Overview

This repository contains computational analysis used in Horste et al., Mol. Cell, 2023 (PMID: 38134885).

Organization

The folders in the repository have the following purposes:

• analysis - primary source code and rendered HTMLs of R Markdown
• data - input data needed to run the code
• envs - Conda environment YAML files for recreating the execution environment
• img - output images
• tbl - output tables

All code is expected to be executed with this repository as the present working directory. If opening as an R Project in RStudio, make sure to set the Project folder as the working directory.

Source Code

The primary source code is found in the analysis folder. Folders and files are numbered in the expected order of execution. The outputs of the 01-preprocess files are already included in the data folder, and therefore are not needed to be rerun. Anyone wishing to do further analysis or replicate the models should be able to immediately run the 03-models files.

Input Data

The data folder contains the input data. We provide clean versions of the tables corresponding to the output of the scripts in 01-preprocess. Raw data versions (needed to run the 01-preprocess code) can be provided upon reasonable request.

Execution Environment

The R instance used to execute the files is captured both in the rendered RMDs themselves (see Runtime Details section in HTMLs) and provided as YAML files in the envs folder.

To recreate on arbitrary platforms (Linux or MacOS), we recommend using Micromamba and the minimal YAML (*.min.yaml):

micromamba create -n brms_r41 -f envs/brms_r41.min.yaml
micromamba activate brms_r41

A fully-solved environment capture is also provided (*.full.yaml). This is only expected to recreate on the osx-64 platform and is primarly intended for exact replication and a statement of record.

Outputs

The img and tbl folders have output files that the source code will generate. The analysis folder also has HTML renders of the R Markdown files.