CCD package for python

Simple implementation of conditional clade distributions in python.

Currently WIP

• Add CCD0 and CCD2
• WIP transmission tree CCDs from BREATH BEAST2 package

Usage

tCCD MAP tree

This package provide a command line interface to compute the tCCD MAP tree. The tool is called transcope and for more information install the package and run

transcope --help

WIW dates data extraction

Note

A detailed example for this tool can be found here

A commandline tool to extract date information about who-infected-whom. After installation you can get more information by running

datesWIW --help

This tool will create a CSV file with the following columns [Infector, Infectee, Start Date of infection, blockcount, Tree index]

The tree index is corrected for burnin and reflect the index of a tree in the input file without burin removed.

To convert the tree distances to dates we need the taxon labels to have date information. The default assumption is that the tip labels are foramted like this:

ID+YYYY-MM-DD
2+2007-11-01

Caution

Use the flags --date-sep and --date-format to specify your layout Be aware that using a separator that is also present in the date format will not work!

Important

It is also currently assumed that the float scale is in years, i.e. 1.0 branch length equals 1 year

Installation

A pre-release can be installed with

pip install https://github.com/Lars-B/pyccd/releases/download/v1.0.0-alpha/pyccd-0.1.0-py3-none-any.whl

Building from source

This uses the hatchling backend for building the package. Clone the repository and then cd into the folder and run

python -m build

which will build the packge wheel file. You can then use pip to install the freshly build package.

pip install dist/*.whl

Or alternatively after cloning the repository install directly with the following:

pip install .