| phylo.impute {phytools} | R Documentation |
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 |
X |
data matrix with species names as row labels. Missing data to be imputed should be coded |
... |
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 liam.revell@umb.edu
References
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.