This repository contains the data and source code for the paper "Indo-European phylogenetics with R: A tutorial introduction," Indo-European Linguistics (Goldstein 2020). This repository is archived at 10.5281/zenodo.8475.
The data used in the paper can be found in the folder Data. The file Multistate_screened.txt was downloaded from Luay Nakhleh's Computational Phylogenetics in Historical Linguistics website (https://www.cs.rice.edu/~nakhleh/CPHL/IEDATA_112603). The code for downloading the file is provided in the R notebook Code_PhylogeneticsRTutorial.Rmd in the Code folder. The file Binary_Screened.txt is a transformation of this dataset into binary traits. The script used to transform the data is provided in the folder code.
The binary phonological and morphological traits are described in the file BinaryTraitDescriptions.pdf.
The script install.R will install the packages used in Code_PhylogeneticsRTutorial.Rmd.
Code_PhylogeneticsRTutorial.Rmd contains an R notebook with all of the code used in the tutorial (plus some additional snippets). The analyses were carried out with R version 3.5.3. Further version information is available in versions.txt in the Code folder.
Program.cs: This is the script used to convert the datasets with multistate characters in the file Multistate_screened.txt into binary character values in Binary_Screened.txt . Characters P1, P3, and M1-M12 were subsequently recoded by hand. The code is written in C-Sharp and was created by Shawn McCreight.