This is a scoping review of the methods applied for the calculation of the probability of causation (PoC) or assigned share of a disease or health outcome due to an (occupational) exposure. The main interests are on uses for lung cancer and its financial compensation in the context of occupational exposures, although flexibility will be allowed within the framework of a scoping review to gain further insight into the concept, methods, and potential alternatives in other use cases.
This study is preregistered in the Open Science Framework: https://doi.org/10.17605/OSF.IO/9EVSY
The suggested use of this repository starts with making sure that R and RStudio are installed in your computer:
- Install R and RStudio on your computer if you haven't done so. (Note that these analyses were conducted under R version 4.4.0 and RStudio 2024.04.0).
- Clone this repository. If you do not know how to do this, you can follow these instructions. Alternatively, you can download the ZIP file, unpack it, and place it in a folder in your computer.
- You should now have all these files in your computer with an identical folder structure (described in the following section).
- In the main directory, open the file named PoC-scoping-review.Rproj in RStudio.
- You can navigate through the folders on the right-bottom panel of R Studio. Open the R folder. You should now see a series of files ending with .qmd.
- Open one of the .qmd files. You can run every chunk of code sequentially to reproduce the analyses. Make sure to respect the order and if something fails, I recommend that you start running al chunks of code from the beginning. If you don't know how to run a chunk of code, you can imitate what this person is doing. If you get a message saying "Access denied", change from Visual to Source mode which can be done with the Ctrl+Shift+F4 command.
- Please note that scripts are meant to be sourced into the flow of analyses in the main .qmd files. You may encounter problems if you attempt to run the scripts independently.
If you are not able to follow the prior steps, you may also consider reviewing the documents explaining and documenting the analyses.
Although I have made significant efforts to ensure reproducibility of this project, I encourage you to contact me or post a request in this repository in case you encounter any issues.
Available in the docs/protocol folder.
The project structure distinguishes three kinds of folders:
- read-only (RO): not edited by either code or researcher
- human-writeable (HW): edited by the researcher only.
- project-generated (PG): folders generated when running the code; these folders can be deleted or emptied and will be completely reconstituted as the project is run.
.
├── .gitignore
├── CITATION.cff
├── LICENSE
├── README.md
├── PoC-scoping-review.Rproj
├── asreview <- ASReview project and data files (RO)
├── data <- All project data files, hidden by default.
│ ├── processed <- The final, canonical data sets for modeling. (PG)
│ ├── raw <- The original, immutable data. (RO)
│ └── temp <- Intermediate data that has been transformed. (PG)
├── docs <- Documentation for users (HW)
│ ├── manuscript <- Manuscript source, docx, html. (HW)
│ ├── presentations <- Presentations, pptx, pdf. (HW)
│ ├── protocol <- Protocol versions, docx. (HW)
│ ├── search_query <- Search query documentation, txt, csv, html. (HW)
│ └── reports <- Project reports, pdf. (HW)
├── results
│ ├── output_figures <- Figures for the manuscript or reports (PG)
│ └── output_tables <- Output tables for the manuscript (PG)
└── R <- Source code for this project (HW)
├── scripts <- Scripts sourced in main R markdown documents (PG)
└── sessions <- Text files with information of R sessions (PG)
This project is licensed under the terms of the MIT License by Utrecht University and Lexces.
For all uses related to Lexces, please refer to their copyright notice.
This project structure repository is adapted from the Utrecht University simple R project template, which builds upon the Good Enough Project Cookiecutter template by Barbara Vreede (2019).