title: Early high rates and disparity in the evolution of ichthyosaurs author:

• name: Benjamin C. Moon affiliation: University of Bristol email: [email protected]
• name: Thomas L. Stubbs affiliation: University of Bristol email: [email protected] date: 2019-12-09 journal: Communications Biology url: https://www.nature.com/articles/s42003-020-0779-6 doi: https://doi.org/10.1038/s42003-020-0779-6 date_published: 2020-02-13 ...

Data and code used in our study ‘Early high rates and disparity in the evolution of ichthyosaurs’, published as

Moon BC & Stubbs TL Early high rates and disparity in the evolution of ichthyosaurs. Communications Biology, 3, 68 doi:10.1038/s42003-020-0779-6

1. supplement-ichthyosaur_macroevolution: supplementary document PDF file with supplementary methods, results, figures, tables, and references.
2. supp_figures: folder of supplementary figures included in the supplementary document.
3. supp_tables: folder of supplementary tables included in the supplementary document.
4. supp_code: supplementary R code to run most analyses.
5. supp_BayesTraits: supplementary code to run the continuous rates analyses in BayesTraits.

ichthyosaur-macroevolution
├ LICENSE
├ README.md
├ supplement-ichthyosaur_macroevolution.tex
├ supplement-ichthyosaur_macroevolution.pdf
├ supplement-ichthyosaur_macroevolution.bib
├ version.dat
├ supp_figures/
├ supp_tables/
├ supp_code/
│  ├ 0-Moon_Stubbs-run_analyses.R
│  ├ 1A-disparity_analyses.R
│  ├ 1B-disparity_stats.R
│  ├ 2-time_scaling.R
│  ├ 3-rates_analyses.R
│  ├ data/
│  ├ fig/
│  ├ functions/
│  ├ output/
│  └ tbl/
└ supp_BayesTraits/
   ├ ichthyosaur_data_BAYESTRAITS.csv
   ├ Moon_Plot_Functions.R
   ├ traitgram.code.R
   ├ BayesTraits/
   └ PostProc/

This uses recent versions of lualatex (compiled with version 1.10.0) and latexmk (version 4.65). Run the following line to compile

> latexmk supplement-ichthyosaur_macroevolution

Most of the analyses are run in the R statistical environment; these were tested using R version 3.6.0. Scripts are contained in the folder supp_code/ All analyses will proceed continuously from the first script from the shell

> Rscript 0-Moon_Stubbs-run_analyses.R

or within R

r$> source("0-Moon_Stubbs-run_analyses.R")

This includes installation of the required packages at the beginning of the first script. Refactoring of Claddis took place during the analyses, so we use a previous version (commit 4f7f1bf); the original version of this code will not function with a later commit. Email notifications are sent using the packages mailR and password storage with keyringr. Vignettes for the set-up of these can be found at https://github.com/rpremraj/mailR and https://bit.ly/2AHUj0A (accessed 2019-09-27).

Individual command scripts and associated trees for 100 runs are included as .cmd and .nex files respectively in the subfolder supp_BayesTraits/BayesTraits. Run these in BayesTraits (version 2.0.2) from http://www.evolution.rdg.ac.uk/BayesTraitsV2.0.2.html for automated analyses

> BayesTraits BayesTraits/ichthyosaur.pca.scores.pruned.singletree.1.nex
ichthyosaur_data_BAYESTRAITS.csv
< BayesTraits/BayesTraits_hetRates_Script.1.cmd

Homogeneous and heterogeneous scripts are separated as homRates or hetRates. Results tables are included in the folder supp_BayesTraits/PostProc. Additional plot are created using the scripts traitgram.code.R and Moon_plot_Functions.R.