SpGeoCodH: A Standard a SpeciesgeocodeR Area Classification

In speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

Description

Run a standard speciesgeocodeR occurrence point to area classification analysis on an object of the class spgeoIN (created by ReadPoints). The results are stored in an object of the class spgeoOUT. See details for more information.

Usage

SpGeoCodH(x, areanames = NULL, occ.thresh = 0)

Arguments

x	an object of the class spgeoIN
areanames	a character string. If the polygons in the spgeoIN object were derived from a shape file, this column indicates the name of the column used for area names. See the Speciesgeocoder tutorial for more information. If the polygons in the spgeoIN object were derived from a text file leave as default (Default = NA).
occ.thresh	numerical. The threshold for the minimum number of occurrences necessary in an area to be counted as present (in percent of the total occurrences of the species). Default = 0.

Details

This function uses an object of the class spgeoIN and performs a point in polygon test classifying each species to a polygon, summarizes the information per samples that could not be classified and calculates a coexistence matrix. These objects are then put together with the input information to an object of the class spgeoOUT.

Value

An object of the class spgeoOUT.

Note

See the speciesgeocodeR tutorial for further information and examples.

Examples

data(lemurs)
data(mdg_poly)

inp <- ReadPoints(lemurs, mdg_poly)
outp <- SpGeoCodH(inp)
names(outp)

Example output

Loading required package: maps
[1] "identifier_in"          "species_coordinates_in" "polygons"              
[4] "sample_table"           "spec_table"             "polygon_table"         
[7] "not_classified_samples" "coexistence_classified" "areanam"               

speciesgeocodeR documentation built on May 30, 2017, 12:34 a.m.