A supplement to Post-Marital Residence Patterns Show Lineage-Specific Evolution (Moravec et al. 2018)
This repository contains code and source files to fully replicate analysis from Post-marital residence patterns show lineage-specific evolution (Moravec et al. 2017). Output files from analysis itself are not included due to size limitations. Input and output files of phylogenetic reconstruction of Pama-Nyungan language family are not included as well for similar reasons.
Analysis was performed on GNU/Linux operating system using BayesTraits v2, R, Python, make/remake and liberal amount of bash scripts. The usage of most recent version of all tools is suggested.
Used R packages: ape, phangorn, phytools, coda, argparser and self-made package simpleSignal (code provided)
Used Python packages: dendropy and argparse
Note that due to usage of GNU tools, Unix systems using POSIX-only compilant tools (e.g., MacOS) might have some problems (e.g., interpretation of special characters in echo). Generally, bash scripts do not form critical part of the pipeline and could be replaced (e.g., by R scripts) to make this analysis possible on Windows operating systems as well.
Folder structure is as follows:
- code -- scripts required for analysis
- coding_schemes -- scripts were written as to enable recoding of data into different format (i.e., recoding ambilocal as unknown state between matrilocality and patrilocality), this folder contain these coding formats
- datasets -- with folders for individual language families, currently contain only pregenerated makefile (which is automatically assembled during analysis) and folder with source files
- documentation -- more detailed documentation
- makefiles -- templates to generate makefiles
To run analysis, run the script execute_make.sh -h and follow its instructions.
For more information, read the documentation: