treeToPoly {treenomial}

Convert trees to coefficient matrices

Description

Converts rooted full binary trees to tree distinguishing polynomials described with coefficient matrices.

Usage

treeToPoly(
  trees,
  type = c("default", "yEvaluated", "tipLabel"),
  y,
  varLabels = FALSE,
  numThreads = -1
)

Arguments

trees

a single phylo object or a list of phylo objects

type

one of:

“real”

tree distinguishing polynomials in two variables x (columns) and y (rows)

“yEvaluated”

tree distinguishing polynomials with y evaluated at a specified argument

“tipLabel”

complex coefficient polynomial that utilize binary trait tip labels on the phylo objects

y

the y value to evaluate the polynomial at when type is “yEvaluated”, ignored otherwise

varLabels

boolean for whether to add row and column names corresponding to the variables in the polynomial

numThreads

number of threads to be used, the default (-1) will use the number of cores in the machine and numThreads = 0 will only use the main thread

Value

the resulting coefficient matrix or matrices of the form:

“real”

a real matrix where the ith row, jth column represents the x^(j-1)*y^(i-1) coefficient

“yEvaluated”

a vector where the kth column represents the x^(k-1) coefficient

“tipLabel”

given trees with two unique tip labels “a”, “b” a complex matrix where the ith row, jth column represents the a^(i-1)*b^(j-1) coefficient

Examples

library(treenomial)
library(ape)

# generate a tree
tree <- rtree(n = 30, rooted = TRUE)

# a real coefficient matrix
treeToPoly(tree, varLabels = TRUE, numThreads = 0)

# complex coefficient vector for the tree
treeToPoly(tree, type = "yEvaluated", y = 1+1i, varLabels = TRUE, numThreads = 0)

# for a list of trees
treeToPoly(rmtree(4, 20), varLabels = TRUE, numThreads = 0)