https://github.com/rmgpanw/codemapper

R package for working with clinical codes
https://github.com/rmgpanw/codemapper

rpackage ukbiobank

Last synced: 8 months ago
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R package for working with clinical codes

• Host: GitHub
• URL: https://github.com/rmgpanw/codemapper
• Owner: rmgpanw
• License: other
• Created: 2022-04-26T20:57:55.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2025-07-15T10:12:53.000Z (11 months ago)
• Last Synced: 2025-09-05T05:16:24.606Z (9 months ago)
• Topics: rpackage, ukbiobank
• Language: R
• Homepage: https://rmgpanw.github.io/codemapper/
• Size: 9.74 MB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Codemeta: codemeta.json

Awesome Lists containing this project

README

          
---

output: github_document

---

```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```

# codemapper

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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.