TreatmentPatterns

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

v3.1.2 · Feb 10, 2026 · Apache License (>= 2)

Description

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>.

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CRAN Check Status

1 ERROR

3 NOTE

10 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	131.8s
r-devel-linux-x86_64-debian-gcc	OK	299.6s
r-devel-linux-x86_64-fedora-clang	OK	640.5s
r-devel-linux-x86_64-fedora-gcc	OK	688.2s
r-devel-macos-arm64	OK	106s
r-devel-windows-x86_64	OK	491s
r-oldrel-macos-arm64	NOTE	105s
r-oldrel-macos-x86_64	NOTE	560s
r-oldrel-windows-x86_64	NOTE	656s
r-patched-linux-x86_64	OK	468.1s
r-release-linux-x86_64	OK	449.3s
r-release-macos-arm64	OK	105s
r-release-macos-x86_64	OK	652s
r-release-windows-x86_64	OK	423s

Check details (15 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘a000_bestPractices.Rmd’ using rmarkdown
--- finished re-building ‘a000_bestPractices.Rmd’

--- re-building ‘a001_DefiningCohorts.Rmd’ using rmarkdown
--- finished re-building ‘a001_DefiningCohorts.Rmd’

--- re-building ‘a010_Computing_Pathways.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


Quitting from a010_Computing_Pathways.Rmd:83-103 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `generateCohortSet()`:
! The package "CirceR" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'a010_Computing_Pathways.Rmd' failed with diagnostics:
The package "CirceR" is required.
--- failed re-building ‘a010_Computing_Pathways.Rmd’

--- re-building ‘a020_Exporting.Rmd’ using rmarkdown
--- finished re-building ‘a020_Exporting.Rmd’

--- re-building ‘a030_Evaluating_Output.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


Quitting from a030_Evaluating_Output.Rmd:31-88 [setup_treatment_patterns]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `CDMConnector::generateCohortSet()`:
! The package "CirceR" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'a030_Evaluating_Output.Rmd' failed with diagnostics:
The package "CirceR" is required.
--- failed re-building ‘a030_Evaluating_Output.Rmd’

--- re-building ‘a998_Strategus.Rmd’ using rmarkdown
--- finished re-building ‘a998_Strategus.Rmd’

--- re-building ‘a999_Publications-Presentations.Rmd’ using rmarkdown
--- finished re-building ‘a999_Publications-Presentations.Rmd’

SUMMARY: processing the following files failed:
  ‘a010_Computing_Pathways.Rmd’ ‘a030_Evaluating_Output.Rmd’

Error: Vignette re-building failed.
Execution halted

ERROR r-devel-linux-x86_64-debian-clang

tests

  Running ‘testthat.R’ [25s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(TreatmentPatterns)
  > 
  > test_check("TreatmentPatterns")
  Starting 2 test processes.
  Saving _problems/test-CRAN-25.R
  > test-computePathways.R: 
  > test-computePathways.R: Attaching package: 'dplyr'
  > test-computePathways.R: 
  > test-computePathways.R: The following objects are masked from 'package:stats':
  > test-computePathways.R: 
  > test-computePathways.R:     filter, lag
  > test-computePathways.R: 
  > test-computePathways.R: The following objects are masked from 'package:base':
  > test-computePathways.R: 
  > test-computePathways.R:     intersect, setdiff, setequal, union
  > test-computePathways.R: 
  > test-export.R: 
  > test-export.R: Attaching package: 'dplyr'
  > test-export.R: 
  > test-export.R: The following objects are masked from 'package:stats':
  > test-export.R: 
  > test-export.R:     filter, lag
  > test-export.R: 
  > test-export.R: The following objects are masked from 'package:base':
  > test-export.R: 
  > test-export.R:     intersect, setdiff, setequal, union
  > test-export.R: 
  [ FAIL 1 | WARN 0 | SKIP 105 | PASS 1 ]
  
  ══ Skipped tests (105) ═════════════════════════════════════════════════════════
  • Eunomia [2.0.0] bug (1): 'test-multipleCohortTables.R:67:3'
  • On CRAN (104): 'test-TreatmentPatternsResults.R:2:3',
    'test-TreatmentPatternsResults.R:24:3',
    'test-TreatmentPatternsResults.R:52:3',
    'test-TreatmentPatternsResults.R:80:3',
    'test-TreatmentPatternsResults.R:85:3',
    'test-TreatmentPatternsResults.R:97:3',
    'test-TreatmentPatternsResults.R:111:3',
    'test-TreatmentPatternsResults.R:125:3',
    'test-TreatmentPatternsResults.R:147:3',
    'test-TreatmentPatternsResults.R:165:3', 'test-createSankeyDiagram.R:13:3',
    'test-createSankeyDiagram.R:18:3', 'test-createSankeyDiagram.R:37:3',
    'test-createSankeyDiagram.R:84:3', 'test-createSankeyDiagram.R:124:3',
    'test-createSankeyDiagram.R:151:3', 'test-computePathways.R:30:3',
    'test-computePathways.R:74:3', 'test-computePathways.R:129:3',
    'test-computePathways.R:144:3', 'test-computePathways.R:182:3',
    'test-computePathways.R:197:3', 'test-computePathways.R:229:3',
    'test-computePathways.R:246:3', 'test-computePathways.R:351:3',
    'test-computePathways.R:508:3', 'test-computePathways.R:557:3',
    'test-computePathways.R:606:3', 'test-computePathways.R:623:3',
    'test-computePathways.R:642:3', 'test-createSunburstPlot.R:17:3',
    'test-createSunburstPlot.R:26:3', 'test-createSunburstPlot.R:39:3',
    'test-executeTreatmentPatterns.R:5:3',
    'test-executeTreatmentPatterns.R:26:3', 'test-exportPatientLevel.R:2:3',
    'test-getResultsDataModelSpecifications.R:2:3', 'test-ggSunburst.R:2:3',
    'test-ggSunburst.R:26:3', 'test-ggSunburst.R:44:3',
    'test-multipleCohortTables.R:6:3', 'test-multipleCohortTables.R:116:3',
    'test-export.R:8:3', 'test-export.R:15:3', 'test-export.R:309:3',
    'test-export.R:373:3', 'test-export.R:419:3', 'test-export.R:458:3',
    'test-export.R:499:3', 'test-export.R:571:3', 'test-export.R:642:3',
    'test-export.R:667:3', 'test-pathwaysMultipleTargetsLogical.R:18:3',
    'test-pathwaysMultipleTargetsLogical.R:224:3',
    'test-pathwaysMultipleTargetsLogical.R:315:3',
    'test-plotEventDuration.R:2:3', 'test-plotEventDuration.R:14:3',
    'test-plotEventDuration.R:41:3', 'test-plotEventDuration.R:69:3',
    'test-pathwaysLogical.R:6:3', 'test-pathwaysLogical.R:46:3',
    'test-pathwaysLogical.R:88:3', 'test-pathwaysLogical.R:130:3',
    'test-pathwaysLogical.R:172:3', 'test-pathwaysLogical.R:214:3',
    'test-pathwaysLogical.R:256:3', 'test-pathwaysLogical.R:299:3',
    'test-pathwaysLogical.R:341:3', 'test-pathwaysLogical.R:383:3',
    'test-pathwaysLogical.R:425:3', 'test-pathwaysLogical.R:467:3',
    'test-pathwaysLogical.R:509:3', 'test-pathwaysLogical.R:551:3',
    'test-pathwaysLogical.R:593:3', 'test-pathwaysLogical.R:636:3',
    'test-pathwaysLogical.R:679:3', 'test-pathwaysLogical.R:720:3',
    'test-pathwaysLogical.R:762:3', 'test-pathwaysLogical.R:804:3',
    'test-pathwaysLogical.R:847:3', 'test-pathwaysLogical.R:887:3',
    'test-pathwaysLogical.R:927:3', 'test-pathwaysLogical.R:967:3',
    'test-pathwaysLogical.R:1008:3', 'test-pathwaysLogical.R:1050:3',
    'test-pathwaysLogical.R:1091:3', 'test-pathwaysLogical.R:1135:3',
    'test-pathwaysLogical.R:1177:3', 'test-pathwaysLogical.R:1219:3',
    'test-pathwaysLogical.R:1261:3', 'test-pathwaysLogical.R:1305:3',
    'test-pathwaysLogical.R:1350:3', 'test-pathwaysLogical.R:1395:3',
    'test-pathwaysLogical.R:1440:3', 'test-pathwaysLogical.R:1485:3',
    'test-pathwaysLogical.R:1528:3', 'test-pathwaysLogical.R:1574:3',
    'test-pathwaysLogical.R:1620:3', 'test-pathwaysLogical.R:1666:3',
    'test-pathwaysLogical.R:1710:3', 'test-pathwaysLogical.R:1754:3',
    'test-pathwaysLogical.R:1801:3', 'test-pathwaysLogical.R:1857:3',
    'test-pathwaysLogical.R:1912:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-CRAN.R:21:3'): CRAN Tests ──────────────────────────────────────
  Error in `validateComputePathways()`: No 'target' cohort specified in `cohorts`.
  Backtrace:
      ▆
   1. └─TreatmentPatterns::computePathways(...) at test-CRAN.R:21:3
   2.   └─TreatmentPatterns:::validateComputePathways()
  
  [ FAIL 1 | WARN 0 | SKIP 105 | PASS 1 ]
  Error:
  ! Test failures.
  Execution halted

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

NOTE r-oldrel-macos-arm64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

NOTE r-oldrel-windows-x86_64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-debian-clang

tests

  Running ‘testthat.R’ [25s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(TreatmentPatterns)

NOTE r-oldrel-macos-arm64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

NOTE r-oldrel-windows-x86_64

installed package size

  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb

Dependency Network

Version History

new 3.1.2 Mar 9, 2026