R: Predicted Niche Occupancy Profiles

pno {phyloclim}

R Documentation

Predicted Niche Occupancy Profiles

Description

Following the approach of Evans et al. (2009), pno integrates species probability (suitability) distributions (e.g. derived with MAXENT) with respect to single climatic (or other environmental) variables in order to get predicted niche occupancy (PNO) profiles for each species and environmenatal variable.

Usage

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

Arguments

`path_bioclim`	The path leading to an ASCII raster map with environmental data (bioclimatic layer) and ArcGIS-compatible header.
`path_model`	The path leading to the directory, where MAXENT probability surfaces are stored as ASCII raster maps with ArcGIS-compatible header.
`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 arguments path_bioclim and path_model point to the directories where the environmental data and the MAXENT probability distributions must be stored as ASCII maps with an ArcGIS-compatible header (as obtained with MAXENT output filetype: asc). An example 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.

Author(s)

Christoph Heibl

References

Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, and diversification of the 'bird-cage evening primroses' (Oenothera, sections Anogra and Kleinia). Am. Nat. 173: 225-240.