# 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.