ancestral: Estimation of traits ancestral states.
In RPANDA: Phylogenetic ANalyses of DiversificAtion

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Reconstruct the ancestral states at the root (and possibly for each nodes) of a phylogenetic tree from models fit obtained using the fit_t_XX functions.

1 2	ancestral(object)

object

A model fit object obtained by the fit_t_XX class of functions.

ancestral is an S3 method that reconstruct the ancestral states at the root and possibly for each nodes of a phylogenetic tree from the models fit obtained by the fit_t_XX class of functions (e.g., fit_t_pl, fit_t_comp and fit_t_env). Ancestral states are estimated using generalized least squares (GLS; Martins & Hansen 1997, Cunningham et al. 1998 ).

a list with the following components

`root`	the reconstructed ancestral states at the root
`nodes`	the reconstructed ancestral states at each nodes (not yet implemented for all the methods)

The function is used internally in phyl.pca_pl.

J. Clavel

Clavel, J., Aristide, L., Morlon, H., 2019. A Penalized Likelihood framework for high-dimensional phylogenetic comparative methods and an application to new-world monkeys brain evolution. Syst. Biol. 68: 93-116.

Cunningham C.W., Omland K.E., Oakley T.H. 1998. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13:361-366.

Martins E.P., Hansen T.F. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.

fit_t_pl, fit_t_env, phyl.pca_pl, GIC, gic_criterion

if(require(mvMORPH)){
set.seed(1)
n <- 32 # number of species
p <- 31 # number of traits

tree <- pbtree(n=n) # phylogenetic tree
R <- Posdef(p)      # a random symmetric matrix (covariance)

# simulate a dataset
Y <- mvSIM(tree, model="BM1", nsim=1, param=list(sigma=R))

# fit a multivariate BM with Penalized likelihood
fit <- fit_t_pl(Y, tree, model="BM", method="RidgeAlt")

# Perform the ancestral states reconstruction
anc <- ancestral(fit)

# retrieve the scores
head(anc$nodes)
}