README.Rmd

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output: github_document
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# 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.