- 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 \pkg{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.