IntoValue 2 Scripts

This repository contains the scripts accompanying the IntoValue2 publication (https://doi.org/10.1101/2021.08.05.21261624). The final, clean dataset generated during the two studies IntoValue 1 + 2 can also be found under https://zenodo.org/record/7633995. This Zenodo deposit also contains a zip file of the raw registry data used in both studies.

Description

The repository is structured into three blocks

• code: contains all the code files
  • 0_get_registry_data.R: script used to download and unzip raw registry data from Zenodo.
    • NOTE: If code-based download fails, please manually download the raw data:
      1. Navigate to https://doi.org/10.5281/zenodo.7633995
      2. Click "Download" by raw-registries.zip
      3. Move zip file to data directory in this project
    • NOTE: If code-based unzipping fails, please manually unzip the raw data:
      1. Navigate to data directory in this project
      2. Unzip raw-registries.zip (e.g., double click on MacOS)
  • 1_sample_generation: scripts involved in creating the trial samples
  • 2_dataset_cleaning: scripts involved in cleaning and combining the data to the final dataset after the manual publication search
  • 3_results analysis: scripts used to create the plots, tables and analyses used in the publication
  • 4_shiny_app: code & data necessary to run the Shiny app https://s-quest.bihealth.org/intovalue/
• data: data files used & generated by the scripts
  • 1_sample_generation: contains the search terms used to identify UMC trials as well as the generated samples
  • 2_dataset_cleaning: contains the results of the manual publication search, intermediate files used in the data cleaning process and the final dataset including readme and data dictionary
• output: contains the output figures & tables generated by the analysis scripts from the final dataset that were used in the publication

License

All analysis code is available under the MIT license. The final dataset is available under CC-BY license from https://doi.org/10.5281/zenodo.5141343. See the LICENSE file for more info.