--- 
title: "Inapplicable data"
author: "Martin Brazeau (m.brazeau@imperial.ac.uk), Thomas Guillerme (guillert@tcd.ie) and Martin Smith (martin.smith@durham.ac.uk)"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::gitbook
documentclass: book
bibliography: [../References.bib, packages.bib]
link-citations: yes
github-repo: TGuillerme/Inapp
description: "Inapplicable data in a parsimony setting"
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Inapplicable data in a parsimony setting {-}

This document provides a detailed explanation of the algorithm for handling
inapplicable data proposed by Brazeau _et al._ [-@ThisStudy].

We first discuss how the [Fitch algorithm](#fitch) works and introduce
the [problems](#problems) that it encounters in the face of inapplicable character states.

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

We close with some [example](#examples) trees that demonstrate how our algorithm behaves in more complicated cases.