ace {ape}R Documentation

Ancestral Character Estimation

Description

This function estimates ancestral character states, and the associated uncertainty, for continuous and discrete characters.

Usage

ace(x, phy, type = "continuous", method = "ML", CI = TRUE,
    model = if (type == "continuous") "BM" else "ER",
    scaled = TRUE, kappa = 1, corStruct = NULL)

Arguments

x a vector or a factor.
phy an object of class "phylo".
type the type of variable; either "continuous" or "discrete" (or an abbreviation of these).
method a character specifying the method used for estimation. Three choices are possible: "ML", "pic", or "GLS".
CI a logical specifying whether to return the 95% confidence intervals of the ancestral state estimates (for continuous characters) or the likelihood of the different states (for discrete ones).
model a character specifying the model (ignored if method = "GLS"), or a numeric matrix if type = "discrete" (see details).
scaled a logical specifying whether to scale the contrast estimate (used only if method = "pic").
kappa a positive value giving the exponent transformation of the branch lengths (see details).
corStruct if method = "GLS", specifies the correlation structure to be used (this also gives the assumed model).

Details

If type = "continuous", the default model is Brownian motion where characters evolve randomly following a random walk. This model can be fitted by maximum likelihood (the default, Schluter et al. 1997), least squares (method = "pic", Felsenstein 1985), or generalized least squares (method = "GLS", Martins and Hansen 1997). In the latter case, the specification of phy and model are actually ignored: it is instead given through a correlation structure with the option corStruct.

For discrete characters (type = "discrete"), only maximum likelihood estimation is available (Pagel 1994). The model is specified through a numeric matrix with integer values taken as indices of the parameters. The numbers of rows and of columns of this matrix must be equal, and are taken to give the number of states of the character. For instance, matrix(c(0, 1, 1, 0), 2) will represent a model with two character states and equal rates of transition, matrix(c(0, 1, 2, 0), 2) a model with unequal rates, matrix(c(0, 1, 1, 1, 0, 1, 1, 1, 0), 3) a model with three states and equal rates of transition (the diagonal is always ignored). There are short-cuts to specify these models: "ER" is an equal-rates model (e.g., the first and third examples above), "ARD" is an all-rates-different model (the second example), and "SYM" is a symmetrical model (e.g., matrix(c(0, 1, 2, 1, 0, 3, 2, 3, 0), 3)). If a short-cut is used, the number of states if determined from the data.

Value

a list with the following elements:

ace if type = "continuous", the estimates of the ancestral character values.
CI95 if type = "continuous", the estimated 95% confidence intervals.
sigma2 if type = "continuous", model = "BM", and method = "ML", the maximum likelihood estimate of the Brownian parameter.
rates if type = "discrete", the maximum likelihood estimates of the transition rates.
loglik if method = "ML", the maximum log-likelihood.
lik.anc if type = "discrete", the scaled likelihoods of each ancestral state.
call the function call.

Note

The current version (as in ape 1.7) is somehow experimental, and the code has not been thoroughly tested. Any feedback will be welcome!

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

References

Felsenstein, J. (1985) Phylogenies and the comparative method. American Naturalist, 125, 1–15.

Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist, 149, 646–667.

Pagel, M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London. Series B. Biological Sciences, 255, 37–445.

Schluter, D., Price, T., Mooers, A. O. and Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699–1711.

See Also

corBrownian, corGrafen, corMartins, compar.ou

Examples

### Just some random data...
data(bird.orders)
x <- rnorm(23)
### Compare the three methods for continuous characters:
ace(x, bird.orders)
ace(x, bird.orders, method = "pic")
ace(x, bird.orders, method = "GLS",
    corStruct = corBrownian(1, bird.orders))
### For discrete characters:
ans <- ace(c(rep(0, 5), rep(1, 18)), bird.orders, type = "d")
#### Showing he likelihood of state "1" on each node:
plot(bird.orders, type = "c", FALSE)
nodelabels(thermo = ans$lik.anc[, 2], cex = 0.75)

[Package ape version 1.7 Index]