phylo.impute: Phylogenetic imputation for multivariate continuous character...

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Phylogenetic imputation for multivariate continuous character data

Description

This function performs phylogenetic multiple imputation using maximum likelihood.

Usage

phylo.impute(tree, X, ...)

Arguments

tree	an object of class "phylo".
X	data matrix with species names as row labels. Missing data to be imputed should be coded NA.
...	optional arguments.

Details

This function performs phylogenetic imputation in which the evolution of the characters in X is assumed to have occurred by correlation multivariate Brownian motion.

Missing values are imputed by maximizing their likelihood jointly with the parameters of the Brownian model. The function evol.vcv is used internally to compute the likelihood.

Note that the Rphylopars package also does phylogenetic imputation for multivariate trait data and it seems to be much faster.

Value

An object of class "phylo.impute" consisting of a complete data frame with missing values imputed.

Since optimization is performed numerically using likelihood, a summary of the optimization can be seen by evaluating attr(object,"optim"), in which object is of class "phylo.impute".

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

evol.vcv

phytools documentation built on June 22, 2024, 10:39 a.m.