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EnvNicheR (version 1.4)

OverlapTaxa: Niche overlap among all species within a taxa

Description

Estimation of the niche overlap among all species within a taxa of a taxonomic level selected by the user (order, family or genus), using the file Polar coordinates.CSV obtained from the function Niche.

Usage

OverlapTaxa(data, Level, digits =2, file1 = "Overlap among taxa.csv", file2 = "Mean overlap among taxa.csv", na = "NA", dec = ",", row.names = FALSE, fileEncoding = "")

Arguments

data
The file Polar coodinates.CSV obtained from the function Niche().
Level
Taxonomic level to be selected, i.e., Class, Order, Family, or Genus
digits
Integer indicating the number of decimal places of the overlap values.
file1
CSV file. A character string naming the file with the overllap among species.
file2
CSV file. A character string naming the file with mean and standard deviation of the overlap for each taxonomic level selected by the user.
na
CSV files. The string to use for missing values in the data.
dec
CSV files. The string to use for decimal points in numeric or complex columns: must be a single character.
row.names
CSV files. Either a logical value indicating whether the row names of x are to be written along with x, or a character vector of row names to be written.
fileEncoding
CSV files. Character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written.

Value

the species for the taxonomic level selected by the user.

Details

In the first CSV file this function estimates the niche overlap, using the file Polar coordinates.CSV obtained from the function Niche(), among all species within the taxonomic level selected by the user. In the second CSV file the function estimates the mean overlap within the taxonomic level selected by the user. If there are many species, e.g. over 5000, the process can take several hours.

Examples

Run this code

data(Polar.coordinates)

OverlapTaxa(data=Polar.coordinates, Level="Genus")

#Remove the data set
rm(Polar.coordinates)

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