plotAncClim {phyloclim}R Documentation

Chronograms with climatic data on the y-axis

Description

This function can be used to plot the history of climatic tolerance for a clade sensu Evans et al. (2009).

Usage

plotAncClim(x, clades = NULL, col, density = TRUE, lwd = 1,
        xspace = c(0, 0.1), ylab = "")

Arguments

x A list with elements tree, data, and (optional) central.density (see details).
clades A list containing vectors of tip labels which define the clades to highlight.
col A vector containing colors for different clades.
density Logical, if TRUE, the central density intervals for recent species are plotted.
lwd The line width, a positive number, defaulting to 1.
xspace A vector of mode numeric; the first element controls the space between tiplabels of different clades, the second element sets the spaces between tiplabels within clades.
ylab A character string, giving a label for the y-axis, i.e., for the bioclimatic dimension of the plot.

Details

The main argument x is a list consisting of at least the first two of the following elements: (1) tree is an ultrametric phylogenetic tree stored as object of class phylo; (2) data is an object of class matrix; its columns correspond to bioclimatic variables and its rows corresond to node numbers such as defined by class phylo objects; (3) central.density must only be included if density = TRUE – it is a list, which for every bioclimatic variable, contains a matrix that contains the some minimum and maximum quantile of the respective bioclimatic variable for every tip in the tree.

Author(s)

Christoph Heibl (heibl@lmu.de)

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, pno.weighted.mean, anc.clim

Examples

# load phylogeny and PNOs of Oxalis sect. Palmatifoliae
data(palmatifoliae_tree)
data(palmatifoliae_pno)

# choose summer precipitation for analysis
clim <- palmatifoliae_pno$PrecipitationWarmestQuarter

# estimate ancestral tolerances
ac <- anc.clim(target = palmatifoliae_tree, pno = clim, n = 100)

# visualize results
plotAncClim(ac) 

[Package phyloclim version 0.0.1 Index]