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sBayes

This software package implements a Bayesian mixture model for reconstructing linguistic contact areas, as described in Contact-tracing in cultural evolution: a Bayesian mixture model to detect geographic areas of language contact (Ranacher P., Neureiter N., Van Gijn R., Sonnenhauser B., Escher A., Weibel R., Muysken P., Bickel B.). sBayes implements a custom MCMC sampler to generate contact areas according to the model. Here we describe the installation process and the basic commands needed to run an analysis. For more detailed instructions explaining each step in the analysis and the various settings, please consult the user manual (sbayes_documentation.pdf).

Installation

To run sBayes, you need Python (version >=3.7) and three required system libraries: GEOS, GDAL, PROJ. The way of installing these system requirements depends on your operating system. E.g. on Linux (Ubuntu/Debian) you can use the following command:

sudo apt-get install -y libproj-dev proj-data proj-bin libgeos-dev

On MAC OS the same can be done using the homebrew package manager:

brew install proj geos gdal

On Windows the three libraries need to be installed manually from the corresponding sources.

Once these system libraries are ready, sBayes can be installed (along with the required python libraries) using:

 pip install --user git+git://github.com/derpetermann/sBayes.git

Running sBayes

sBayes can be used as a python library or through a command line interface. Here we describe the command line interface, which offers a convenient way to run the standard workflow of a sBayes analysis. To run sBayes from the command line, simply call:

sbayes <path_to_config_file>

The config file is a JSON file which contains all the settings for the analysis. The results are written to CSV files, which can be visualized using the plotting functions. The format of the config file and details about the set-up and visualization are described in the user manual.