NEWS

# 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.

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.

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

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.

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.

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().

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.

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.

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.