https://github.com/epiverse-trace/readepi
An R package for importing epi data into R.
https://github.com/epiverse-trace/readepi
data-import epidemiology epiverse health-information-systems r r-package
Last synced: 3 months ago
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An R package for importing epi data into R.
- Host: GitHub
- URL: https://github.com/epiverse-trace/readepi
- Owner: epiverse-trace
- License: other
- Created: 2022-08-23T12:34:04.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-10-28T14:21:02.000Z (12 months ago)
- Last Synced: 2024-10-28T17:20:37.997Z (12 months ago)
- Topics: data-import, epidemiology, epiverse, health-information-systems, r, r-package
- Language: R
- Homepage: https://epiverse-trace.github.io/readepi/
- Size: 22.5 MB
- Stars: 6
- Watchers: 7
- Forks: 5
- Open Issues: 12
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
---
output: github_document
editor_options:
markdown:
wrap: 72
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# readepi: Read data from health information systems 
[](https://opensource.org/license/mit/)
[](https://github.com/epiverse-trace/readepi/actions/workflows/R-CMD-check.yaml) [](https://app.codecov.io/gh/epiverse-trace/readepi?branch=main) [](https://www.reconverse.org/lifecycle.html#concept)
**{readepi}** is an R package for reading data from several health information systems (HIS) including public repositories, relational database management systems (RDBMS).
**{readepi}** currently supports reading data from the followings:
- RDBMS (Relational Database Management Systems) such as MS SQL, MySQL, and PostgreSQL\
- [REDCap](https://projectredcap.org/software/): Research Electronic Data Capture - a secure web application for building and managing online surveys and databases\
- [DHIS2](https://dhis2.org/about/): an open source and web-based platform for managing health information\
- [Fingertips](https://fingertips.phe.org.uk/): a repository of public health indicators in England
**{readepi}** returns a list object containing one or more data frames. **{readepi}** also has a number of auxiliary functions that allow importing a subset of the original dataset.
**{readepi}** is developed by [Epiverse-TRACE](https://data.org/initiatives/epiverse/) team at the [Medical Research Center, The Gambia unit at London School of Hygiene and Tropical Medicine](https://www.lshtm.ac.uk/research/units/mrc-gambia).
## Installation
You can install the development version of **{readepi}** from [GitHub](https://github.com/epiverse-trace/readepi) with:
```{r message=FALSE}
if (!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/readepi")
library(readepi)
```
## Quick start
The main function in **{readepi}** is `readepi()`. It reads data from a specified source. The `readepi()` function accepts a user-supplied string (the API's URL) as argument. Other specific arguments can be provided depending on the data source (see the **vignette** for more details). The examples below show how to use the `readepi()` function to import data from a variety of sources.
### Reading data from RDBMS and HIS
The `readepi()` function can import data from a variety of RDBMS, including MS SQL, MySQL, and PostgreSQL. Reading data from a RDBMS requires the following:
1. A MS SQL driver that is compatible with the version of DBMS of interest. The **vignette** describes how to install the appropriate driver for each database management system.\
2. Valid Credentials to access the server. The user credential details are expected to be stored in a file that will be supplied as an argument of the `readepi()` function. Use the `show_example_file()` function to visualize the structure of the template credential file.
Users can read data from a RDBMS by providing the details of the tables of interest or an SQL query (for more information, see the **vignette**).
```{r eval=FALSE}
# DEFINE THE PATH TO THE CREDENTIAL FILE
credentials_file <- system.file("extdata", "test.ini", package = "readepi")
# DISPLAY THE STRUCTUTRE OF THE TEMPLATE CREDENTIAL FILE
show_example_file()
# READING FILE FROM A PROJECT IN A REDCap DATABASE
dat <- readepi(
data_source = "https://bbmc.ouhsc.edu/redcap/api/",
credentials_file = credentials_file
)
project_data <- dat$data # accessing the actual data
project_metadeta <- dat$metadata # accessing the metadata associated with project
# VIEWING THE LIST OF ALL TABLES IN A MySQL DATABASE
show_tables(
data_source = "mysql-rfam-public.ebi.ac.uk",
credentials_file = credentials_file,
driver_name = "" # note that this example MySQL server does not require a driver
)
# VISUAIZE FIRST 5 ROWS OF THE TABLE 'AUTHOR'
visualise_table(
data_source = "mysql-rfam-public.ebi.ac.uk",
credentials_file = credentials_file,
from = "author", # this is the table name
driver_name = ""
)
# READING ALL FILEDS AND RECORDS FROM A MySQL SERVER
dat <- readepi(
data_source = "mysql-rfam-public.ebi.ac.uk",
credentials_file = credentials_file,
from = "author", # this is the table name
driver_name = ""
)
# READING DATA FROM DHIS2
dat <- readepi(
data_source = "https://play.dhis2.org/dev",
credentials_file = credentials_file,
dataset = "BfMAe6Itzgt",
organisation_unit = "Umh4HKqqFp6",
data_element_group = NULL,
start_date = "2014",
end_date = "2023"
)
# READING DATA FROM THE FINGERTIPS REPOSITORY
dat <- readepi(
indicator_id = 90362,
area_type_id = 202,
parent_area_type_id = 6 # optional
)
```
## Package Vignettes
The vignette of the **{readepi}** package contains detailed illustrations about the use of each function and the description of every argument. This can be accessed by typing the command below:
```{r eval=FALSE}
# OPEN THE VIGNETTE WITHIN RSTUDIO
vignette("readepi")
# OPEN THE VIGNETTE IN YOUR WEB BROWSER.
browseVignettes("readepi")
```
## Development
### Lifecycle
This package is currently a *maturing*, as defined by the [RECON software
lifecycle](https://www.reconverse.org/lifecycle.html). This means that it can be used in production with the understanding that the interface may still undergo minor changes.
### Contributions
Contributions are welcome via [pull requests](https://github.com/{{ gh_repo }}/pulls).
### Code of Conduct
Please note that the {{ packagename }} project is released with a
[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.