Sex-disaggregated analysis of neutropenic fever in high-risk patients with hematological malignancies - a pooled re-analysis - analysis code

Analysis code in R accompanying the paper "Sex-disaggregated analysis of neutropenic fever in high-risk patients with hematological malignancies - a pooled re-analysis" by Alva Seltmann, Tobias Sachs, Karin Mayer, Corinna Hahn-Ast, Annamaria Brioli, Maria Madeleine Rüthrich, Peter Brossart, Andreas Hochhaus and Marie von Lilienfeld-Toal. Reproducible Environment Setup The original environment was set up using conda / mamba and the conda-env.yml file. After setting up conda / mamba on your system, navigate to the project directory containing conda-env.yml and use conda env create -f conda-env.yml to create the conda environment. For further details, check the conda documentation. Alternatively, we provide an environment setup via a nix flake. After setting up nix on your system, navigate to the project directory containing flake.nix and set up the environment andautostart a jupyter lab instance via nix develop For further details, check the nix documentation. Note: While constructing the nix flake, there were some build problems using the exact versions given in the original conda environment, thus we had to move to R 4.5.0. Also, some minor version differences are possible (e.g. officer 0.6.9 instead of 0.6.8). All results were reproducible using both approaches. Literate org mode document The analysis files are provided in the src-R directory. Additionally, we provide a literate org mode document (feb-neutro-reproduce.org) which references these scripts (via "transclusion", see the org-transclusion repository) and executes jupyter-R source blocks (see the emacs-jupyter repository). The org document provides an interactive way of executing scripts and saving the output, simular to a jupyter notebook. It also annotates the source files and makes it clear in which order to execute them to get to the desired outputs. For further details, check the org-mode documentation. Additionally, we provide a HTML export of the document (feb-neutro-reproduce.html), which is not interactive, but provides an easily accessible view of the literate document. Open this file in any browser. Output files We currently provide the raw .rds files of the tables, as well as the supplementary correlation plots in this repository. For .docx outputs and main and supplementary figures, we refer to the connected publication.