R Observatory: Metrics for PheVis version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheVis

1.0.4Package record

Automatic Phenotyping of Electronic Health Record at Visit Resolution

0packages depend

3Kdownloads / year

76.9%test coverage

13/13flavors OK

Overview

About

Maintained by Thomas FerteCRAN 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.

Changes in 1.0.4

Patch

Correct test failure by increasing tolerance.

From NEWS.md in the release

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. 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-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). 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: 5.3 min · r-devel-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
OK14 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 147 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 25 (1 internal)includes a package overview page
Examples that run: 33%1 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

TutoPheVis HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #15,218 · ~8/day · ~249/mo

Releases R versions

Daily download trend is not available in this view yet.

31730 days

80590 days

3K1 year

Compare downloads with other packages →

Also on349 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing PheVis adds 50 packages (26 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, lme4 4.3 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Thomas Ferte

Author, Maintainer since 1.0.1 (2021)

Boris P. Hejblum

Author

Releases (4)

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
1.0.4Latest
record
2023-10-20 · current release · diff ↗
1.0.3
record
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
record
2021-02-23 · diff ↗
1.0.1
record
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

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 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 PheVis version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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