SpeciesGeoCoder: A Complete SpeciesgeocodeR Analysis

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

Description

A complete occurrence to area classification with a set of standard output files saved to the working directory.

Usage

SpeciesGeoCoder(x, y, coex = FALSE, graphs = TRUE, areanames = "",
                occ.thresh = 0, elevation = FALSE, threshold,
		verbose = FALSE, cleaning = FALSE, ...)

Arguments

x	a data.frame with three columns named identifier, XCOOR, YCOOR or a character string. If x is a character string it can be the path to a tab-delimited text file containing the coordinates of points of interest (tab delimited, three columns with header: identifier, XCOOR, YCOOR) OR a shape file OR a vector of species names. In the latter cases GBIF is search for occurrence data using the rgbif function.
y	a character string giving the path to a text file containing the polygons of points of interest (tab delimited, three columns with header: identifier, XCOOR, YCOOR) OR an object of the class SpatialPolygons OR an object of the class SpatialPolygonsDataframe.
coex	logical. Indicating if a coexistence matrix should be calculated and shown as a heat plot (default = FALSE). Only for small to medium-sized datasets.
graphs	logical. Defines if the summary plots and maps are created as pdf files in the working directory (default = TRUE).
areanames	a character string. If the input polygon file is a shape and not a text file, this column indicates the name of the column used for area names. See the SpeciesgeocodeR documentation for more information, if the polygon input file is a text file leave as default (default = "").
occ.thresh	numerical. Threshold for the minimum number of occurrences necessary in a polygon to be counted as present (in percent of the total occurrences of the species). Default = 0.
elevation	logical. Should the results be split by elevation class? (default = FALSE)
threshold	numeric vector. Indicating the elevation thresholds.
verbose	logical. If TRUE, reports the progress of the analyses.
cleaning	logical. If TRUE, GeoClean is applied to the input coordinates.
...	Further arguments to be passed to GeoClean.

Details

This performs a complete speciesgeocodeR occurrences to area classification analysis and produces the standard set of output files: 1. classification of all samples to a polygon, 2. Summary of species (identifier) occurrence per polygon, 3. a table of samples that could not be classified to any of the input polygons, 4. a nexus-file, including the species classification, 5. a coexistence matrix, showing to which percentage species to co-occur in the input polygons, 5. a table giving species numbers per polygon. Furthermore produces a set of .pdf files in the output directory: 1. a bar chart showing the number of species per polygon, 2. a bar chart summarizing numbers of each species for each polygon, 3. a bar chart summarizing the occurrences in each polygon per species, 4. a map of all polygons with the points classified to them, colored for species (identifier), 5. a map of the occurrences of all species, a map showing all points used and all unclassified points in the geographic context, 6. a heat plot showing the co-occurrence patterns of all species in the polygons. If elevation = T, the input dataset is split at the elevation(s) provided by threshold, and separate output files are generated for each elevation class.

Value

A set of output tables (.txt) and graphics (.pdf).

Note

See the speciesgeocodeR documentation for further information and examples.

Examples

## Not run: 
data(lemurs)
data(mdg_poly)
SpeciesGeoCoder(lemurs, mdg_poly
## End(Not run)

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