Fixed issue where doubles casted to numeric were reported in
scientific notation.
Fixed issue when parallelizing multiple computePathways(), caused by
database-side conflicts.
Fixed issue where the same subject_id was assigned a different
pseudo-subject_id when using multiple cohort tables.
Fixed issue when multiple target cohorts and multiple cohort tables
were specified.
Added export of problematic records when combination check
fails.
Deprecated SQL implementation for fetching cohort information.
Internal change to always use CDMConnector internally (either using
ODBC or JDBC).
Require CDMConnector >= 2.0.0.
Gracefully exit when there is no internet connection when running
internal helper functions for testing.
# TreatmentPatterns 3.1.1
Fixed issue when setting filterTreatments = "Changes"
and made it ambiguous regardless of the Andromeda version.
Fixed issue where combination treatments were ordered differently
when using Andromeda >= 1.0.0.
Fixed compatibility with Spark when using CDMConnector with
ODBC.
Updated the way data is copied from the cdm_reference
to andromeda.
# TreatmentPatterns 3.1.0
Added exportPatientLevel() function to export patient
level data.
Added startAnchor parameter to dictate the window of
interest.
Added windowStart parameter to dictate the window of
interest.
Added endAnchor parameter to dictate the window of
interest.
Added windowEnd parameter to dictate the window of
interest.
Added concatTargets parameter to specify if multiple
target cohorts should be treated separately, or continuously.
Added overlapMethod parameter to pick a method how to
deal with non-combination overlap between events.
Removed indexOffset parameter.
Removed includeTreatments parameter.
Disabled failing test on CRAN environment
Significantly reduced tests that run on CRAN.
# TreatmentPatterns 3.0.3
Added compatibility with Andromeda 0.6.7 and 1.0.0
# TreatmentPatterns 3.0.2
Added unit-testing for CDMInterface on Postgres,
Redshift, SQL Server, Oracle, BigQuery, Spark, Snowflake
Fixed some SQL issues for specific databases
Fixed issue where a crash occurred on R 4.2.x, when saving the input
arguments.
Uncapped pathway length from 5.
Fixed edge case on long repeating events to collapse.
# TreatmentPatterns 3.0.1
Deprecated shiny app
Removed shiny-related dependencies
Added ggplot2 version of sunburst plot
Fixed failing examples
# TreatmentPatterns 3.0.0
Save parameters from computePathways() and
export()
A TreatmentPatternsResults (TPR) object is now returned
from export()
Updated output file and column names to be snake_case rather than
camelCase
The TPR object houses all the different tables, and has methods for
plotting.
Writing CSV-files on export() is now optional
(export(outputPath = "some/path/"))
The TPR object has the following methods: saveAsCsv(),
saveAsZip(), uploadResultsToDb(),
load(), plotSunburst(),
plotSankey(), plotEventDuration()
The TPR object has the following fields:, attrition,
metadata, treatment_pathways,
summary_event_duration, counts_age,
counts_sex, counts_year,
cdm_source_info, analyses,
arguments
Added ResultModelManager support
Multiple target cohorts are now supported
Allow target, event, and exit
cohorts to be in different tables
Stratification is now optional
export(stratify = TRUE)
When data is pulled from the database, subjects are assigned a new
subject ID. This prevents rounding subject ID’s, and unintentional
grouping of subjects.
# 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.