R Observatory: Metrics for TreatmentPatterns version 3.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TreatmentPatterns

3.1.2Package record

Analyzes Real-World Treatment Patterns of a Study Population of Interest

0packages depend

18Kdownloads / year

94.9%test coverage

13/13flavors OK

Overview

About

Maintained by Maarten van KesselCRAN page ↗GitHub ↗Website ↗Issues ↗

Computes treatment patterns within a given cohort using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM). As described in Markus, Verhamme, Kors, and Rijnbeek (2022) doi:10.1016/j.cmpb.2022.107081.

Changes in 3.1.2

---------

Fixes run-to-run stability of TreatmentPatterns.
Fixes issue for andromeda >= 1.0.0
Fixed issue where doubles casted to numeric were reported in scientific notation.
Fixed issue when parallelizing multiple computePathways(), caused by database-side conflicts.
Fixed issue where the same subject_id was assigned a different pseudo-subject_id when using multiple cohort tables.
Fixed issue when multiple target cohorts and multiple cohort tables were specified.
Added export of problematic records when combination check fails.
Deprecated SQL implementation for fetching cohort information.
Internal change to always use CDMConnector internally (either using ODBC or JDBC).
Require CDMConnector >= 2.0.0.
Gracefully exit when there is no internet connection when running internal helper functions for testing.

From NEWS.md in the release

Install

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

install.packages("TreatmentPatterns", 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("darwin-eu/TreatmentPatterns")

Development version from darwin-eu/TreatmentPatterns. 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-treatmentpatterns

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-TreatmentPatterns

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-TreatmentPatterns

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

Additional issues

donttest

CRAN check page ↗

Slowest check: 10.9 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-29
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 9 earlier changesHide 9 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-06
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-04
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.1.2

READMEYes · 279 wordsVignettesYes · 7 · dynamicNEWSYes · 100% structured · mentions 3.1.2Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 12 (1 internal)includes a package overview page
Examples that run: 56%5 run in a plain check (1 of them under a condition) · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 90%
Documented parameters: 100%
Return-value docs: 90%
Help pages citing references: 0%

Vignettes (7)

How these are measured

Downloads

18K

CRAN downloads in the past year

Rank #5,099 · ~49/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

58330 days

1.6K90 days

18K1 year

Compare downloads with other packages →

Also on93 r2u4 autocran

How downloads are counted

Repository

darwin-eu/treatmentpatterns ↗Organization: darwin-euFork of darwin-eu-dev/TreatmentPatterns

2Stars

4Forks

10Open issues

0Open PRs

12Releases

1,434Commits

10Commit identities

License file reads as Apache-2.0 · 1,434 commits · Last activity 2026-02-11

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-06-03 · 22026-07-07 · 2

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/darwin-eu/treatmentpatterns on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Issue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-11 · The repository has a site deploy workflow

pkgdown site last built 2026-02-11

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

CRAN release process (1)

CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing TreatmentPatterns adds 48 packages (27 with compiled code, 35 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 4.6 MB, CDMConnector 4.0 MB.

Depends (1)

R >= 4.2

Imports (11)

utilsstatsR6 stringi jsonlite checkmate dplyr tidyr dbplyr Andromeda CDMConnector

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Maarten van Kessel

Maintainer since 2.5.0 (2023)

Aniek Markus

Author

Releases (21)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.1.2Latest
record
2026-02-10 · current release · diff ↗
3.1.1
record
2025-08-25 · diff ↗
3.1.0
record
2025-06-03 · diff ↗ ·
added 1 export
exportPatientLevel
3.0.3
record
2025-04-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.2
record
2025-04-04 · diff ↗
3.0.1
record
2025-03-10 · diff ↗ ·
removed 6 exports
CharacterizationPlots, InputHandler, SankeyDiagram, ShinyModule, SunburstPlot, launchResultsExplorer

added 1 export
ggSunburst
3.0.0
record
2025-02-06 · diff ↗ ·
added 2 exports
TreatmentPatternsResults, getResultsDataModelSpecifications
2.7.0
record
2024-11-27 · diff ↗ ·
removed 2 exports
createSankeyDiagram2, createSunburstPlot2

added 1 export
plotEventDuration
unarchivedReturned to CRAN
2024-09-02
2.6.9
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2024-09-02 · diff ↗
archivedRemoved from CRAN
2024-09-01
issues were not corrected in time
2.6.8
record
2024-08-29 · diff ↗
2.6.7
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2024-05-24 · diff ↗
R
R 4.4.0 released · 2024-04-24

Show 11 earlier eventsHide 11 earlier events

2.6.6
record
2024-04-16 · diff ↗ ·
removed 2 exports
InteractivePlots, Module

added 3 exports
SankeyDiagram, ShinyModule, SunburstPlot
2.6.5
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2024-02-19 · diff ↗
2.6.4
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2024-01-26 · diff ↗
2.6.3
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2024-01-25 · diff ↗ ·
added 2 exports
createSankeyDiagram2, createSunburstPlot2
2.6.2
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2023-12-13 · diff ↗ ·
removed 2 exports
createSankeyDiagram2, createSunburstPlot2
2.6.1
record
2023-12-11 · diff ↗ ·
added 5 exports
CharacterizationPlots, InputHandler, InteractivePlots, Module, launchResultsExplorer
2.6.0
record
2023-11-13 · diff ↗ ·
added 2 exports
createSankeyDiagram2, createSunburstPlot2
2.5.2
record
2023-09-15 · diff ↗
2.5.1
record
2023-09-07 · diff ↗
2.5.0
record
2023-08-16
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-16
Total releases: 21 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.2
Download size: 3.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("TreatmentPatterns")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.cmpb.2022.107081.

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 TreatmentPatterns version 3.1.2 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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