adjust_data: Adjusts the tree and traits to meet the requirements of...

In khabbazian/l1ou: Tools for detecting past changes in the expected mean trait values and studying trait evolution from comparative data

Adjusts the tree and traits to meet the requirements of estimate_shift_configuration

Description

Returns a new tree and new data matrix, where the tree edges are in postorder, and the data row names match the order of the tree tip labels.

Usage

adjust_data(tree, Y, normalize = TRUE, quietly = FALSE)

Arguments

tree	ultrametric tree of class phylo with branch lengths.
Y	trait vector/matrix without missing entries.
normalize	logical. If TRUE, normalizes branch lengths to a unit tree height.
quietly	logical. If FALSE, changes in tree/trait are printed.

Value

tree	tree of class phylo, with the same topology as the input tree but adjusted edge order.
Y	trait vector/matrix with adjusted row names and row order.

Examples

data(lizard.tree, lizard.traits)
# here, lizard.traits is a matrix, so columns retain row names:
names(lizard.traits[,1])
lizard <- adjust_data(lizard.tree, lizard.traits[,1])

# for a data frame, make sure to retain row names if a single column is selected:
lizard.traits <- as.data.frame(lizard.traits)
lizard <- adjust_data(lizard.tree, subset(lizard.traits, select=1))

khabbazian/l1ou documentation built on Aug. 10, 2022, 7:41 p.m.