This repository contains code for the project “Improving research transparency with individualized report cards: A feasibility study in clinical trials at a large university medical center.”

📝 The manuscript is computationally reproducible using this repository. Note that a few manual formatting tweaks to tables and figures were done for the final published article. The manuscript is also available in HTML format.

To reproduce the manuscript:

1. Clone this repository
2. Run renv::restore() to ensure you have the necessary packages and versions
3. Knit manuscript.Rmd

📊 Personally identifiable information from the trial contacts and survey are kept local-only and are not provided in the data folders. Therefore, not all R scripts can be re-run using a clone of this repository. Additionally, communication-materials are kept locally, with only templates share publicly. The repository file tree below, .gitignore, and _environment.required provide additional details on local-only materials.

Repository File Tree

Note: Files related to renv are not shown below.

├── R
│   ├── 01_get-data.R
│   ├── 02_create-trial-sample.R
│   ├── 03_check-crossreg.R
│   ├── 04_get-euctr-data.R
│   ├── 05_check-oa.R
│   ├── 06_correct-trials.R
│   ├── 07_download-historical-registries.R
│   ├── 08_prep-contacts.R
│   ├── 09_render-communication-materials.R
│   ├── 10_check-email-logs.R
│   ├── 11_update-contacts.R
│   ├── 12_download-clean-survey.R
│   ├── 13_prepare-trials-practices.R
│   ├── functions.R
│   └── global.R
├── README.Rmd
├── _environment.local
├── _environment.required
├── analysis
│   ├── analyze-survey-text.R
│   ├── analyze-trials.R
│   ├── create-characteristics-table.R
│   ├── plot-survey-likert.R
│   ├── plot-survey-roles.R
│   ├── plot-survey-timeline.R
│   └── prepare-screening-flowcharts.R
├── communication-materials
│   ├── materials
│   │   ├── 0_email
│   │   ├── 0_letter
│   │   ├── 1_email
│   │   ├── 2_corrected_email
│   │   ├── 2_email
│   │   ├── 2_letter
│   │   └── 3_email
│   └── templates
│       ├── 0_email_multi.Rmd
│       ├── 0_email_one.Rmd
│       ├── 0_letter_multi.Rmd
│       ├── 0_letter_one.Rmd
│       ├── 1_email.Rmd
│       ├── 2_corrected_email.Rmd
│       ├── 2_email.Rmd
│       ├── 3_email.Rmd
│       ├── body-multi.Rmd
│       ├── body-one.Rmd
│       ├── quest-letterfoot.pdf
│       ├── quest-letterhead.pdf
│       ├── signature-email-csc.Rmd
│       ├── signature-email.Rmd
│       ├── signature-letter.pdf
│       └── template.html
├── data
│   ├── local
│   │   ├── contacts-pii.csv
│   │   ├── email-parameters.csv
│   │   ├── emails
│   │   │   ├── 0_email.txt
│   │   │   ├── 1_email.txt
│   │   │   ├── 2_email.txt
│   │   │   ├── 3_email.txt
│   │   │   └── autoreplies.txt
│   │   ├── survey-changes-comments.csv
│   │   ├── survey-corrections.csv
│   │   └── survey-raw.csv
│   ├── manual
│   │   ├── contacts
│   │   │   ├── charite-contacts-missing-email.csv
│   │   │   └── charite-contacts-missing-email_coded.csv
│   │   ├── crossreg
│   │   │   ├── cross-registrations_codebook.csv
│   │   │   ├── cross-registrations_extracted-msh.csv
│   │   │   ├── cross-registrations_extracted-sy.csv
│   │   │   ├── cross-registrations_reconciled.csv
│   │   │   ├── cross-registrations_to-extract.csv
│   │   │   └── pdfs
│   │   └── survey-text
│   │       ├── survey-changes-comments_coded.csv
│   │       ├── survey-changes-comments_to-code.csv
│   │       └── survey-email-corrections.csv
│   ├── processed
│   │   ├── contacts-analysis.csv
│   │   ├── contacts.csv
│   │   ├── email-delivery-info.csv
│   │   ├── oa-checks.csv
│   │   ├── survey-items.csv
│   │   ├── survey.csv
│   │   ├── trials-corrected.csv
│   │   ├── trials-crossreg-euctr-data.csv
│   │   ├── trials-crossreg.csv
│   │   ├── trials-filtered.csv
│   │   └── trials-practices.csv
│   ├── queries.log
│   ├── raw
│   │   ├── 2021-08-15_intovalue.csv
│   │   ├── 2022-11-01_intovalue.csv
│   │   ├── historical-ctgov.csv
│   │   ├── historical-drks.csv
│   │   ├── intovalue-crossreg.csv
│   │   ├── intovalue.csv
│   │   ├── open-access
│   │   │   ├── 2022-02-20_oa-unpaywall.csv
│   │   │   ├── 2022-08-20_oa-unpaywall.csv
│   │   │   └── 2023-05-08_oa-unpaywall.csv
│   │   └── survey-items.csv
│   └── timestamped
│       ├── 2022-05-25_trials-corrected.csv
│       ├── 2022-06-03_trials-corrected.csv
│       └── 2022-06-29_trials-corrected.csv
├── manuscript
│   ├── _extensions
│   │   └── pandoc-ext
│   │       └── abstract-section
│   │           ├── _extension.yaml
│   │           └── abstract-section.lua
│   ├── appendix.qmd
│   ├── elife.csl
│   ├── figures
│   │   ├── flowchart-practices.pdf
│   │   ├── flowchart-survey.pdf
│   │   ├── flowchart-trials.pdf
│   │   ├── flowchart.png
│   │   ├── infosheet.png
│   │   ├── pipeline-schematic.png
│   │   ├── report-card.png
│   │   ├── survey-likert-means.png
│   │   ├── survey-likert.png
│   │   ├── survey-roles.png
│   │   ├── survey-timeline.png
│   │   ├── tbl-characteristics.png
│   │   └── transparency-practices.png
│   ├── manuscript.html
│   ├── manuscript.qmd
│   └── references.bib
├── report-cards
│   ├── create-package.py
│   ├── gen-report-cards-merged.py
│   ├── gen-report-cards.py
│   ├── infosheet.pdf
│   ├── report-card-merged.afpub
│   ├── report-card-merged.svg
│   ├── report-card.afpub
│   ├── report-card.svg
│   └── requirements.txt
└── trackvalue.Rproj