- In the default setting (\code{method = "ML"} and \code{model = "BM"})
- the maximum likelihood estimation is done simultaneously on the
- ancestral values and the variance of the Brownian motion process;
- these estimates are then used to compute the confidence intervals in
- the standard way. The REML method first estimates the ancestral value
- at the root (aka, the phylogenetic mean), then the variance of the
- Brownian motion process is estimated by optimizing the residual
- log-likelihood. The ancestral values are finally inferred from the
- likelihood function giving these two parameters. If \code{method =
- "pic"} or \code{"GLS"}, the confidence intervals are computed using
- the expected variances under the model, so they depend only on the
- tree.
+ In the setting \code{method = "ML"} and \code{model = "BM"} (this used
+ to be the default until ape 3.0-7) the maximum likelihood estimation
+ is done simultaneously on the ancestral values and the variance of the
+ Brownian motion process; these estimates are then used to compute the
+ confidence intervals in the standard way. The REML method first
+ estimates the ancestral value at the root (aka, the phylogenetic
+ mean), then the variance of the Brownian motion process is estimated
+ by optimizing the residual log-likelihood. The ancestral values are
+ finally inferred from the likelihood function giving these two
+ parameters. If \code{method = "pic"} or \code{"GLS"}, the confidence
+ intervals are computed using the expected variances under the model,
+ so they depend only on the tree.