R Observatory: Metrics for EHR version 0.4-11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EHR

0.4-11Package record

Electronic Health Record (EHR) Data Processing and Analysis Tool

0packages depend

3.5Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Leena ChoiCRAN page ↗Website ↗

Process and analyze electronic health record (EHR) data. The 'EHR' package provides modules to perform diverse medication-related studies using data from EHR databases. Especially, the package includes modules to perform pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden, Stein, Bejan, Denny, and Van Driest (2020) doi:10.1002/cpt.1787. Additional modules will be added in future. In addition, this package provides various functions useful to perform Phenome Wide Association Study (PheWAS) to explore associations between drug exposure and phenotypes obtained from EHR data, as outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018) doi:10.1093/bioinformatics/bty306.

Install

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

install.packages("EHR", 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-ehr

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-EHR

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-EHR

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) build_lastdose.Rd:10: Lost braces
    10 | code{build_lastdose}: build PK oral with lastdose information
       |     ^
checkRd: (-1) mod-internal.Rd:18: Lost braces
    18 | code{colflow_mod}: build a comparison of potentially duplicate flow data
       |     ^
checkRd: (-1) mod-internal.Rd:21: Lost braces
    21 | code{findMedFlowRow_mod}: find row numbers for matching ID and time
       |     ^
checkRd: (-1) mod-internal.Rd:23: Lost braces
    23 | code{flowData_mod}: correct flow data
       |     ^
checkRd: (-1) mod-internal.Rd:25: Lost braces
    25 | code{concData_mod}: correct concentration data
       |     ^
checkRd: (-1) mod-internal.Rd:27: Lost braces
    27 | code{infusionData_mod}: combine flow and MAR data; standardize hourly rate,
       |     ^
checkRd: (-1) mod-internal.Rd:30: Lost braces
    30 | code{resolveDoseDups_mod}: correct duplicated infusion and bolus doses
       |     ^
checkRd: (-1) mod-internal.Rd:32: Lost braces
    32 | code{writeCheckDat
...[truncated]...
rence (in minutes) of time vector
       |     ^
checkRd: (-1) pk-internal.Rd:28: Lost braces
    28 | code{fixDates}: add leading zeroes to date
       |     ^
checkRd: (-1) pk-internal.Rd:30: Lost braces
    30 | code{joinFlowMar}: rbind two data sets
       |     ^
checkRd: (-1) pk-internal.Rd:32: Lost braces
    32 | code{updateInterval_mod}: replace maxint with difference between surgery time
       |     ^
checkRd: (-1) pk-internal.Rd:35: Lost braces
    35 | code{fix_serum_time}: create time variable
       |     ^
checkRd: (-1) pk-internal.Rd:37: Lost braces
    37 | code{merge_by_time}: impute in x by closest time in y
       |     ^
checkRd: (-1) pk-internal.Rd:39: Lost braces
    39 | code{merge_inf_bolus}: combine infusion and bolus into one hourly dose file
       |     ^
checkRd: (-1) pk-internal.Rd:41: Lost braces
    41 | code{addZeroDose}: add rows of zero dose, after a gap
       |     ^
checkRd: (-1) pk-internal.Rd:43: Lost braces
    43 | code{pkdata}
       |     ^

CRAN check page ↗

Slowest check: 6.9 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-04
ERROR12 NOTE, 1 ERROR2026-08-31
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE12 NOTE2026-04-25

Show 2 earlier changesHide 2 earlier changes

ERROR13 NOTE, 1 ERROR2026-03-30
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4-11

READMENoVignettesYes · 4 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 52 (9 internal)includes a package overview page
Examples that run: 97%37 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 88%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 4%

Vignettes (4)

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #12,211 · ~10/day · ~290/mo

Releases R versions

Daily download trend is not available in this view yet.

33430 days

91190 days

3.5K1 year

Compare downloads with other packages →

Also on682 r2u8 autocran

How downloads are counted

Repository

choileena/choileena.github.io ↗Account: choileena

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-06-09

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/choileena/choileena.github.io on 2026-10-21.

Docs source (1)

GitHub Pages site last deployed 2026-06-09

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing EHR adds 6 packages (3 with compiled code, 6.6 MB of source tarballs). Heaviest: data.table 5.7 MB, lubridate 420 KB, cpp11 298 KB.

Depends (1)

R >= 2.10

Imports (6)

statsutilsdata.tablemethodslubridate pkdata

LinkingTo (0)

none

Suggests (7)

glmnet logistf medExtractR knitr rmarkdown ggplot2 markdown

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 (6)

Leena Choi

Author, Maintainer since 0.1-3 (2017)

Cole Beck

Author

Nathan James

Author · added in 0.4-0

Elizabeth McNeer

Author · added in 0.3-0

Hannah Weeks

Author · added in 0.3-0

Michael Williams

Author · added in 0.4-0

Releases (10)

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
0.4-11Latest
record
2022-12-19 · current release · diff ↗
0.4-10
record
2022-10-11 · diff ↗
unarchivedReturned to CRAN
2022-06-21
0.4-8
record
2022-06-21 · diff ↗
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-04-07
resubmitted without corrected check error 'coercion to logical' errors
unarchivedReturned to CRAN
2022-04-06
0.4-5
record
2022-04-06 · diff ↗
archivedRemoved from CRAN
2022-04-04
'coercion to logical' errors were not corrected in time See https://www.stats.ox.ac.uk/pub/bdr/LENGTH1/
0.4-4
record
2021-10-07 · diff ↗
0.4-1
record
2021-06-09 · diff ↗
0.4-0
record
2021-06-05 · diff ↗ ·
added 12 exports
idCrosswalk, pullFakeId, pullRealId, run_Build_PK_IV, run_Build_PK_Oral, run_Demo, run_DrugLevel, run_Labs, run_MedStrI, run_MedStrII, stdzDoseChange, stdzDoseSchedule

Show 10 earlier eventsHide 10 earlier events

R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-10-08
0.3-1
record
2020-10-08 · diff ↗
archivedRemoved from CRAN
2020-09-20
problems were not corrected in time Calls model.frame with 'data = sys.parent()', which has never worked and is now an error
0.3-0
record
2020-09-12 · diff ↗ ·
added 18 exports
addLastDose, buildDose, collapseDose, dataTransformation, extractMed, freqNum, makeDose, parseCLAMP, parseMedEx, parseMedExtractR, parseMedXN, processLastDose, readTransform, stdzDose, stdzDuration, stdzFreq, stdzRoute, stdzStrength
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1-3
record
2017-10-20
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-10-20
Total releases: 10 / 9 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 231 KB / 7 files
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EHR")

Format

Choi, L., Beck, C., James, N., McNeer, E., Weeks, H., & Williams, M. (2022). EHR: Electronic Health Record (EHR) Data Processing and Analysis Tool (Version 0.4-11) [Computer software]. https://doi.org/10.32614/CRAN.package.EHR

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 EHR version 0.4-11 [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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