plotAncClim {phyloclim} | R Documentation |
This function can be used to plot the history of climatic tolerance for a clade sensu Evans et al. (2009).
plotAncClim(x, clades = NULL, col, density = TRUE, lwd = 1, xspace = c(0, 0.1), ylab = "")
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. |
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.
Christoph Heibl (heibl@lmu.de)
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
, pno.weighted.mean
, anc.clim
# 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)