databaseToAssignedSubspecies: Species Occurrences to Subspecies Occurrences

In kaiyaprovost/subsppLabelR: Subspecies Labeled Occurences Generator

Species Occurrences to Subspecies Occurrences

Usage

databaseToAssignedSubspecies(
  spp,
  subsppList,
  pointLimit,
  dbToQuery,
  quant = 0.95,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  plotIt = F,
  bgLayer = NULL,
  outputDir,
  datafile = NULL,
  epsilon = 1e-06,
  restrictNominate = F,
  cleanup_nominate = T,
  num_digits_latlong = 2,
  ...
)

Arguments

spp	Genus and species to query, as string
subsppList	Strings of subspecies to query
pointLimit	Maximum point limit to return for each database – see spocc::occ
dbToQuery	List of databases to search through – see spocc::occ
quant	quant for density, below which points are removed. E.g., if set to 0.95, removes 95 \item xminMinimum longitude extent to clip rasters to \item xmaxMaximum longitude extent to clip rasters to \item yminMinimum latitute extent to clip rasters to \item ymaxMaximum latitude extent to clip rasters to \item plotItWhether to generate plots \item bgLayerA background layer for generating plots \item outputDirWhat directory to output to \item datafileif already ran and saved output from spocc:occ, put file here – default NULL \item epsilonParameter for anomaly detection

This function is a wrapper for the package and takes a species with a list of subspecies, and then assigns points to subspecies. Points that have problems with assignment are listed as "suspect" and points without problems are listed as "good." Also returns polygons used to make subspecies assignments.

Env = raster::stack(list.files(path='~/wc2-5/',pattern="\\.bil$",full.names=T)) ext = raster::extent(c(-125,-60,10,50)) Env = raster::crop(Env, ext) bg = Env[[1]] phainopeplaNitens = databaseToAssignedSubspecies(spp="Phainopepla nitens", subsppList=c("nitens","lepida"), pointLimit=500,dbToQuery=c("gbif","bison","inat","ebird","ecoengine","vertnet"), quant=0.95,xmin=-125,xmax=-60,ymin=10,ymax=50,plotIt=T,bgLayer=bg, outputDir="~/project/") suspect_occurrences = phainopeplaNitens$loc_suspect, good_occurrences = phainopeplaNitens$loc_good, subspecies_polygons = phainopeplaNitens$pol

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