R Observatory: Metrics for PheCAP version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheCAP

1.2.1

High-Throughput Phenotyping with EHR using a Common Automated Pipeline

0packages depend

2.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by PARSE LTDFirst published 2020-05-022 releasesCRAN page ↗GitHub ↗

Implement surrogate-assisted feature extraction (SAFE) and common machine learning approaches to train and validate phenotyping models. Background and details about the methods can be found at Zhang et al. (2019) doi:10.1038/s41596-019-0227-6, Yu et al. (2017) doi:10.1093/jamia/ocw135, and Liao et al. (2015) doi:10.1136/bmj.h1885.

Install

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

install.packages("PheCAP", 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("celehs/PheCAP")

Development version from celehs/PheCAP. 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-phecap

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-PheCAP

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: 5.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 240 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 89%
References docs: 9%

Downloads

2.8K

CRAN downloads in the past year

Rank #13,197 · ~8/day · ~233/mo

Releases R versions

Daily download trend is not available in this view yet.

18930 days

76490 days

2.8K1 year

Compare downloads with other packages →

Also on175 r2u

Repository

GitHub ↗ celehs/phecap

22Stars

1Forks

0Open issues

0Open PRs

1Releases

88Commits

5Contributors

88 commits · Last activity 2021-06-24 · -4.3% stars, 30d

Stars over time

2026-07-14 · 232026-08-10 · 22

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/celehs/phecap on 2026-08-16.

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (6)

graphicsmethodsstatsutilsglmnet RMySQL

LinkingTo (0)

none

Suggests (6)

ggplot2 e1071 randomForestSRC xgboost knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

PARSE LTD

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.1Latest
2020-09-17 · current release · diff ↗
unarchivedReturned to CRAN
2020-09-17
archivedRemoved from CRAN
2020-05-29
check problems were not corrected in time
1.1.0
2020-05-02
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-05-02
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.3.0
Bundled data: 1.5 MB / 2 files
Download size: 2.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PheCAP")

Format

PARSE LTD, , Cai, T., Hong, C., & Zhang, Y. (2020). PheCAP: High-Throughput Phenotyping with EHR using a Common Automated Pipeline (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.PheCAP

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 PheCAP version 1.2.1 [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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