readepi

1.0.6

Read Data from Relational Database Management Systems and Health Information Systems

0packages depend

78.3Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Bubacarr BahFirst published 2025-10-016 releasesCRAN page ↗GitHub ↗

Import Data from Relational Database Management Systems (RDBMS) and Health Information Systems ('HIS'). The current version of the package supports importing data from RDBMS including 'MS SQL', 'MySQL', 'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and 'SORMAS'.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("readepi", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("epiverse-trace/readepi")

Development version from epiverse-trace/readepi. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-readepi

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-readepi

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.21

0.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 467 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 19%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

78.3K

CRAN downloads in the past year

Rank #2,463 · ~214/day · ~6.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

35630 days

9.1K90 days

78.3K1 year

Compare downloads with other packages →

Also on82 r2u

Repository

GitHub ↗ epiverse-trace/readepi

6Stars

5Forks

4Open issues

1Open PRs

4Releases

377Commits

10Contributors

epidemiologyrr-packagedata-importepiversehealth-information-systems

377 commits · Last activity 2026-06-16

Stars over time

2024-06-01 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

9 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/epiverse-trace/readepi on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (11)

checkmate cli DBI dplyr httr2 odbc pool purrr RMySQL RSQLite tidyr

LinkingTo (0)

none

Suggests (7)

cyclocomp DiagrammeR httptest kableExtra knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,611 (57%)Rd 1,235 (27%)Vignettes 740 (16%)

Code characteristics

Cyclomatic complexity: 2.0 median / 7 max
Test cases: 20 / 0.21 per code line
System requirements: 2 external

Test coverage

Line coverage

Expression

0.0%

Tests / Examples

0.0% / 4% ex

Functions

38 16 exported

Complexity

2.7 avg / 7 max

Call network

38 nodes / 41 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

38 functions

Function	Cyclo	Coverage
dhis2_login exp	1	0%
get_api_version exp	1	0%
get_data_elements exp	1	0%
get_organisation_units exp	5	0%
get_program_org_units exp	2	0%
get_program_stages exp	7	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
lookup_table	data.frame	11 × 3	–
request_parameters	data.frame	3 × 12	–

People & History

People (11)

Maintainer (1)

Bubacarr Bah

Author, Maintainer

Authors (3)

Bubacarr Bah

Author, Maintainer

Emmanuel Kabuga

Author

Karim Mané

Author

Contributors (3)

Bankolé Ahadzie

Contributor

Abdoelnaser Degoot

Contributor

Nuredin Mohammed

Contributor

London School of Hygiene and Tropical Medicine, LSHTM

Funders (1)

data.org

Funder

Reviewers (3)

Hugo Gruson

Reviewer

Pratik Gupte

Reviewer

Andree Valle-Campos

Reviewer

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.6Latest
2026-04-23 · current release · diff ↗
1.0.5
2026-04-23 · diff ↗
1.0.4
2026-01-29 · diff ↗
1.0.3
2025-10-29 · diff ↗
1.0.2
2025-10-27 · diff ↗
1.0.1
2025-10-01
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-01
Total releases: 6 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 0.7 KB / 2 files
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →