--- 
title: "Supplementary Information for: \\newline\\newline The sclerite bearing ancestry of Lophotrochozoa"
author: "Martin R. Smith"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: 
  bookdown::pdf_book:
    includes:
      in_header: preamble.tex
    keep_tex: true
documentclass: book
classoption: openany
bibliography: [References.bib]
csl: http://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
biblio-style: apalike-doi
link-citations: yes
github-repo: ms609/halkieria
description: "Supplementary materials, including details of phylogenetic analysis"
---

# Supplementary Text {-}

This document comtains supplementary material to @SmithInPrep.  `r if (knitr::is_latex_output()) 'It is best viewed in HTML format at [ms609.github.io/halkieria](https://ms609.github.io/halkieria/).'`

It describes the [morphological dataset](#dataset) and the results of tree searches using [Fitch parsimony](#fitch) and a [Bayesian method](#bayesian): approaches that are subject to errors resulting from logically incoherent treatment of inapplicable data [@Maddison1993].
We also present the  [results](#treesearch) of tree searches with the algorithm described by @Brazeau2018, which reduces error due to inapplicable data in a parsimony setting. Finally, we document how each character is parsimoniously [reconstructed](#reconstructions) on `r if(knitr::is_html_output()) "optimal trees" else "an optimal tree"`.

Supplementary [figures](#figures) and [tables](#table) appear after the text.

```{r setup-index, include=FALSE, message=FALSE}
Sys.setlocale('LC_ALL','English_United Kingdom.1252');
set.seed(0)
knitr::opts_chunk$set(echo = TRUE)
library('ape'); library('phangorn'); library('TreeSearch');
if (!require('Inapp')) devtools::install_github('TGuillerme/Inapp')
library('Inapp')
if (!require('MorphoBank')) devtools::install_github('ms609/MorphoBank')
library('MorphoBank')

source('bibFunctions.R')
source('plotFunctions.R')
source('treeFunctions.R')
source('italicize.R')
```

```{R setup-more, include=FALSE, message=FALSE}
options(GitHubUser='ms609', GitHubRepo='halkieria', 
        MorphoBankProject=3262, ProjectName='Scleritomorph_phylogeny',
        svgHeight=720, svgWidth=682)
tntFiles <- list.files('TNT/', pattern='xpiwe.*\\.tre', full=TRUE)
tntKs <- as.double(gsub(".*xpiwe([\\d\\.]+)\\..*", "\\1", tntFiles, perl=TRUE))
tntFiles <- tntFiles[order(tntKs)]
tntFile <- gsub(".*(mbank_.*\\.tnt).*", "\\1", readLines(tntFiles[1], n=1))
nexusFile <- MostRecentNexus()
my_data <- ReadAsPhyDat(nexusFile)
ignoredTaxa <- c('Conotheca', 'Maxilites', 'Pauxillites', 'Alisina',
                 'Amathia', # There because it has setae; Flustra doesn't
                 'Yuganotheca_elegans', 'Lingulellotreta_malongensis',
                 'Glyptoria', 'Nisusia_sulcata', 'Kutorgina_chengjiangensis',
                 'Tomteluva_perturbata', 'Salanygolina', 'Coolinia_pecten',
                 'Antigonambonites_planus', 'Askepasma_toddense',
                 'Longtancunella_chengjiangensis', 'Lingulosacculus', 
                 'Mummpikia_nuda', 'Cupitheca_holocyclata',
                 'Siphonobolus_priscus', 'Acanthotretella_spinosa',
                 'Clupeafumosus_socialis', 'Botsfordia', 'Eoobolus', 'Ussunia',
                 'Craniops', 'Paramicrocornus', 'Bactrotheca')
                 # Also manually update tnt.run using `taxcode-`
#ignoredTaxa <- character(0)
my_data[ignoredTaxa] <- NULL

# my_data contains an inapplicable state that we should convert to ambiguous for 
# standard fitch, for CI etc.
iw_data <- PrepareDataIW(my_data)
fitch_data <- my_data
cont <- attr(fitch_data, 'contrast')
cont[cont[, '-'] == 1, ] <- 1
colnames(cont)[colnames(cont) == '-'] <- '?'
attr(fitch_data, 'contrast') <- cont
attr(fitch_data, 'allLevels')[attr(fitch_data, 'allLevels') == '-'] <- '?'
attr(fitch_data, 'levels')[attr(fitch_data, 'levels') == '-'] <- '?'
fitch_data <- PrepareDataIW(fitch_data)

my_chars <- ReadCharacters(nexusFile)
char_notes <- ReadNotes(nexusFile)
my_states <- attr(my_chars, 'state.labels')
my_chars <- my_chars[!(rownames(my_chars) %in% ignoredTaxa), ]

neomorphic <- vapply(my_states, IsNeomorphic, logical(1))

kValues <- c(3, 4.5, 7, 10.5, 16, 24)

outgroup <- 'Yilingia_spiciformis'
# rootingTips <- c('Tonicella', 'Serpula', 'Loxosomella')
rootingTips <- outgroup
```

(ref:first-panels) at _k_ = `r kValues[1]` and `r kValues[2]`.

(ref:second-panels) at _k_ = `r kValues[3]` and `r kValues[4]`.

(ref:third-panels) at _k_ = `r kValues[5]` and `r kValues[6]`.

