pno: 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.

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.

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: rll{ ncols 958 nrows 376 xllcorner -73.440304 yllcorner -55.27622 cellsize 0.0166 NODATA_value -9999 }

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.