Files for phylogenetic analysis

Main_analyses.zip contains files necessary to replicate the results of Smith &amp; Long <i>et al.</i> These are modelled on Workflows for phylogenetic analysis of morphological data.Conservative.zip contains a repeat of our phylogenetic analyses after re-coding as ambiguous any character in <i>Youti yuanshi</i> whose state at adulthood is not unequivocal.Each archive contains files within a common subdirectory structure:MrBayesFolder containing input and output files for analysis in MrBayes.<code>mbank_X27231_2024-03-22-1117.nex</code>: NEXUS format character matrix downloaded from MorphoBank (project 3927), with addition of <code>MrBayes</code> block specifying search parameters.Other files are output files in the standard MrBayes format; sampled trees are contained in files ending <code>.t</code>.Phylogenetics.zip also contains marginal likelihood estimates under topological constraints that impose Tactopoda (Euarthropoda + Tardigrada) and Arthropoda (Euarthropoda + Onychophora):Output of stepping stone analyses are contained within files ending <code>.ss</code>.<code>marginal_likelihood.R</code> is a simple R script that computes marginal likelihoods and Bayes Factors from stepping stone analysis; it can be executed in R or RStudio.TreeSearchScripts for phylogenetic analysis under parsimony, with an approximate correction for inapplicable data.<code>analyse.R</code>: R script used to perform analysis. Can be executed within R / RStudio, or run directly on Windows by modifying <code>Analyse.lnk</code> to point to a local R installation.<code>common.R</code>: R file included from other scripts; loads packages and defines utility functions<code>plot.R</code>: R file included from other scripts; defines plotting parameters, including colour and format of tip labels.<code>visualize.R</code>: R script for visualizing search results generated by <code>analyse.R</code>, and the distribution of trees in tree space. Can be executed within R / RStudio, or run directly on Windows by modifying <code>Visualize.lnk</code> to point to a local R installation.<code>mbank_X27231_2024-03-22-1117.nex</code>: NEXUS format character matrix downloaded from MorphoBank (project 3927).<code>XXX_mbank_X27231_2024-03-22-1117.nex.trees</code>: NEXUS file containing results of parsimony search under the weighting system specified by <code>XXX</code>. <code>ew</code> = equal weights; <code>iw#</code> = implied weighting under concavity constant (k) = <code>#</code>.<code>Character_report.Rmd</code>: R Markdown file used to generate character report. Can be compiled into a standalone document using the "knit" command in RStudio.<code>Character_report_template.docx</code>: Word Document file providing style templates used when rendering the character report and the supplementary information (see folder <code>SI</code>).TNTScripts for phylogenetic analysis under parsimony, with no correction for inapplicable data.<code>mbank_X27231_2024-03-22-1117.tnt</code>: TNT format character matrix downloaded from MorphoBank (project 3927).<code>tnt.run</code>: TNT script used to perform analysis. Can be executed within TNT.<code>XXX.tre</code>: Most parsimonious trees in TNT format, as recovered under the weighting strategy denoted by <code>XXX</code>. <code>ew</code> = equal weights; <code>iw#</code> = implied weighting under concavity constant (k) = <code>#</code>.<code>XXX.sym</code>: Strict consensus trees under each weighting strategy, with symmetric resampling node support values, in TNT format.<code>XXX.pdf</code>: Visualization of strict consensus trees under each weighting strategy, after removal of rogue taxa using 'fast' heuristic of Smith (2022); tips coloured by stability.<code>visualize.R</code>: R script used to produce PDF visualizations.SIFiles used to render supplementary information documents.<code>map_trees.Rmd</code>: R Markdown document used to compile and summarise results of tree search under Bayesian and parsimony analyses. Can be compiled as a standalone document using the "knit" command in RStudio.<code>SI.Rmd</code>: Wrapper file used to collate components into a single output file. Using the "knit" command in RStudio will compile the supplementary information document.<code>_bookdown.yml</code>: YAML-formatted configuration file to control output settings.<br>