apply.reconstruction: Apply reconstruction

In TGuillerme/Inapp: Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees

Apply reconstruction

Description

Apply a series of passes for an ancestral states reconstruction

Usage

apply.reconstruction(
  tree,
  character,
  passes = 4,
  method = "NA",
  inapplicable = 1,
  match.tip.char = FALSE
)

Arguments

tree	phylo, a tree
character	character, a vector of character states
passes	numeric, the number of passes in the tree; from 1 to 4 (default)
method	either "Fitch" or "NA"
inapplicable	When method is "Fitch", how do deal with inapplicable data: 1, 2 for respectively treating them as ? or an extra state.
match.tip.char	logical, TRUE to match the character to the tip labels (e.g character 1 matches with tip "a" or "1") or FALSE (default) to match the character to the tips entry (e.g. character 1 matches with the first tip)

Value

A states.matrix object that is a list of:

$Char	a list of character (numeric) where "NA" is equal to -1
$Dp1	a list of character from the first downpass
$Up1	a list of character from the first uppass
$Dp2	a list of character from the second downpass
$Up2	a list of character from the second uppass
$tracker	a list of the same Dp1, Up1, Dp2 and Up2 elements but tracking the applicable regions
$region	a vector of numeric value indicating the number of additional applicable regions
$changes	a vector of numeric values indicating the nodes where a state change was recorded
$score	a single numeric value that is the score of the tree (X$score = length(X$region) + length(X$changes))
$tree	the tree (phylo)

Author(s)

Thomas Guillerme

See Also

plot.states.matrix, runInapp

Examples

set.seed(1)
## Random tree with 12 taxa
tree <- ape::rtree(12, br = NULL)
## A character with inapplicable data
character <- "23--1??--032"

## Normal Fitch algorithm (NA states are missing data)
apply.reconstruction(tree, character, passes = 2, method = "Fitch",
                     inapplicable = 1)
## Same but NA states are an extra state and character now match the tips
apply.reconstruction(tree, character, passes = 2, method = "Fitch",
                     inapplicable = 2, match.tip.char = TRUE)

## NA algorithm
apply.reconstruction(tree, character, passes = 4, method = "NA")

## 1st pass of the NA algorithm
apply.reconstruction(tree, character, passes = 1, method = "NA")

TGuillerme/Inapp documentation built on Feb. 4, 2024, 7:26 a.m.