pno: Predicted Niche Occupancy Profiles

Description Usage Arguments Details Value References See Also

View source: R/pno.R

Description

Following the approach of \insertCiteevanssmith2009;textualphyloclim, pno integrates species probability (suitability) distributions (e.g. derived with MAXENT) with respect to single climatic (or other environmental) variable in order to get predicted niche occupancy (PNO) profiles for each species and environmental variable.

Usage

1
pno(path_bioclim, path_model, subset = NULL, bin_width = 1, bin_number = NULL)

Arguments

path_bioclim

A character string, giving the path to an ASCII raster map with environmental data (bioclimatic layer) and ArcGIS-compatible header (see Details).

path_model

A character string, giving the path to the directory, where MAXENT probability surfaces are stored as ASCII raster maps with ArcGIS-compatible header (see Details).

subset

A vector of mode 'character' giving taxon names if only a subset of the species ENMs in path_model is to be used

bin_width

A numeric, giving the bin interval.

bin_number

An integer, giving the number of bins used.

Details

The path argument path_model points to the directory where the MAXENT probability distributions must be stored as ASCII maps with an ArcGIS-compatible header (as obtained with MAXENT output filetype: asc).

An example for an ArcGIS-compatible header:

ncols 958
nrows 376
xllcorner -73.440304
yllcorner -55.27622
cellsize 0.0166
NODATA_value -9999

Value

A data frame of cumulative probalities of suitability for each value on an environmental gradient (rows) for the a set of studied taxa (rows). The first column gives the mean of each category.

References

\insertRef

evanssmith2009phyloclim

See Also

pno.weighted.mean, niche.overlap, anc.clim


heibl/phyloclim documentation built on Jan. 19, 2020, 4:54 a.m.