partitionsNumber: Number of different models

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Number of different models

Description

partitionsNumber computes the number of different models with a given number of shifts K. It is also the number of colorings of the tips to the tree in npart = K + 1 colors.

Usage

partitionsNumber(phylo, npart)

Arguments

phylo	a phylogenetic tree of class phylo.
npart	the numbers of partitions (colors) allowed at the tips. This is the number of shifts plus one (npart = K + 1).

Value

an object of class partitionsNumber. This is made of a matrix with (Nnode + ntaxa) rows and (2*npart) columns. Each column contains two vectors: for k=1:npart it contains the number of partitions with k groups compatible with the tree and the shift process; and for k=(npart+1):2*npart, it contains the number of "marked" partitions with (k-npart) groups compatible with the tree and the shift process. The actual number can be extracted with function extract.partitionsNumber (see examples below).

See Also

extract.partitionsNumber, parsimonyNumber, equivalent_shifts

Examples

if (requireNamespace("combinat", quietly = TRUE)) {
  npart <- 8 # number of colors at the tips allowed
  tree <- read.tree(text="(A,(A,(A,A,A),A,A));") # a tree with polytomies
  plot(tree)
  parts_num <- partitionsNumber(tree, npart)
  parts_num
  
  ## Number of possible colorings of the tips in npart colors
  extract(parts_num)
  
  ## Get all the solutions for colorings with 1 to nparts colors
  extract(parts_num, npart = 1:npart)
  
  ## Number of possible colorings of the tips in npart colors
  ## For the sub-tree starting at node 17
  extract(parts_num, node = 10)
  
  ## Number of possible colorings of the tips in npart colors
  ## with one marked color
  extract(parts_num, marked = TRUE)
}

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.