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

library('Inapp')
library('ape')
knitr::opts_chunk$set(echo = TRUE)
labelRow <- function(text) text(-3, 9, text, font=2, pos=4, cex=1.2)
goloPar <- function () par(mfrow=c(1, 2), mar=c(0.5, 0.2, 0.6, 0.2), oma=c(0, 0, 2, 0), cex=0.5)
goloPlot <- function (tai, clr, nodeLabels=FALSE) {
    goloPar()
    vignettePlot(comb, tai, legend.pos='topleft', FALSE, passes=2, state.labels=ap)
    vignettePlot(comb, clr, legend.pos='topleft', passes=4, state.labels = rb)
    if (nodeLabels) {
        text((1:15) - 1 , 1:15, LETTERS[1:15])
        text((1:14) + 2.5 , (1:14) - 0.5, 1:14)
    }
}
SankoffMatrix <- function (states) {
  nr <- prod(vapply(states, length, 0L)) + 1L
  nchar <- length(states)
  ret <- matrix(0, nr, nr)
  ret[1, -1] <- nchar + 1L # +1 for gain of character
  ret[-1, 1] <- 1L # Just a loss

  listing <- vapply(seq_len(nr - 1L) - 1L, function (x) {
      ret <- integer(nchar)
      if (x == 0) return (ret)
      bin <- TreeSearch::AsBinary(x)
      ret[seq_along(bin)] <- bin
      ret
  }, double(nchar))
  rownames(ret) <- c('(0), absent', vapply(seq_len(nr - 1L), function (x) {
      paste0(paste0('(', x, '), present, '), 
             paste(vapply(seq_len(nchar), 
                          function (char) states[[char]][listing[char, x]+ 1L],
                          character(1)),
                   collapse=', ')
             )
      }, character(1)))
  ret[-1, -1] <- vapply(seq_len(nr-1), function (i) 
      vapply(seq_len(nr-1), function (j) sum(listing[, i] != listing[, j]), 0L),
      integer(nr - 1L))
  colnames(ret) <- paste0('**', seq_len(nr) - 1L, '**')

  # Return: 
  ret
}
ap <- c('Absent', 'Present')
rb <- c('Red', 'Blue')
oap <- c('', ap)
orb <- c('', rb)
whitey <- '#ffffff42'
greeny <- '#7fbf7ba7'
purply <- '#af8dc3e0'
number <- function (n) ifelse (n %in% 1:14, c('one', 'two', 'three', 'four', 'five', 'six', 'seven', 'eight', 'nine', 'ten', 'eleven', 'twelve', 'thirteen', 'fourteen')[n], n)

Inapplicable data in a parsimony setting {-}

This document r if(knitr::is_latex_output()) "(also available as an [HTML webpage*](https://rawgit.com/TGuillerme/Inapp/master/inst/gitbook/_book/index.html))" provides a detailed explanation of the algorithm for handling inapplicable data proposed by @Brazeau2018.

We first discuss how the Fitch algorithm works and introduce the problems that it encounters in the face of inapplicable character states.

We then introduce our solution, a new algorithm, implemented in various software packages, and discuss its implications for the coding of characters and ambiguity.

We close with some example trees that demonstrate how our algorithm behaves in more complicated cases.

r if(knitr::is_latex_output()) "* [rawgit.com/TGuillerme/Inapp/master/inst/gitbook/_book/](https://rawgit.com/TGuillerme/Inapp/master/inst/gitbook/_book/index.html)"

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