readepi

An R package for importing epi data into R.

https://github.com/epiverse-trace/readepi

Science Score: 54.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
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Committers with academic emails
2 of 9 committers (22.2%) from academic institutions
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Low similarity (21.0%) to scientific vocabulary

Keywords

data-import epidemiology epiverse health-information-systems r r-package

Keywords from Contributors

best-practices internal-docs onboarding r-package-development standard-operating-procedure standards

Last synced: 6 months ago · JSON representation ·

Repository

An R package for importing epi data into R.

Basic Info

Host: GitHub
Owner: epiverse-trace
License: other
Language: R
Default Branch: main
Homepage: https://epiverse-trace.github.io/readepi/
Size: 19.9 MB

Statistics

Stars: 6
Watchers: 6
Forks: 5
Open Issues: 14
Releases: 1

Topics

data-import epidemiology epiverse health-information-systems r r-package

Created over 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
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 


[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
[![R-CMD-check](https://github.com/epiverse-trace/readepi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/readepi/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/epiverse-trace/readepi/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/readepi?branch=main) [![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-maturing.svg)](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.

Owner

Name: Epiverse-TRACE
Login: epiverse-trace
Kind: organization

Website: https://epiverse.org
Repositories: 17
Profile: https://github.com/epiverse-trace

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "readepi" in publications use:'
type: software
license: MIT
title: 'readepi: Read Data from Health Information Systems'
version: 0.1.0
abstract: Data import from several health information systems ('HIS'). The current
  version of the package covers 'HIS' such as 'MS SQL', 'MySQL', and 'PostGRESQL'
  servers, 'REDCap', 'DHIS2' and 'Fingertips'.
authors:
- family-names: Mané
  given-names: Karim
  email: karim.mane@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-9892-2999
preferred-citation:
  type: manual
  title: Read Data From Health Information Systems
  authors:
  - family-names: Mané
    given-names: Karim
    email: karim.mane@lshtm.ac.uk
    orcid: https://orcid.org/0000-0002-9892-2999
  - family-names: Mohammed
    given-names: Nuredin
  - family-names: Bah
    given-names: Bubacarr
  - family-names: Ahadzie
    given-names: Bankolé
  - family-names: Degoot
    given-names: Abdoelnaser
  year: '2023'
  url: https://github.com/epiverse-trace/readepi
repository-code: https://github.com/epiverse-trace/readepi
url: https://epiverse-trace.github.io/readepi/
contact:
- family-names: Mané
  given-names: Karim
  email: karim.mane@lshtm.ac.uk
  orcid: https://orcid.org/0000-0002-9892-2999
keywords:
- data-import
- epidemiology
- epiverse
- health-information-systems
- r
- r-package
references:
- type: software
  title: checkmate
  abstract: 'checkmate: Fast and Versatile Argument Checks'
  notes: Imports
  url: https://mllg.github.io/checkmate/
  repository: https://CRAN.R-project.org/package=checkmate
  authors:
  - family-names: Lang
    given-names: Michel
    email: michellang@gmail.com
    orcid: https://orcid.org/0000-0001-9754-0393
  year: '2024'
- type: software
  title: DBI
  abstract: 'DBI: R Database Interface'
  notes: Imports
  url: https://dbi.r-dbi.org
  repository: https://CRAN.R-project.org/package=DBI
  authors:
  - name: R Special Interest Group on Databases (R-SIG-DB)
  - family-names: Wickham
    given-names: Hadley
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2024'
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2024'
- type: software
  title: fingertipsR
  abstract: 'fingertipsR: Fingertips Data for Public Health'
  notes: Imports
  url: https://fingertips.phe.org.uk
  authors:
  - family-names: Westermann
    given-names: Annabel
    email: annabel.westermann@dhsc.gov.uk
  - family-names: Fox
    given-names: Sebastian
    email: sebsfox@gmail.com
  - family-names: Nanayakkara
    given-names: Hadley
    email: hadley.nanayakkara@dhsc.gov.uk
  - family-names: Flowers
    given-names: Julian
  year: '2024'
  version: '>= 1.0.10.9001'
- type: software
  title: glue
  abstract: 'glue: Interpreted String Literals'
  notes: Imports
  url: https://glue.tidyverse.org/
  repository: https://CRAN.R-project.org/package=glue
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2024'
- type: software
  title: httr2
  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
  notes: Imports
  url: https://httr2.r-lib.org
  repository: https://CRAN.R-project.org/package=httr2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
- type: software
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  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  url: https://magrittr.tidyverse.org
  repository: https://CRAN.R-project.org/package=magrittr
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2024'
- type: software
  title: odbc
  abstract: 'odbc: Connect to ODBC Compatible Databases (using the DBI Interface)'
  notes: Imports
  url: https://odbc.r-dbi.org
  repository: https://CRAN.R-project.org/package=odbc
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Gjoneski
    given-names: Oliver
  year: '2024'
- type: software
  title: pool
  abstract: 'pool: Object Pooling'
  notes: Imports
  url: http://rstudio.github.io/pool/
  repository: https://CRAN.R-project.org/package=pool
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Borges
    given-names: Barbara
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
- type: software
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  abstract: 'REDCapR: Interaction Between R and REDCap'
  notes: Imports
  url: https://ouhscbbmc.github.io/REDCapR/
  repository: https://CRAN.R-project.org/package=REDCapR
  authors:
  - family-names: Beasley
    given-names: Will
    email: wibeasley@hotmail.com
    orcid: https://orcid.org/0000-0002-5613-5006
  year: '2024'
- type: software
  title: RMySQL
  abstract: 'RMySQL: Database Interface and ''MySQL'' Driver for R'
  notes: Imports
  url: https://downloads.mariadb.org/connector-c/
  repository: https://CRAN.R-project.org/package=RMySQL
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: James
    given-names: David
  - family-names: DebRoy
    given-names: Saikat
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Horner
    given-names: Jeffrey
  year: '2024'
- type: software
  title: DiagrammeR
  abstract: 'DiagrammeR: Graph/Network Visualization'
  notes: Suggests
  url: https://rich-iannone.github.io/DiagrammeR/
  repository: https://CRAN.R-project.org/package=DiagrammeR
  authors:
  - family-names: Iannone
    given-names: Richard
    email: riannone@me.com
    orcid: https://orcid.org/0000-0003-3925-190X
  - family-names: Roy
    given-names: Olivier
    email: olivierroy71@hotmail.com
  year: '2024'
- type: software
  title: httptest
  abstract: 'httptest: A Test Environment for HTTP Requests'
  notes: Suggests
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  repository: https://CRAN.R-project.org/package=httptest
  authors:
  - family-names: Richardson
    given-names: Neal
    email: neal.p.richardson@gmail.com
    orcid: https://orcid.org/0009-0002-7992-3520
  year: '2024'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  version: '>= 3.0.0'
identifiers:
- type: url
  value: https://github.com/epiverse-trace/readepi/

GitHub Events

Total

Issues event: 2
Delete event: 5
Issue comment event: 2
Push event: 11
Pull request review event: 2

Last Year

Issues event: 2
Delete event: 5
Issue comment event: 2
Push event: 11
Pull request review event: 2

Committers

Last synced: 9 months ago

All Time

Total Commits: 229
Total Committers: 9
Avg Commits per committer: 25.444
Development Distribution Score (DDS): 0.371

Past Year

Commits: 28
Committers: 4
Avg Commits per committer: 7.0
Development Distribution Score (DDS): 0.214

Top Committers

Name	Email	Commits
Karim-Mane	k**e@o**m	144
Hugo Gruson	B****o	19
Thibaut Jombart	t**t@g**m	18
GitHub Action	a**n@g**m	18
Karim Mane	k**e@i**l	17
Karim Mane	k**e@L**l	8
banky	4****e	2
=	d**t@a**a	2
Abdoelnaser M Degoot	d**t@a**a	1

Committer Domains (Top 20 + Academic)

aims.ac.za: 1 aimsa.ac.za: 1 github.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 51
Total pull requests: 31
Average time to close issues: 3 months
Average time to close pull requests: about 1 month
Total issue authors: 8
Total pull request authors: 5
Average comments per issue: 0.84
Average comments per pull request: 1.23
Merged pull requests: 21
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: 2
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

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Issue Authors

Karim-Mane (21)
avallecam (10)
Bisaloo (8)
adamkucharski (4)
bahadzie (2)
pratikunterwegs (1)
avinashladdha (1)
wibeasley (1)

Pull Request Authors

Karim-Mane (22)
Bisaloo (12)
Degoot-AM (3)
bahadzie (2)
pitmonticone (1)

Top Labels

Issue Labels

enhancement (13) help wanted (3) Full review (1) documentation (1)

Pull Request Labels

documentation (2) bug (2) enhancement (2)

Dependencies

DESCRIPTION cran

checkmate * imports
covr * suggests
testthat >= 3.0.0 suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/render_readme.yml actions

actions/checkout v2 composite
ad-m/github-push-action master composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/test-coverage.yaml actions

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

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Data

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Open Source Science

readepi

Science Score: 54.0%

Keywords

Keywords from Contributors

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README.Rmd

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