epitest 0.1

Tests for detecting such epidemic aspects as contact-tracing, incubation and superspreading in transmission trees.

epitest

Quick non-parametric tests for detecting if such aspects as contact tracing, incubation, superspreading or transmission/detection rate changes over time are present in an epidemic represented by a time-scaled phylogenetic trees.

Input data

One needs to supply a time-scaled phylogenetic tree in newick format, or a collection of trees (one per line in the newick file), which will be treated as all belonging to the same epidemic.

Installation

There are 4 alternative ways to run epitest on your computer: with docker, apptainer, in Python3, or via command line (requires installation with Python3).

Run in python3 or command-line (for linux systems, recommended Ubuntu 21 or newer versions)

You could either install python (version 3.10 or higher) system-wide and then install epitest via pip:

sudo apt install -y python3 python3-pip python3-setuptools python3-distutils
pip3 install epitest

or alternatively, you could install python (version 3.10 or higher) and epitest via conda (make sure that conda is installed first). Here we will create a conda environment called epitestenv:

conda create --name epitestenv python=3.10
conda activate epitestenv
pip install epitest

Basic usage in a command line

If you installed epitest in a conda environment (here named epitestenv), do not forget to first activate it, e.g.

conda activate epitestenv

Run the following commands to check for the presence of contact tracing, superspreading, incubation, and changes in transmission and detection patterns over time in a given tree. Here we will use an early SARS-CoV-2 tree real_data/covid.resolved.nwk as an example. The command will produce a tab-separated file covid.resolved.epitest.tsv, containing the results of the tests (can be viewed with a text editor, Excel or Libre Office Calc). The results are presented as p-values, where the values lower than a certain threshold (e.g., 0.05) suggest the presence of the epidemic aspect in question (e.g., incubation).

epitest --nwk covid.resolved.nwk --log covid.resolved.epitest.tsv

Help

To see detailed options, run:

epitest --help

Run with docker

Basic usage

Once docker is installed, run the following command to to check for the presence of contact tracing, superspreading, incubation, and changes in transmission and detection patterns over time in a given tree:

docker run -v <path_to_the_folder_containing_the_tree>:/data:rw -t modpath/epitest --nwk /data/<tree_file>.nwk --log /data/<test_results>.tsv

This will produce a tab-separated file in the <path_to_the_folder_containing_the_tree> folder, containing the test results (can be viewed with a text editor, Excel or Libre Office Calc).

Help

To see advanced options, run

docker run -t modpath/epitest -h

Run with apptainer

Basic usage

Once apptainer is installed, run the following command to to check for the presence of contact tracing, superspreading, incubation, and changes in transmission and detection patterns over time in a given tree:

apptainer run docker://modpath/epitest --nwk <tree_file>.nwk --log <test_results>.tsv

This will produce a tab-separated file, containing the test results (can be viewed with a text editor, Excel or Libre Office Calc).

Help

To see advanced options, run

apptainer run docker://modpath/epitest -h