CPRD-analysis-package/README.Rmd at master · AGEexeter/CPRD-analysis-package · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

# CPRD-analysis-package

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This package provides functions to query a CPRD Aurum database on a local or remote MySQL server. It uses the dbplyr package (part of the tidyverse) to translate dplyr code into SQL. Analyses and outputs are run/stored on the remote server.


## Installation

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

``` r
# install.packages("devtools")
devtools::install_github("drkgyoung/Exeter_diabetes_aurum_package")
```

## Configuration

### Setup

Data and lookup MySQL tables are named as per data-raw/data-tables.yaml and data-raw/lookup-tables.yaml.

As per vignettes/getting-started.Rmd, users must make a configuration text file containing username, password and server details to connect to the MySQL server. The example below will use CPRD Aurum data in a MySQL database called 'cprd_data' and store outputs in a database called 'cprd_analysis_dev'.

```YAML
default:
  user: <mysql username>
  password: <sql password>
  server: "localhost"
  port: 3306

test-analysis:
  dataDatabase: cprd_data
  analysisDatabase: cprd_analysis_dev

test-remote:
  dataDatabase: cprd_data
  analysisDatabase: cprd_analysis_dev
  server: 127.0.0.1
  port: 3307

test-vpn:
  dataDatabase: cprd_data
  analysisDatabase: cprd_analysis_dev
  server: <dbserver>
  port: 3306
```

Use 'test-analysis' to connect to MySQL on a local server, 'test-remote' when to connect with MySQL on a remote server to which an SSH connection has been established, and 'test-vpn' to connect with MySQL on a remote server to which a VPN connection has been established.

Users can then connect by running e.g.

``` r
cprd = CPRDData$new(cprdEnv = "test-remote",cprdConf = "~/.aurum.yaml")
```
where ~/.aurum.yaml is the configuration file detailed above.

### Codelists

Codelists (e.g. of medcodeids or prodcodeids) for use with CPRD Aurum can be added and deleted from MySQL as outlined in vignettes/loading-and-using-codesets.Rmd. Codelists developed by the Exeter Diabetes team can be found at [CPRD-Codelists](https://github.com/Exeter-Diabetes/CPRD-Codelists).

### Analysis functions

Analysis functions e.g. computing and caching results are stored in CPRDAnalysis.R and explained in vignettes/setting-up-an-analysis.Rmd. These can only be executed when connected to a MySQL server.