pno: Predicted Niche Occupancy Profiles
In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

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

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.

1 2	pno(path_bioclim, path_model, subset = NULL, bin_width = 1, bin_number = NULL)

`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.

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.

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

phyloclim documentation built on May 2, 2019, 8:07 a.m.