asr: Ancestral state reconstruction
In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

View source: R/reconstruct.R

asr	R Documentation

Ancestral state reconstruction

Description

Reconstruct the ancestral states of a vector or matrix object by using either parsimony or maximum-likelihood methods to infer the states at the internal nodes of a phylogenetic tree.

Usage

asr(
  var,
  tree,
  type = c("parsimony", "ML", "ace"),
  method = c("discrete", "continuous"),
  unique.cols = FALSE
)

Arguments

`var`	Either a matrix or a vector containing the state of a variable (eg. SNPs or a phenotype) for all individuals (ie. for all terminal nodes in the tree).
`tree`	A phylo object containing the tree representing the ancestral relationships between the individuals for which snps and phen are known.
`type`	A character string specifying whether ancestral state reconstruction should be performed by `parsimony` or `ML` (as performed by the `ace` function in package ape).
`method`	A character string specifying the type of ASR method to implement, either `'discrete'` or `'continuous'` (only used if `type` is set to "ML").
`unique.cols`	A logical indicating whether only unique column patterns are present in `var`, if `var` is a matrix (if so (`TRUE`), a time-consuming step can be skipped); by default, `FALSE`.

Value

Depending on the dimensions of the input var object, either a matrix or a vector containing both the known states of the variable at the terminal nodes (in positions 1:Nterminal) and the inferred states at internal nodes (in positions (Nterminal+1):Ntotal).