{"id":46252901,"url":"https://github.com/steno-aarhus/legliv","last_synced_at":"2026-03-03T22:38:39.014Z","repository":{"id":245874360,"uuid":"695145606","full_name":"steno-aarhus/legliv","owner":"steno-aarhus","description":"Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort 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of Red Meat with Legumes and Risk of Primary Liver Cancer in UK Biobank: A Cohort Study*\n\n-   Protocol:\n    [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11670569.svg)](https://doi.org/10.5281/zenodo.11670569)\n-   Preprint:\n    [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12666778.svg)](https://doi.org/10.5281/zenodo.12666778)\n-   Code:\n    [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12702170.svg)](https://doi.org/10.5281/zenodo.12702170)\n-   Paper:\n    [![DOI](https://img.shields.io/badge/DOI-10.3390%2Fnu16152383-blue?style=flat)](https://doi.org/10.3390/nu16152383)\n\nWith this project, we will statistically model replacement of red meat\nconsumption with legumes in relation to incident primary liver cancer\nand assess whether the association is mediated through non-alcoholic\nfatty liver disease (NAFLD).\n\nThis research project uses the UK Biobank Resource under Application\nNumber 81520.\n\n# Installing and setting up the project\n\nIf dependencies have been managed by using\n`usethis::use_package(\"packagename\")` through the `DESCRIPTION` file,\ninstalling dependencies is as easy as opening the `.Rproj` file and\nrunning this command in the console:\n\n``` r\npak::pak()\n```\n\nTo build the reports and papers to PDF, you'll need to install TinyTeX:\n\n``` r\ntinytex::install_tinytex()\n```\n\n## Steps to download the data and reproduce the analysis\n\nThe `data-raw/` folder contains the scripts to select, process, and\nprepare the data on the RAP to eventually be downloaded.\n\nThe steps to take to select the variables you want, create the CSV file\non the RAP and download to your project on RAP. The order is:\n\n1.  Select the variables you want in `data-raw/project-variables.csv`.\n2.  Follow the instructions in the `data-raw/create-data.R` script and\n    run it to create the CSV file on the RAP server.\n3.  Run `targets::tar_make()` to download the CSV file to `data/` and\n    get the project analysis to the current state.\n\n# Brief description of folder and file contents\n\nThe following folders contain:\n\n-   `data/`: Will contain the UK Biobank data (not saved to Git) as well\n    as the intermediate results output files.\n\n-   `data-raw/`: Contains the R script to download the data, as well as\n    the CSV files that contain the project variables and the variable\n    list as named in the RAP.\n\n-   `doc/`: This file contains the R Markdown, Word, or other types of\n    documents with written content, like the manuscript and protocol.\n\n-   `R/`: Contains the R scripts and functions to create the figures,\n    tables, and results for the project.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsteno-aarhus%2Flegliv","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsteno-aarhus%2Flegliv","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsteno-aarhus%2Flegliv/lists"}