Westerfeld analyses

Accompanying repository. This repository contains the analysis scripts.

Getting started

The following few steps are necessary to get started.

Get the repository

Clone the repository with Git:

git clone https://github.com/laschuet/westerfeld_analyses.git

Alternatively, download and unzip the repository as a file.

Install Python dependencies

The scripts provided are written in Python 3.

We recommend using uv for managing all dependencies. Please follow the official installation instructions.

Create the project environment in the root directory of this repository:

uv sync

Get the dataset

Get the dataset from the BonaRes Repository for Soil and Agricultural Research Data.

Move the dataset into the root directory of this repository, i.e., the dataset should be located next to this README.

Analyses

Run the analyses:

uv run westerfeld/ncm.py

Using Docker

We provide a pre-build docker image which contains all necessary dependencies. This requires a docker installation.

Run the scripts usind docker run:

Analyses:

docker run \
-v /path/to/data:/app/input \
-v /path/to/results:/app/out \
ghcr.io/laschuet/westerfeld_analyses:latest westerfeld/ncm.py

Co-occurence network analysis:

docker run \
-v /path/to/data:/app/input \
-v /path/to/results:/app/out \
ghcr.io/laschuet/westerfeld_analyses:latest westerfeld/cooccurence.py

This maps both the data folder to /app/input and the results at /app/out.

Building Docker Image Manually

The docker image can also be build locally:

docker build -t westerfeld-analyses -f docker/Dockerfile .

To run this image, run the commands above but replace ghcr.io/laschuet/westerfeld_analyses:latest with westerfeld-analyses.

License

This work is licensed under the MIT License.