dtt {geiger}R Documentation

Disparity-through-time

Description

Functions for calculating and plotting disparity-through-time for a phylogenetic tree and phenotypic data.

Usage

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))

Arguments

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)

Details

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
Calculate morphological disparity for a set of species. Disparity measure can be one of the following:
avg.sq
Average squared euclidean distance among all pairs of points. This is a good choice if all of the axes are in the same units, or PC axes.
avg.manhattan
Average Manhattan distance among all pairs of points. This is a good choice if the axes are all in different units, like colors and lengths.
nb.states
Number of unique character states; this is the only option for discrete character data, for now.
dtt
Evaluates disparity-through-time for either a single data set or multiple data sets (for example, from simulations).
dtt.full
Calculates dtt for the actual data, runs simulations using univariate or multivariate Brownian motion, calculates dtt for all simulations and finds the mean, and plots dtt for both data and simulations on the output device.

Value

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:
dtt.data
DTT for the data
dtt.sims
DTT for each simulated data set
times
Times for each value in the dtt plot; this is just the branching times of the phylogeny
MDI
Value of the MDI statistic, which is the area between the DTT plot for the data and the mean of the simulations
Plot
Creates a DTT plot

Author(s)

Luke J. Harmon

References

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.

Examples


data(geospiza)
attach(geospiza)

disp.calc(geospiza.data)
disp.data<-dtt(geospiza.tree, geospiza.data)
full.output<-dtt.full(geospiza.tree, geospiza.data)


[Package geiger version 1.2-14 Index]