R Observatory: Metrics for PheCAP version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheCAP

1.2.1Package record

High-Throughput Phenotyping with EHR using a Common Automated Pipeline

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by PARSE LTDCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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

CRAN check page ↗

Slowest check: 5.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 240 wordsVignettesYes · 5 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 11includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 9%

Vignettes (5)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #17,776 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

26830 days

71890 days

2.8K1 year

Compare downloads with other packages →

Also on105 r2u

How downloads are counted

Repository

celehs/phecap ↗Account: celehs

22Stars

1Forks

1Open issues

0Open PRs

1Releases

88Commits

5Commit identities

88 commits · Last activity 2021-02-23 · 0% stars, 30d · Default branch at 1.2.2, ahead of CRAN 1.2.1 (checked 2026-10-18)

Responsiveness

not measured

Stars over time

2026-07-14 · 232026-08-10 · 22

How these are measured

PracticesBeta

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

Checks run against github.com/celehs/phecap on 2026-10-18.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2021-02-23

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing PheCAP adds 8 packages (4 with compiled code, 7.9 MB of source tarballs). Heaviest: glmnet 2.7 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

PARSE LTD

Author, Maintainer since 1.1.0 (2020)

Tianxi Cai

Author

Chuan Hong

Author

Yichi Zhang

Author

Releases (2)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2020-09-17
1.2.1Latest
record
2020-09-17 · current release · diff ↗
archivedRemoved from CRAN
2020-05-29
check problems were not corrected in time
1.1.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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