R Observatory: Metrics for eHDPrep version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

eHDPrep

2.0.1Package record

Quality Control and Semantic Enrichment of Datasets

0packages depend

3.5Kdownloads / year

51.0%test coverage

13/13flavors OK

Overview

About

Maintained by Ian OvertonCRAN page ↗GitHub ↗Issues ↗

A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) doi:10.1093/gigascience/giad030). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.

Changes in 2.0.1

Added Kluivert Boakye Duah as package author.
Updated the quality control workflow to include impute_missing_values().

From NEWS.md in the release

Install

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

install.packages("eHDPrep", 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("overton-group/eHDPrep")

Development version from overton-group/eHDPrep. 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-ehdprep

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-eHDPrep

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-eHDPrep

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 10.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-12

Show 2 earlier changesHide 2 earlier changes

WARNING12 OK, 1 WARNING2026-05-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 126 wordsVignettesYes · 1 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 2.0.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 72 (2 internal)includes a package overview page
Examples that run: 98%48 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 17%

Vignettes (1)

Introduction to eHDPrep

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #8,139 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

53130 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on729 r2u5 autocran

How downloads are counted

Repository

overton-group/ehdprep ↗Organization: overton-group

8Stars

3Forks

1Open issues

0Open PRs

5Releases

115Commits

4Commit identities

health-informaticsrdata-qualitysemantic-enrichment

License file reads as GPL-3.0 · 115 commits · Last activity 2026-09-22

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-03-23 · 72026-07-07 · 8

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/overton-group/ehdprep on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing eHDPrep adds 83 packages (45 with compiled code, 78 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.6.0

Imports (20)

ggplot2 dplyr forcats stringr purrr tidyr kableExtra magrittr tibble scales rlang quanteda tm pheatmap igraph tidygraph readr readxl knitr (>= 1.31)tidyselect

LinkingTo (0)

none

Suggests (4)

testthat ggraph rmarkdown VIM

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Ian Overton

Author, Maintainer since 1.2.1 (2022)

Kluivert Boakye Duah

Author · added in 2.0.1

Tom Toner

Author

Releases (7)

Pick two releases to compare their code metrics.

2.0.1Latest
record
2026-10-21 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-21 10:55 UTC, so it stayed less than the time between readings.
2.0.0
record
2026-09-22 · diff ↗ ·
added 3 exports
coerce_dates, coerce_numeric_vars, impute_missing_values
R
R 4.6.0 released · 2026-04-24
1.4.0
record
2026-02-20 · diff ↗
1.3.4
record
2025-09-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.3.3
record
2023-06-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.2
record
2023-02-01 · diff ↗ ·
added 2 exports
edge_tbl_to_graph, metavariable_variable_descendants
1.2.1
record
2022-09-07
R
R 4.2.0 released · 2022-04-22

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2022-09-07
Total releases: 7 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 26 KB / 4 files
Download size: 2.4 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("eHDPrep")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/gigascience/giad030.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for eHDPrep version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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