R Observatory: Metrics for rplec version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rplec

0.1.3

Placental Epigenetic Clock to Estimate Aging by DNA Methylation

0packages depend

1.9Kdownloads / year

92.5%test coverage

13/13checks pass

Overview

About

Maintained by Herdiantri SufriyanaFirst published 2025-01-271 releasesCRAN page ↗

Placental epigenetic clock to estimate aging based on gestational age using DNA methylation levels, so called placental epigenetic clock (PlEC). We developed a PlEC for the 2024 Placental Clock DREAM Challenge (https://www.synapse.org/Synapse:syn59520082/wiki/628063). Our PlEC achieved the top performance based on an independent test set. PlEC can be used to identify accelerated/decelerated aging of placenta for understanding placental dysfunction-related conditions, e.g., great obstetrical syndromes including preeclampsia, fetal growth restriction, preterm labor, preterm premature rupture of the membranes, late spontaneous abortion, and placental abruption. Detailed methodologies and examples are documented in our vignette, available at https://herdiantrisufriyana.github.io/rplec/doc/placental_aging_analysis.html.

Install

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

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

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

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-rplec

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-rplec

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-rplec

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 8.0 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.20

92.5%

Coverage · measured lines

100%

Documentation · exports

13

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-10
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-03
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-07-01
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 479 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.9K

CRAN downloads in the past year

Rank #20,696 · ~5/day · ~157/mo

Releases R versions

Daily download trend is not available in this view yet.

16330 days

53290 days

1.9K1 year

Compare downloads with other packages →

Also on169 r2u

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4

Imports (13)

doParallel dplyr foreach ggplot2parallelpbapply purrr RPMMstatsstringr tibble tidyrutils

LinkingTo (0)

none

Suggests (3)

tidyverse knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Herdiantri Sufriyana

Author, Maintainer

Authors (2)

Herdiantri Sufriyana

Author, Maintainer

Emily Chia-Yu Su

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-01-27
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.4
Bundled data: 2.8 MB / 8 files
Download size: 3.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rplec")

Format

Sufriyana, H., & Su, E. C. (2025). rplec: Placental Epigenetic Clock to Estimate Aging by DNA Methylation (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.rplec

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 rplec version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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