# TreatmentPatterns 2.7.0
- 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
- 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.