pno: Predicted Niche Occupancy Profiles

Description Usage Arguments Details Value Author(s) References See Also

View source: R/pno.R


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.


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



The path leading to an ASCII raster map with environmental data (bioclimatic layer) and ArcGIS-compatible header.


The path leading to the directory, where MAXENT probability surfaces are stored as ASCII raster maps with ArcGIS-compatible header.


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


A numeric, giving the bin interval.


An integer, giving the number of bins used.


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


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.


Christoph Heibl


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.

See Also

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

phyloclim documentation built on May 29, 2017, 9:18 p.m.

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