Changes in version 3.1.2 (2026-02-10) - Fixes run-to-run stability of TreatmentPatterns. - Fixes issue for andromeda >= 1.0.0 - 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. Changes in version 3.1.1 (2025-08-25) - 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. Changes in version 3.1.0 (2025-06-03) - 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. Changes in version 3.0.3 (2025-04-16) - Added compatibility with Andromeda 0.6.7 and 1.0.0 Changes in version 3.0.2 (2025-04-04) - 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. Changes in version 3.0.1 (2025-03-10) - Deprecated shiny app - Removed shiny-related dependencies - Added ggplot2 version of sunburst plot - Fixed failing examples Changes in version 3.0.0 (2025-02-06) - 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. Changes in version 2.7.0 (2024-11-27) - 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. - Changes in version 2.6.9 (2024-09-02) - Disabled tests when required suggested packages are not available. - Updated examples to only run when required suggested packages are available. Changes in version 2.6.8 (2024-08-29) - 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. Changes in version 2.6.7 (2024-05-24) - Updated URLs in description - Updated examples to fix compatibility with CDMConnector >1.4.0 - Updated so more tests run on CRAN Changes in version 2.6.6 (2024-04-16) - Internal update to shinyApp. - Update to createSankeyDiagram() to properly handle combinations consisting of >2. - Added article to package website about best practices. Changes in version 2.6.5 (2024-02-19) - 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. Changes in version 2.6.4 (2024-01-26) - Fixed issue with minPostCombinationWindow broken by the fix for re-occurring treatments. - Added unit tests for minPostCombinationWindow. Changes in version 2.6.3 (2024-01-25) - 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. Changes in version 2.6.2 (2023-12-13) - 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. Changes in version 2.6.1 (2023-12-11) - 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(). Changes in version 2.6.0 (2023-11-13) - 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. Changes in version 2.5.2 (2023-09-15) - Resolved issue with finalize method of CDMInterface class. - Resolved issue with schema references. - Unified case style. - Refactored code for createSunburstPlot(). Changes in version 2.5.1 (2023-09-07) - 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. Changes in version 2.5.0 (2023-08-16) - 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.