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Changelog

Source: NEWS.md

# TreatmentPatterns 3.0.0

CRAN release: 2025-02-06

  • Save parameters from computePathways() and export()
  • A TreatmentPatternsResults (TPR) object is now returned from export()
  • Updated output file and column names to be snake_case rather than camelCase
    • The TPR object houses all the different tables, and has methods for plotting.
    • Writing CSV-files on export() is now optional (export(outputPath = "some/path/"))
    • The TPR object has the following methods: saveAsCsv(), saveAsZip(), uploadResultsToDb(), load(), plotSunburst(), plotSankey(), plotEventDuration()
    • The TPR object has the following fields:, attrition, metadata, treatment_pathways, summary_event_duration, counts_age, counts_sex, counts_year, cdm_source_info, analyses, arguments
  • Added ResultModelManager support
  • Multiple target cohorts are now supported
  • Allow target, event, and exit cohorts to be in different tables
  • Stratification is now optional export(stratify = TRUE)
  • When data is pulled from the database, subjects are assigned a new subject ID. This prevents rounding subject ID’s, and unintentional grouping of subjects.

# TreatmentPatterns 2.7.0

CRAN release: 2024-11-27

  • Converted subject_id’s to pseudo_subject_id’s when pulling in data from the database. Actual subject_id’s are stored as character().
  • Added copyright statements in R-files.
  • Renamed periodPriorToIndex to indexDateOffset.
  • Added life cycle badge to ReadMe
  • Added more informative error / warning messaging when no data is available to compute pathways.
  • Extended output for event duration in pathways.
  • Renamed summaryStatsTherapyDuration.csv to summaryEventDuration.csv.
  • Updated status messaging in the console.
  • Added attrition.csv that capture status messaging and time stamps.

  • # TreatmentPatterns 2.6.9

    CRAN release: 2024-11-27

  • Disabled tests when required suggested packages are not available.
  • Updated examples to only run when required suggested packages are available.

# TreatmentPatterns 2.6.8

CRAN release: 2024-08-29

  • Updated some tests to work with later versions of omopgenerics.
  • Fixed issue with where combinations sometimes got miss-classified.
  • Fixed issue when event starts and ends on end-date of target.
  • Fixed issue when collapsing events when there is also a combination, when filterTreatments = "All".
  • Added check in tests to only run if packages are availible. (noSuggests, M1).
  • createSankeyDiagram() now supports pathways over 3 levels long.

# TreatmentPatterns 2.6.7

CRAN release: 2024-05-24

  • Updated URLs in description
  • Updated examples to fix compatibility with CDMConnector >1.4.0
  • Updated so more tests run on CRAN

# TreatmentPatterns 2.6.6

CRAN release: 2024-04-16

  • Internal update to shinyApp.
  • Update to createSankeyDiagram() to properly handle combinations consisting of >2.
  • Added article to package website about best practices.

# TreatmentPatterns 2.6.5

CRAN release: 2024-02-19

  • Removed stringi, rjson, and googleVis as dependencies.
  • Fixed unit tests that had dummy data outside of observation data.
  • Fix for complex edge-case paths with re-occuring treatments.
  • Added unit tests for edge-cases.
  • Added warning when minEraDuration > minPostCombinationWindow or combinationWindow.
  • Fixed issue when filterTreatments was set to "changes", age and sex columns were dropped from output.
  • datatypes of cohort_table are now checked.

# TreatmentPatterns 2.6.4

CRAN release: 2024-01-26

  • Fixed issue with minPostCombinationWindow broken by the fix for re-occurring treatments.
  • Added unit tests for minPostCombinationWindow.

# TreatmentPatterns 2.6.3

CRAN release: 2024-01-25

  • Fixed issue where there were duplicate rows in the exported treatmentPathways.csv file.
  • Added more comprehensive description for parameter ageWindow for export().
  • Added additional tests validating the counts per pathway being exported by export().
  • Fixed issue with re-occurring treatments in pathways.
  • Added dedicated logical tests for various pathways.
  • Added dedicated tests for target-event cohort overlaps.
  • Fixed spelling error in outputs, and interaction with them in shiny module.

# TreatmentPatterns 2.6.2

CRAN release: 2023-12-13

  • Fixed spelling mistake ‘summaryStatsTherapyDuraion’ to ‘summaryStatsTherapyDuration’.
  • Added error when only one level of data is available in the data when computing a sankey diagram.
  • Removed createSankeyDiagram
  • Renamed createSankeyDiagram2 to createSankeyDiagram
  • Removed createSunburstPlot
  • Renamed createSunburstPlot2 to createSunburstPlot
  • Fixed issue where target cohorts had to be at least 1 day long to be included when using DatabaseConnector.
  • Fixed CRAN error when running examples.
  • Renamed cellCount to minCellCount in export documentation.
  • Fixed issue where counts of pathways were not computed correctly.
  • Fixed spelling error summaryStatsTherapyDuraion to summaryStatsTherapyDuration.
  • Fixed issue in export where merging two tables could fail, if one was empty.

# TreatmentPatterns 2.6.1

CRAN release: 2023-12-11

  • Bumped R version to 4.2.1
  • Added additional unit-tests for createSunburstPlot2() and createSankeyDiagram2()
  • Updated to use DATEDIFF to compute difference between dates when fetching data from the database.
  • Added functionality to choose how groups below the minimum cell count are censored.
  • Made some parameters ambiguous for createSankeyDiagram2 and createSunburstPlot2() for more control over the figures.
  • Removed addNoPath parameter.
  • Renamed minFreq parameter to minCellCount.
  • Added Shiny app with exported module classes.
  • Added censoring options of treatment pathways falling below the minCellCount.
  • Simplified part of computePathways().
  • Significantly improved performance of export().

# TreatmentPatterns 2.6.0

CRAN release: 2023-11-13

  • Added createSunburstPlot2() as a replacement of createSunburstPlot(). createSunburstPlot2() will fully replace createSunburstPlot() in a future version.
  • Moved DatabaseConnector and SqlRender to Suggests
  • Removed obsolete dependencies: data.table, fs, and glue.
  • Internal performance updates.
  • Internal code style updates.
  • Moved basic filtering when fetching cohort table.
  • Updated ReadMe with functionalities
  • Internal updates to LRFS paths, to allow paths of identical duration.

# TreatmentPatterns 2.5.2

CRAN release: 2023-09-15

  • Resolved issue with finalize method of CDMInterface class.
  • Resolved issue with schema references.
  • Unified case style.
  • Refactored code for createSunburstPlot().

# TreatmentPatterns 2.5.1

CRAN release: 2023-09-07

  • Added checks for user input: cohorts and cohortTableName.
  • Added option to directly return HTML when using createSankeyDiagram.
  • Added option to directly return HTML when using createSunburstPlot.
  • Added option for ageWindow to be a vector.
  • Added input checking for export().
  • Added additional check for frequency for createSunburstPlot.
  • Resolved issue in createSunburstPlot, when converting from data.table to nested JSON.

# TreatmentPatterns 2.5.0

CRAN release: 2023-08-16

  • Updated interface
  • Some internal OO usage
  • CDM & DatabaseConnector
  • Uses Andromeda to be able to handle bigger than RAM data sets.
    • Shift from data.table to dplyr.
  • Updated vignettes using new interface
  • General code clean up
  • Intermediate files are cached and accessable through Andromeda for review.
  • Outputted CSV-files re-imagined to be more flexible for use post TreatmentPatterns.
  • Sunburst and Sankey plots are now directly usable with treatmentPathways.csv.