OverlapTaxa: Niche overlap among all species within a taxa

In EnvNicheR: Niche Estimation

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.

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.

Value

Two CSV files with the overlap among species and the mean overlap among the species for the taxonomic level selected by the user.

Author(s)

Cástor Guisande González, Universidad de Vigo, Spain.

Examples

## Not run: 

data(Polar.coordinates)

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

#Remove the data set
rm(Polar.coordinates)


## End(Not run)

EnvNicheR documentation built on Oct. 8, 2023, 1:07 a.m.