R Observatory: Metrics for PheVis version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheVis

1.0.4

Automatic Phenotyping of Electronic Health Record at Visit Resolution

0packages depend

2.7Kdownloads / year

76.9%test coverage

13/13checks pass

Overview

About

Maintained by Thomas FerteFirst published 2021-02-164 releasesCRAN page ↗

Using Electronic Health Record (EHR) is difficult because most of the time the true characteristic of the patient is not available. Instead we can retrieve the International Classification of Disease code related to the disease of interest or we can count the occurrence of the Unified Medical Language System. None of them is the true phenotype which needs chart review to identify. However chart review is time consuming and costly. 'PheVis' is an algorithm which is phenotyping (i.e identify a characteristic) at the visit level in an unsupervised fashion. It can be used for chronic or acute diseases. An example of how to use 'PheVis' is available in the vignette. Basically there are two functions that are to be used: `train_phevis()` which trains the algorithm and `test_phevis()` which get the predicted probabilities. The detailed method is described in preprint by Ferté et al. (2020) doi:10.1101/2020.06.15.20131458.

Install

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

install.packages("PheVis", 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-phevis

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-PheVis

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-PheVis

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

Health

CRAN checks

13OK

Slowest check: 5.2 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.06

76.9%

Coverage · measured lines

100%

Documentation · exports

12

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
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 147 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #16,217 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

13930 days

65190 days

2.7K1 year

Compare downloads with other packages →

Also on388 r2u20 autocran

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (12)

dplyr ggplot2 glmnet knitr lme4 purrr randomForest Rcppstatstidyr viridis zoo

LinkingTo (1)

Rcpp

Suggests (3)

PRROC rmarkdown 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)

Thomas Ferte

Author, Maintainer

Authors (2)

Thomas Ferte

Author, Maintainer

Boris P. Hejblum

Author

Package Timeline

4 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
1.0.4Latest
2023-10-20 · current release · diff ↗
1.0.3
2023-09-21 · diff ↗
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
1.0.2
2021-02-23 · diff ↗
1.0.1
2021-02-16
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-16
Total releases: 4 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 257 KB / 2 files
Download size: 329 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PheVis")

Format

Ferte, T., & Hejblum, B. P. (2023). PheVis: Automatic Phenotyping of Electronic Health Record at Visit Resolution (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.PheVis

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 PheVis version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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