plotAncClim: Chronograms with Climatic Data on the Y-Axis

In heibl/phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

Chronograms with Climatic Data on the Y-Axis

Description

Plot the history of climatic tolerance for a clade sensu \insertCiteevanssmith2009;textualphyloclim.

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

\insertRef

evanssmith2009phyloclim

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)

heibl/phyloclim documentation built on April 23, 2024, 2:39 a.m.