TreatmentPatterns

3.1.2

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

0packages depend

18.1Kdownloads / year

94.9%test coverage

13/13checks pass

Overview

About

Maintained by Maarten van KesselFirst published 2023-08-1621 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 11.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 1.38

94.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-06
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 279 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 56%
Documented parameters: 100%
Return-value docs: 90%
References docs: 0%

Downloads

18.1K

CRAN downloads in the past year

Rank #7,576 · ~50/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

1.4K90 days

18.1K1 year

Compare downloads with other packages →

Also on133 r2u22 autocran

Repository

GitHub ↗ darwin-eu/treatmentpatterns

2Stars

4Forks

9Open issues

0Open PRs

12Releases

1,434Commits

10Contributors

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

Stars over time

2024-06-03 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/darwin-eu/treatmentpatterns on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

CRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 8,983 (79%)Vignettes 1,237 (11%)Rd 1,092 (10%)

Code characteristics

Object systems

R61

Cyclomatic complexity: 1.0 median / 6 max
Test cases: 126 / 1.38 per code line

Test coverage

Line coverage

95%

Expression

93.2%

Tests / Examples

94.9% / 0% ex

Functions

69 9 exported

Complexity

1.7 avg / 6 max

Call network

69 nodes / 80 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

69 functions

Function	Cyclo	Coverage
doEraCollapse	2	0%
checkInstall	2	50%
doFilterTreatments	6	60%
computePathways exp	2	87%
addLabels	4	88%
doCombinationWindow	4	94%

People & History

People (2)

Maintainer (1)

Maarten van Kessel

Maintainer

Authors (1)

Aniek Markus

Author

Package Timeline

21 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
3.1.2Latest
2026-02-10 · current release · diff ↗
3.1.1
2025-08-25 · diff ↗
3.1.0
2025-06-03 · diff ↗
3.0.3
2025-04-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.0.2
2025-04-04 · diff ↗
3.0.1
2025-03-10 · diff ↗
3.0.0
2025-02-06 · diff ↗
2.7.0
2024-11-27 · diff ↗
2.6.9
2024-09-02 · diff ↗
unarchivedReturned to CRAN
2024-09-02
archivedRemoved from CRAN
2024-09-01
issues were not corrected in time
2.6.8
2024-08-29 · diff ↗
2.6.7
2024-05-24 · diff ↗
R
R 4.4.0 released · 2024-04-24

Show 11 earlier events

2.6.6
2024-04-16 · diff ↗
2.6.5
2024-02-19 · diff ↗
2.6.4
2024-01-26 · diff ↗
2.6.3
2024-01-25 · diff ↗
2.6.2
2023-12-13 · diff ↗
2.6.1
2023-12-11 · diff ↗
2.6.0
2023-11-13 · diff ↗
2.5.2
2023-09-15 · diff ↗
2.5.1
2023-09-07 · diff ↗
2.5.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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