(Reasonably) fast estimation of ML ancestral states
This function performs (reasonably) fast estimation of the ML ancestral states for a continuous trait by taking advantage of the fact that the state computed for the root node of the tree during Felsenstein's (1985) contrasts algorithm is also the MLE of the root node. Thus, the function re-roots the tree at all internal nodes and computes the contrasts state at the root each time. The function can also (optionally) compute variances or 95-percent confidence intervals on the estimates.
fastAnc(tree, x, vars=FALSE, CI=FALSE, ...)
tree |
an object of class |
x |
a vector of tip values for species; |
vars |
a logical value indicating whether or not to compute variances on the ancestral state estimates. Variances are based on Equation (6) of Rohlf (2001). |
CI |
a logical value indicating whether or not to compute 95-percent confidence intervals on state estimates. |
... |
optional arguments. Presently this consists of |
An object of class "fastAnc" consisting of either: a named vector containing the states at internal nodes - names are node numbers; or a list containing ancestral state estimates (ace), variances on the estimates (var), and/or 95-percent confidence intervals (CI95).
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
## load data from Garland et al. (1992)
data(mammal.tree)
data(mammal.data)
## extract character of interest
ln.bodyMass<-log(setNames(mammal.data$bodyMass,
rownames(mammal.data)))
## estimate ancestral body sizes
fit.BM<-fastAnc(mammal.tree,ln.bodyMass,CI=TRUE)
print(fit.BM,printlen=10)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.