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‎.gitattributes‎

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*.rds filter=lfs diff=lfs merge=lfs -text

‎README.md‎

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date: 2019-09-27
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# ichthyosaur-macroevolution
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# ichthyosaur-macroevolution #
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Data and code used in our study ‘Early high rates and disparity in the evolution of fish-shaped reptiles’.
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Data and code used in our study ‘Early high rates and disparity in the evolution of fish-shaped reptiles’, published as
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> Moon BC & Stubbs TL Early high rates and disparity in the evolution of fish-shaped reptiles. <Journal> doi:
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# Contents #
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1. supplement-ichthyosaur_macroevolution: supplementary document PDF file with supplementary methods, results, figures, tables, and references.
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2. supp_figures: folder of supplementary figures included in the supplementary document.
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3. supp_tables: folder of supplementary tables included in the supplementary document.
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4. supp_code: supplementary R code to run most analyses.
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5. supp_BayesTraits: supplementary code to run the continuous rates analyses in BayesTraits.
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## Repository layout ##
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ichthyosaur-macroevolution
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├ LICENSE
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├ README.md
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├ supplement-ichthyosaur_macroevolution.tex
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├ supplement-ichthyosaur_macroevolution.pdf
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├ supplement-ichthyosaur_macroevolution.bib
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├ version.dat
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├ supp_figures/
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├ supp_tables/
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├ supp_code/
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│ ├ 0-Moon_Stubbs-run_analyses.R
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│ ├ 1A-disparity_analyses.R
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│ ├ 1B-disparity_stats.R
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│ ├ 2-time_scaling.R
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│ ├ 3-rates_analyses.R
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│ ├ data/
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│ ├ fig/
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│ ├ functions/
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│ ├ output/
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│ └ tbl/
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└ supp_BayesTraits/
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├ ichthyosaur_data_BAYESTRAITS.csv
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├ Moon_Plot_Functions.R
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├ traitgram.code.R
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├ BayesTraits/
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└ PostProc/
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# Running the code #
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## Compiling the supplement ##
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This uses recent versions of `lualatex` (compiled with version 1.10.0) and `latexmk` (version 4.65). Run the following line to compile
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> latexmk supplement-ichthyosaur_macroevolution
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## R code analyses ##
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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
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> Rscript 0-Moon_Stubbs-run_analyses.R
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or within R
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r$> source("0-Moon_Stubbs-run_analyses.R")
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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).
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## BayesTraits analyses ##
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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
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> BayesTraits BayesTraits/ichthyosaur.pca.scores.pruned.singletree.1.nex ichthyosaur_data_BAYESTRAITS.csv < BayesTraits/BayesTraits_hetRates_Script.1.cmd
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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_Funtions.R`.

‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.1.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.10.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.100.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.11.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.12.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.13.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.14.cmd‎

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‎supp_BayesTraits/BayesTraits/BayesTraits_hetRates_Script.15.cmd‎

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