createAssignedSubspecies: Species Occurrences to Subspecies Occurrences

In kaiyaprovost/subsppLabelR: Subspecies Labeled Occurences Generator

Species Occurrences to Subspecies Occurrences

Description

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.

Usage

createAssignedSubspecies(
  spp,
  subsppList,
  pointLimit,
  dbToQuery,
  method = "raster",
  quant = 0.95,
  xmin = -180,
  xmax = 180,
  ymin = -90,
  ymax = 90,
  plotIt = F,
  bgLayer = NULL,
  outputDir,
  datafile = NULL,
  epsilon = 1e-06,
  spp_epsilon = epsilon,
  subspp_epsilon = epsilon,
  restrictNominate = F,
  cleanup_nominate = T,
  num_digits_latlong = 2,
  cells_per_bgLayer = 50,
  downloadOnly = FALSE,
  ...
)

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
method	Whether to calculate overlaps with rasters or polygons
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 rasters to
xmax	Maximum longitude extent to clip rasters to
ymin	Minimum latitute extent to clip rasters to
ymax	Maximum latitude extent to clip rasters to
plotIt	Whether to generate plots
bgLayer	A background layer for generating plots
outputDir	What directory to output to
datafile	if already ran and saved output from spocc:occ, put file here – default NULL
epsilon	Parameter for anomaly detection
spp_epsilon	Parameter for anomly detection specifically for species
subspp_epsilon	Parameter for anomaly detection specifically for subspecies
restrictNominate	Whether or not to restrict the nominate and remove extra points
cleanup_nominate	Whether or not to clean up the nominate
num_digits_latlong	The number of digits to round the coordinates to
cells_per_bgLayer	How many cells to include per background layer
downloadOnly	Whether to run as download occurrences only

Examples

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

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