Getting started with TreePPL
We have developed R and Python interfaces to facilitate installation, data preparation, program compilation and execution, post-processing, and visualization of inference results. We strive to provide the same functionalities in R and Python, but there might be small differences between the two interfaces because the project is under active development.
If you want to contribute to TreePPL development, see Instructions for developers.
We currently support Linux and MacOS only. For Windows users there are two options: use a virtual machine/server/cluster or use TreePPL with WSL (see Windows installation instructions).
For R users
When you install the R package treepplr, TreePPL and everything it requires is also installed. For that, run within R or RStudio:
devtools::install_github("treeppl/treepplr")
treepplr converts data to a format readable by TreePPL, reads the TreePPL output, and connects to downstream analyses in model-specific packages, such as the evolnets package for the host repertoire evolution model.
For complete treepplr documentation, see treepplr. There you will find the complete list of package functions (Reference) and all vignettes (Articles).
For Python users
TreePPL can also be installed with the package treeppl-python. For that, got to list of releases and download the wheel from the most recent release for your operating system. Then, run within Python:
pip install name-of-file.whl
For more information, check treeppl-python Github repository.