Impute duplication events based on a vector of species — imputate

Uses a simple algorithm to impute duplication events based on the terminal genes of the tree. An interior node is a duplication event if a specie has two or more leafs within its clade.

imputate_duplications(tree, species)

Arguments

tree: An object of class ape::phylo.
species: A character vector of length ape::Ntip(tree) (see details).

Value

A logical vector of length ape::Nnode(tree, internal.only = FALSE)

with TRUE to indicate that the corresponding node is a duplication event. The order matches that in the input tree.

Details

This function will take a vector of species and, based on that, assign duplication events throughout the interior nodes. An interior node is labeled as a duplication event if two or more of the leaves within it are from the same species.

Examples


# Data from PANTHER
path <- system.file("tree.tree", package="aphylo")
ptree <- read_panther(path)

# Extracting the species
sp <- gsub(".+[:]|[|].+", "" , ptree$tree$tip.label)

# Imputing duplications
imputate_duplications(ptree$tree, species = sp)
#>   [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [97] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [145] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE
#> [157]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE
#> [169] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
#> [181] FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE
#> [193] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE
#> [205]  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE
#> [217]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE
#> [229] FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE
#> [241]  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE