plotAncClim: Chronograms with Climatic Data on the Y-Axis

In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

Description

Plot the history of climatic tolerance for a clade sensu Evans et al. (2009).

Usage

plotAncClim(x, layer, clades = NULL, col, density = TRUE, tipmode = 1,
  nchar = 3, cex, tipspace, cladespace = 1, lwd, ylab = "")

Arguments

x	A list with elements tree, data, and (optional) central.density (see details).
layer	Do not use.
clades	A list containing vectors of tip labels which define the clades to highlight.
col	A vector containing colors for different clades (see Examples).
density	Logical, if TRUE, the central density intervals for recent species are plotted.
tipmode	Integer: tipmode = 0 means no tiplabels (and no central density intervals) are plotted; values 1, 2, and 3 define different ways of plotting the tiplabels (see Examples).
nchar	An integer giving the number of characters to which the tiplabels are truncated.
cex	Numeric character expansion factor for tiplabels; multiplied by par("cex") yields the final character size. NULL is are equivalent to 1.0.
tipspace	The fraction of the x-axis that is reserved for tiplabel plotting. If no value is given (default), plotAncClim calculates the fraction as 1 - (4 / nbtips), but this can be overridden by specifiying a fixed value for tipspace in ]0, 1[.
cladespace	A positive reel number; tentative: a factor controlling the space between tiplabels of different clades.
lwd	The line width, a positive number, defaulting to 1.
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.

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(tree)
 data(PNO)

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

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

# visualize results with default branch coloration
plotAncClim(ac)

# alternative clade colors are given according to the order
# in which tip labels appear from left to right
plotAncClim(ac, col = c("red", "purple", "blue"))

# the 'tipmode' argument
plotAncClim(ac, tipmode = 0)
plotAncClim(ac, tipmode = 1)
plotAncClim(ac, tipmode = 2, nchar = 5)
plotAncClim(ac, tipmode = 3, nchar = 4)

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.