codemapper

R package for working with clinical codes

https://github.com/rmgpanw/codemapper

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (18.0%) to scientific vocabulary

Keywords

rpackage ukbiobank

Last synced: 6 months ago · JSON representation

Repository

R package for working with clinical codes

Basic Info

Host: GitHub
Owner: rmgpanw
License: other
Language: R
Default Branch: master
Homepage: https://rmgpanw.github.io/codemapper/
Size: 9.73 MB

Statistics

Stars: 3
Watchers: 1
Forks: 0
Open Issues: 2
Releases: 1

Topics

rpackage ukbiobank

Created almost 4 years ago · Last pushed 9 months ago

Metadata Files

Readme Contributing License Codemeta

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# codemapper



[![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)



The goal of codemapper is to facilitate working with clinical codes used in electronic health records. 

This 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.

## Installation

You can install the development version from [GitHub](https://github.com/) with:

```{r eval=FALSE}
# install.packages("devtools")
devtools::install_github("rmgpanw/codemapper")
```

## Basic example

A data analyst using electronic health records for research into hypertension may wish to build a list of clinical codes that capture this condition.

First, build a local resource containing lookup and mapping tables for various clinical codings systems. A dummy dataset is used here:

```{r example}
library(codemapper)

all_lkps_maps_dummy <- build_all_lkps_maps_dummy()
```

Look up Read 2 codes for hypertension:

```{r}
htn_read2 <- code_descriptions_like("Hypertension",
                       code_type = "read2",
                       all_lkps_maps = all_lkps_maps_dummy)

htn_read2
```

Map these to ICD10:

```{r}
htn_icd10 <- map_codes(
  codes = htn_read2$code,
  from = "read2",
  to = "icd10",
  all_lkps_maps = all_lkps_maps_dummy
)

htn_icd10
```

See `vignette('codemapper')` for further details, including how to build a clinical codelist with R Shiny using `RunCodelistBuilder()`.

## UK Biobank

Also included are functions for using CALIBER code lists (`vignette('caliber')`) and Phecodes (`vignette('phecodes')`) with UK Biobank data.

Owner

Login: rmgpanw
Kind: user

Repositories: 1
Profile: https://github.com/rmgpanw

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "codemapper",
  "description": "Functions for mapping between clinical coding systems.",
  "name": "codemapper: Functions for mapping between clinical coding systems",
  "relatedLink": "https://rmgpanw.github.io/codemapper/",
  "codeRepository": "https://github.com/rmgpanw/codemapper",
  "issueTracker": "https://github.com/rmgpanw/codemapper/issues",
  "license": "https://spdx.org/licenses/MIT",
  "version": "0.0.0.9001",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.2.0 (2022-04-22)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Alasdair",
      "familyName": "Warwick",
      "email": "alasdair.warwick06@gmail.com",
      "@id": "https://orcid.org/0000-0002-0800-2890"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Alasdair",
      "familyName": "Warwick",
      "email": "alasdair.warwick06@gmail.com",
      "@id": "https://orcid.org/0000-0002-0800-2890"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "covr",
      "name": "covr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=covr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "PheWAS",
      "name": "PheWAS",
      "sameAs": "https://github.com/PheWAS/PheWAS"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "shinytest",
      "name": "shinytest",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=shinytest"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "assertthat",
      "name": "assertthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=assertthat"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "DBI",
      "name": "DBI",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=DBI"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "magrittr",
      "name": "magrittr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=magrittr"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "purrr",
      "name": "purrr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=purrr"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "reactable",
      "name": "reactable",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=reactable"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "readr",
      "name": "readr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=readr"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "readxl",
      "name": "readxl",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=readxl"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "RSQLite",
      "name": "RSQLite",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=RSQLite"
    },
    "11": {
      "@type": "SoftwareApplication",
      "identifier": "shiny",
      "name": "shiny",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=shiny"
    },
    "12": {
      "@type": "SoftwareApplication",
      "identifier": "shinyFeedback",
      "name": "shinyFeedback",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=shinyFeedback"
    },
    "13": {
      "@type": "SoftwareApplication",
      "identifier": "stats",
      "name": "stats"
    },
    "14": {
      "@type": "SoftwareApplication",
      "identifier": "stringr",
      "name": "stringr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=stringr"
    },
    "15": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "16": {
      "@type": "SoftwareApplication",
      "identifier": "tidyr",
      "name": "tidyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidyr"
    },
    "17": {
      "@type": "SoftwareApplication",
      "identifier": "tidyselect",
      "name": "tidyselect",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidyselect"
    },
    "18": {
      "@type": "SoftwareApplication",
      "identifier": "ukbwranglr",
      "name": "ukbwranglr",
      "sameAs": "https://github.com/rmgpanw/ukbwranglr"
    },
    "19": {
      "@type": "SoftwareApplication",
      "identifier": "utils",
      "name": "utils"
    },
    "SystemRequirements": null
  },
  "fileSize": "1171852.156KB",
  "readme": "https://github.com/rmgpanw/codemapper/blob/master/README.md",
  "contIntegration": [
    "https://github.com/rmgpanw/codemapper/actions",
    "https://codecov.io/gh/rmgpanw/codemapper?branch=master",
    "https://github.com/rmgpanw/codemapper/actions"
  ],
  "keywords": [
    "rpackage",
    "ukbiobank"
  ]
}

GitHub Events

Total

Watch event: 2
Push event: 38
Create event: 1

Last Year

Watch event: 2
Push event: 38
Create event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 155
Total Committers: 3
Avg Commits per committer: 51.667
Development Distribution Score (DDS): 0.097

Past Year

Commits: 4
Committers: 1
Avg Commits per committer: 4.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
rmgpanw	r**w@u**k	140
Chuin Ying Ung	c**6@g**m	12
Alasdair Warwick	a**6@g**m	3

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 1

Issues and Pull Requests

Last synced: about 2 years ago

All Time

Total issues: 2
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 1
Total pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rmgpanw (2)

Pull Request Authors

Top Labels

Issue Labels

enhancement (1) bug (1)

Pull Request Labels

Dependencies

.github/workflows/check-standard.yaml actions

actions/cache v1 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite

.github/workflows/deploy-app.yml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

DESCRIPTION cran

DBI * imports
RSQLite * imports
assertthat * imports
dplyr * imports
magrittr * imports
purrr * imports
reactable * imports
readr * imports
readxl * imports
rlang * imports
shiny * imports
shinyFeedback * imports
stats * imports
stringr * imports
tibble * imports
tidyr * imports
tidyselect * imports
ukbwranglr * imports
utils * imports
PheWAS * suggests
covr * suggests
knitr * suggests
rmarkdown * suggests
shinytest * suggests
testthat >= 3.0.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

codemapper

Science Score: 46.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies