custom_branch: Bind PUTs to customized sets of phylogenetic edges

In iramosgutierrez/randtip: A generalized framework to expand incomplete phylogenies with taxonomic information

Bind PUTs to customized sets of phylogenetic edges

Description

Bind PUTs to customized sets of phylogenetic edges

Usage

custom_branch(
  tree,
  edges,
  rand.type = "random",
  forceultrametric = FALSE,
  prob = TRUE
)

Arguments

tree	backbone tree of class phylo.
edges	matrix with five columns (character vectors). Each row defines a set of consecutive edges between two nodes, and multiple rows can be used for the same PUT. Column 1 includes the PUTs. Columns 2 and 3 include a pair of species whose MRCA defines the older node, whereas the MRCA of the species in columns 4 and 5 defines the younger node. Using the same species in columns 4 and 5 will define a terminal node as the younger node. If columns 2-3 are filled with a species and columns 4-5 are filled with another species, then all edges below the MRCA of the two species will be set as candidates. If the four columns are filled with the same species, the PUT will be bound as sister to this species.
rand.type	"random" or "polytomy". Default is "random".
forceultrametric	Whether or not to force the backbone tree to be ultrametric (in case it is detected as non-ultrametric). Default is FALSE.
prob	Whether or not the probability for selecting edges must be proportional to their length. If FALSE (default is TRUE), all edges have equal probability.

Value

An expanded phylogeny.

Author(s)

Ignacio Ramos-Gutierrez, Rafael Molina-Venegas, Herlander Lima

Examples

#Create a 'edges' dataframe
cats.edges <- data.frame(
 "PUT"= "Felis_catus",
 "parent1"= "Felis_silvestris",
 "parent2"= "Felis_silvestris",
 "child1"= "Felis_silvestris",
 "child2"= "Felis_silvestris")

#Bind the PUT to any of the candidate edges as defined in cats.edges 
cats.expanded <- custom_branch(tree=cats, 
 edges=cats.edges, forceultrametric=TRUE)

iramosgutierrez/randtip documentation built on March 19, 2024, 6:35 p.m.