{"id":31741546,"url":"https://github.com/rmgpanw/codemapper","last_synced_at":"2025-10-09T10:53:06.663Z","repository":{"id":119298768,"uuid":"485945478","full_name":"rmgpanw/codemapper","owner":"rmgpanw","description":"R package for working with clinical codes","archived":false,"fork":false,"pushed_at":"2025-07-15T10:12:53.000Z","size":10217,"stargazers_count":3,"open_issues_count":3,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-05T05:16:24.606Z","etag":null,"topics":["rpackage","ukbiobank"],"latest_commit_sha":null,"homepage":"https://rmgpanw.github.io/codemapper/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rmgpanw.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2022-04-26T20:57:55.000Z","updated_at":"2025-03-10T22:38:05.000Z","dependencies_parsed_at":"2023-10-14T17:03:10.316Z","dependency_job_id":"b4ce96cd-0911-444d-be21-4f12c7ede34d","html_url":"https://github.com/rmgpanw/codemapper","commit_stats":{"total_commits":155,"total_committers":3,"mean_commits":"51.666666666666664","dds":0.09677419354838712,"last_synced_commit":"6a07af611bd50c7dfbc5cac73967a98c1ef0defb"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/rmgpanw/codemapper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rmgpanw%2Fcodemapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rmgpanw%2Fcodemapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rmgpanw%2Fcodemapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rmgpanw%2Fcodemapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rmgpanw","download_url":"https://codeload.github.com/rmgpanw/codemapper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rmgpanw%2Fcodemapper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279001269,"owners_count":26083040,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-09T02:00:07.460Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["rpackage","ukbiobank"],"created_at":"2025-10-09T10:53:05.327Z","updated_at":"2025-10-09T10:53:06.658Z","avatar_url":"https://github.com/rmgpanw.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# codemapper\n\n\u003c!-- badges: start --\u003e\n\n[![R-CMD-check](https://github.com/rmgpanw/codemapper/workflows/R-CMD-check/badge.svg)](https://github.com/rmgpanw/codemapper/actions) [![Codecov test coverage](https://codecov.io/gh/rmgpanw/codemapper/branch/master/graph/badge.svg)](https://codecov.io/gh/rmgpanw/codemapper?branch=master) [![pkgdown](https://github.com/rmgpanw/codemapper/workflows/pkgdown/badge.svg)](https://github.com/rmgpanw/codemapper/actions) [![Launch RStudio Cloud](https://img.shields.io/badge/RStudio-Cloud-blue)](https://rstudio.cloud/project/4007004) [![DOI](https://zenodo.org/badge/485945478.svg)](https://zenodo.org/badge/latestdoi/485945478) [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)\n\n\u003c!-- badges: end --\u003e\n\nThe goal of codemapper is to facilitate working with clinical codes used in electronic health records. \n\nThis package relies primarily on UK Biobank resource 592 ([Clinical coding classification systems and maps](https://biobank.ndph.ox.ac.uk/ukb/refer.cgi?id=592)) and the UK Biobank [data codings file](https://biobank.ctsu.ox.ac.uk/crystal/exinfo.cgi?src=accessing_data_guide), both of which are publicly available.\n\n## Installation\n\nYou can install the development version from [GitHub](https://github.com/) with:\n\n```{r eval=FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"rmgpanw/codemapper\")\n```\n\n## Basic example\n\nA data analyst using electronic health records for research into hypertension may wish to build a list of clinical codes that capture this condition.\n\nFirst, build a local resource containing lookup and mapping tables for various clinical codings systems. A dummy dataset is used here:\n\n```{r example}\nlibrary(codemapper)\n\nall_lkps_maps_dummy \u003c- build_all_lkps_maps_dummy()\n```\n\nLook up Read 2 codes for hypertension:\n\n```{r}\nhtn_read2 \u003c- code_descriptions_like(\"Hypertension\",\n                       code_type = \"read2\",\n                       all_lkps_maps = all_lkps_maps_dummy)\n\nhtn_read2\n```\n\nMap these to ICD10:\n\n```{r}\nhtn_icd10 \u003c- map_codes(\n  codes = htn_read2$code,\n  from = \"read2\",\n  to = \"icd10\",\n  all_lkps_maps = all_lkps_maps_dummy\n)\n\nhtn_icd10\n```\n\nSee `vignette('codemapper')` for further details, including how to build a clinical codelist with R Shiny using `RunCodelistBuilder()`.\n\n## UK Biobank\n\nAlso included are functions for using CALIBER code lists (`vignette('caliber')`) and Phecodes (`vignette('phecodes')`) with UK Biobank data.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frmgpanw%2Fcodemapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frmgpanw%2Fcodemapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frmgpanw%2Fcodemapper/lists"}