",]
locs_ful = labeledLoc[labeledLoc$subspecies=="fulvescens",]
dens_sin = subspeciesDensityMap(localities=locs_sin,quant=0.95,xmin=-125,xmax=-60,ymin=10,ymax=50)
dens_ful = subspeciesDensityMap(localities=locs_ful,quant=0.95,xmin=-125,xmax=-60,ymin=10,ymax=50)
densPol_sin = densityMapToPolygons(densityMap=dens_sin)
densPol_ful = densityMapToPolygons(densityMap=dens_ful)
polyLocations = labeledLoc
polyLocations = locatePolygonPoints(test_points=polyLocations,polygonA=densPol_sin,polygonB=densPol_ful,crs="+proj=longlat +ellps=WGS84",setcoord = TRUE,nameA="sinuatus",nameB="fulvescens")
checked = subspeciesMatchChecker(locfile = polyLocations)
checked_suspect = checked$suspect
checked_good = checked$good

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