dtt {geiger} | R Documentation |
Functions for calculating and plotting disparity-through-time for a phylogenetic tree and phenotypic data.
disp.calc(data, disp = "avg.sq") dtt(phy, data, data.names=NULL, disp = "avg.sq") dtt.full(phy, data, data.names=NULL, disp="avg.sq", nsims=1000, mdi.range=c(0,1))
data |
Data matrix - either actual or simulated |
data.names |
Tip names for data vector that match tree species; ignored if data includes names |
phy |
Phylogenetic tree in 'phylo' format |
disp |
Disparity measure: see below for currently implemented options. |
nsims |
Number of simulations used to calculate null dtt plot |
mdi.range |
Time range over which to calculate MDI statistic (area between curves). Time is relative to the total tree length of 1; default is the whole tree from 0 (root) to 1 (tips) |
The most complete function, dtt.plot, carries out the entire disparity-through-time procedure described in Harmon et al. 2003. Other functions are for various parts of this, as follows:
disp.calc |
Disparity of the supplied data |
dtt |
Average disparity for clades whose stem crosses each time interval in the tree. |
dtt.full |
A list with the following items:
|
Luke J. Harmon
Foote, M. 1997. The evolution of morphological diversity. Annual Review of Ecology and Systematics 28:129-152. Harmon, L. J., J. A. Schulte, J. B. Losos, and A. Larson. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. Science 301: 961-964.
data(geospiza) attach(geospiza) disp.calc(geospiza.data) disp.data<-dtt(geospiza.tree, geospiza.data) full.output<-dtt.full(geospiza.tree, geospiza.data)