# TreatmentPatterns 2.6.9

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

# TreatmentPatterns 2.6.8

• 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

• 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

• 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

• 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

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

# TreatmentPatterns 2.6.3

• 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

• 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

• 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

• 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

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

# TreatmentPatterns 2.5.1

• 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

• 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.