plotPNO: Plot Predicted Niche Occupancy Profiles

In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

Description

This function can be used to plot predicted niche occupancy profiles (PNOs). PNOs can be obtained in a geographical information system by summing the cumulative probabilies of each climatical value for a species distribution model (SDM).

Usage

plotPNO(x, subset = NULL, thinning = NULL, xlab = NULL, 
	tail_threshold = 0, wm = FALSE, legend.pos = "topleft")

Arguments

x	A data frame or matrix with columns corresponding to species and rows corresponding to values along an environmental gradient. The first columns contains the environmental variable, the remaining colums probabilities of suitability.
subset	A vector of mode "character" which can be used to restrict the calculation of weighted means to those columsn in x whose column names match subset; defaults to NULL.
thinning	An integer that can be used to thin fuzzy PNOs prior to plotting; defaults to NULL.
xlab	A character string given the label for the x-axis.
tail_threshold	A numeric that can be used cut long tails of PNOs; defaults to 0.
wm	A logical indicating if weighted mean should added for each species.
legend.pos	Controls the position of the legend. Might eihter be a list object containing x and y coordinates (such as e.g. returned by locator) of the topleft corner of the legend box or one of the following: "topleft" (default), "bottomleft", "topright", or "bottomright". If legend.pos == NULL the plotting of the legend is suppressed.

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.

See Also

pno

Examples

# load PNOs for Oxalis sect. Palmatifoliae
data(PNO)

# plot predicted niche occupany for annual mean temperature
plotPNO(x = PNO$AnnualMeanTemperature, 
	xlab = "Annual Mean Temperature (degree C)")
	
# same plot, but with weighted means added
plotPNO(x = PNO$AnnualMeanTemperature, 
	xlab = "Annual Mean Temperature (degree C)", wm = TRUE)

Example output

Loading required package: ape
Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

The following objects are masked from 'package:ape':

    rotate, zoom

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