NEWS
TreatmentPatterns 2.6.9 (2024-09-02)
- Disabled tests when required suggested packages are not available.
- Updated examples to only run when required suggested packages are available.
TreatmentPatterns 2.6.8 (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 (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 (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 (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 (2024-01-26)
- Fixed issue with minPostCombinationWindow broken by the fix for re-occurring treatments.
- Added unit tests for minPostCombinationWindow.
TreatmentPatterns 2.6.3 (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 (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 (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 (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 (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 (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 (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.