diff --git a/DESCRIPTION b/DESCRIPTION index 9ceb6d4..521f730 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: FeatureExtraction Type: Package Title: Generating Features for a Cohort Version: 3.13.0 -Date: 2026-02-28 +Date: 2026-03-05 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")), person("Marc", "Suchard", role = c("aut")), diff --git a/R/Aggregation.R b/R/Aggregation.R index 53a48e6..afb70f4 100644 --- a/R/Aggregation.R +++ b/R/Aggregation.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/CompareCohorts.R b/R/CompareCohorts.R index fffa07f..c1f7beb 100644 --- a/R/CompareCohorts.R +++ b/R/CompareCohorts.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/CovariateData.R b/R/CovariateData.R index 3a0dfff..772ac09 100644 --- a/R/CovariateData.R +++ b/R/CovariateData.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/DefaultCovariateSettings.R b/R/DefaultCovariateSettings.R index 4a45f71..b5acf68 100644 --- a/R/DefaultCovariateSettings.R +++ b/R/DefaultCovariateSettings.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/DefaultTemporalCovariateSettings.R b/R/DefaultTemporalCovariateSettings.R index 5d1004b..c0bba9b 100644 --- a/R/DefaultTemporalCovariateSettings.R +++ b/R/DefaultTemporalCovariateSettings.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/DefaultTemporalSequenceCovariateSettings.R b/R/DefaultTemporalSequenceCovariateSettings.R index aac1c59..e40d297 100644 --- a/R/DefaultTemporalSequenceCovariateSettings.R +++ b/R/DefaultTemporalSequenceCovariateSettings.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/DetailedCovariateSettings.R b/R/DetailedCovariateSettings.R index 2ea8132..92d6dd8 100644 --- a/R/DetailedCovariateSettings.R +++ b/R/DetailedCovariateSettings.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/FeatureExtraction.R b/R/FeatureExtraction.R index 7132f6c..6346da6 100644 --- a/R/FeatureExtraction.R +++ b/R/FeatureExtraction.R @@ -1,6 +1,6 @@ # @file FeatureExtraction.R # -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/GetCovariates.R b/R/GetCovariates.R index f2bf40f..94b55c0 100644 --- a/R/GetCovariates.R +++ b/R/GetCovariates.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # @@ -71,7 +71,7 @@ #' privileges where temp tables can be created. #' @param covariateCohortDatabaseSchema The database schema where the cohorts used to define the covariates can be found. #' @param covariateCohortTable The table where the cohorts used to define the covariates can be found. -#' +#' #' @param exportToTable Whether to export to a table rather than Andromeda object #' @param dropTableIfExists If targetDatabaseSchema, drop any existing tables. Otherwise, results are merged #' into existing table data. Overides createTable. @@ -85,10 +85,10 @@ #' @param targetCovariateContinuousTable (Optional) The name of the table where the resulting continuous covariates will #' be stored. If not provided, results will be fetched to R. The table can be #' a permanent table in the \code{targetDatabaseSchema} or a temp table. If -#' it is a temp table, do not specify \code{targetDatabaseSchema}. +#' it is a temp table, do not specify \code{targetDatabaseSchema}. #' @param targetCovariateRefTable (Optional) The name of the table where the covariate reference will be stored. If #' it is a temp table, do not specify \code{targetDatabaseSchema}. -#' +#' #' @param targetAnalysisRefTable (Optional) The name of the table where the analysis reference will be stored. If #' it is a temp table, do not specify \code{targetDatabaseSchema}. #' @param targetTimeRefTable (Optional) The name of the table for the time reference. If @@ -187,22 +187,23 @@ getDbCovariateData <- function(connectionDetails = NULL, } else { cohortDatabaseSchemaTable <- paste(cohortDatabaseSchema, cohortTable, sep = ".") } - + # check for temporal features in any of the settings - if(inherits(covariateSettings, 'covariateSettings')){ + if (inherits(covariateSettings, "covariateSettings")) { anyTemporal <- covariateSettings$temporal | covariateSettings$temporalSequence - } else{ + } else { anyTemporal <- sum(unlist(lapply( - X = covariateSettings, - FUN = function(x){ - sum(c(x$temporal,x$temporalSequence)) == 1 - }))) > 0 + X = covariateSettings, + FUN = function(x) { + sum(c(x$temporal, x$temporalSequence)) == 1 + } + ))) > 0 } - + # Create export tables # figure out tables if (exportToTable) { - if(is.null(targetDatabaseSchema)){ + if (is.null(targetDatabaseSchema)) { # turn off create table since the tables are temp tempOutputTables <- TRUE # covariate tables @@ -235,7 +236,6 @@ getDbCovariateData <- function(connectionDetails = NULL, } else { targetTimeRefTable <- paste0("#", targetTimeRefTable) } - } else { tempOutputTables <- FALSE targetCovariateTable <- paste(targetDatabaseSchema, targetCovariateTable, sep = ".") @@ -244,13 +244,13 @@ getDbCovariateData <- function(connectionDetails = NULL, targetAnalysisRefTable <- paste(targetDatabaseSchema, targetAnalysisRefTable, sep = ".") targetTimeRefTable <- paste(targetDatabaseSchema, targetTimeRefTable, sep = ".") } - + # drop table if required - if(dropTableIfExists){ - message('Dropping export tables') + if (dropTableIfExists) { + message("Dropping export tables") sql <- SqlRender::loadRenderTranslateSql( - sqlFilename = 'DropExportTables.sql', - packageName = 'FeatureExtraction', + sqlFilename = "DropExportTables.sql", + packageName = "FeatureExtraction", dbms = attr(connection, "dbms"), tempEmulationSchema = tempEmulationSchema, temp_tables = tempOutputTables, @@ -260,45 +260,42 @@ getDbCovariateData <- function(connectionDetails = NULL, analysis_ref_table = targetAnalysisRefTable, time_ref_table = targetTimeRefTable ) - + DatabaseConnector::executeSql( - connection = connection, + connection = connection, sql = sql ) } - - if(dropTableIfExists & !createTable){ - stop('Seem to be exporting to tables but create table is FALSE and dropTable is TRUE') + + if (dropTableIfExists & !createTable) { + stop("Seem to be exporting to tables but create table is FALSE and dropTable is TRUE") } - + # create the cohort tables if required - if(createTable){ - message('Creating export tables') + if (createTable) { + message("Creating export tables") sql <- SqlRender::loadRenderTranslateSql( - sqlFilename = 'CreateExportTables.sql', - packageName = 'FeatureExtraction', + sqlFilename = "CreateExportTables.sql", + packageName = "FeatureExtraction", dbms = attr(connection, "dbms"), tempEmulationSchema = tempEmulationSchema, - aggregated = aggregated, temporal = anyTemporal, - row_id_field = 'row_id', - + row_id_field = "row_id", covariate_table = targetCovariateTable, covariate_continuous_table = targetCovariateContinuousTable, covariate_ref_table = targetCovariateRefTable, analysis_ref_table = targetAnalysisRefTable, time_ref_table = targetTimeRefTable ) - + DatabaseConnector::executeSql( - connection = connection, + connection = connection, sql = sql ) } - } - + sql <- "SELECT cohort_definition_id, COUNT_BIG(*) AS population_size FROM @cohort_database_schema_table {@cohort_ids != -1} ? {WHERE cohort_definition_id IN (@cohort_ids)} GROUP BY cohort_definition_id;" sql <- SqlRender::render( sql = sql, @@ -336,7 +333,7 @@ getDbCovariateData <- function(connectionDetails = NULL, covariateCohortTable ) } - + for (i in 1:length(covariateSettings)) { fun <- attr(covariateSettings[[i]], "fun") args <- list( @@ -374,33 +371,33 @@ getDbCovariateData <- function(connectionDetails = NULL, } else if (hasData(tempCovariateData$covariatesContinuous)) { covariateData$covariatesContinuous <- tempCovariateData$covariatesContinuous } - - if(hasData(tempCovariateData$covariateRef)){ + + if (hasData(tempCovariateData$covariateRef)) { Andromeda::appendToTable(covariateData$covariateRef, tempCovariateData$covariateRef) } - if(hasData(tempCovariateData$analysisRef)){ + if (hasData(tempCovariateData$analysisRef)) { Andromeda::appendToTable(covariateData$analysisRef, tempCovariateData$analysisRef) } - - if(!exportToTable){ - for (name in names(attr(tempCovariateData, "metaData"))) { - if (is.null(attr(covariateData, "metaData")[[name]])) { - attr(covariateData, "metaData")[[name]] <- attr(tempCovariateData, "metaData")[[name]] - } else { - attr(covariateData, "metaData")[[name]] <- list( - c( - unlist(attr(covariateData, "metaData")[[name]]), - attr(tempCovariateData, "metaData")[[name]] + + if (!exportToTable) { + for (name in names(attr(tempCovariateData, "metaData"))) { + if (is.null(attr(covariateData, "metaData")[[name]])) { + attr(covariateData, "metaData")[[name]] <- attr(tempCovariateData, "metaData")[[name]] + } else { + attr(covariateData, "metaData")[[name]] <- list( + c( + unlist(attr(covariateData, "metaData")[[name]]), + attr(tempCovariateData, "metaData")[[name]] + ) ) - ) + } } - } } # if not exporting } } } - - if(!is.null(covariateData)){ + + if (!is.null(covariateData)) { attr(covariateData, "metaData")$populationSize <- populationSize attr(covariateData, "metaData")$cohortIds <- cohortIds } diff --git a/R/GetCovariatesFromCohortAttributes.R b/R/GetCovariatesFromCohortAttributes.R index 47b3b58..9e265f9 100644 --- a/R/GetCovariatesFromCohortAttributes.R +++ b/R/GetCovariatesFromCohortAttributes.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/GetCovariatesFromOtherCohorts.R b/R/GetCovariatesFromOtherCohorts.R index f295d77..dca900e 100644 --- a/R/GetCovariatesFromOtherCohorts.R +++ b/R/GetCovariatesFromOtherCohorts.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # @@ -28,10 +28,10 @@ #' be stored. If not provided, results will be fetched to R. The table can be #' a permanent table in the \code{targetDatabaseSchema} or a temp table. If #' it is a temp table, do not specify \code{targetDatabaseSchema}. -#' +#' #' @param targetCovariateContinuousTable (Optional) The name of the table where the resulting continuous covariates should be stored. #' @param targetCovariateRefTable (Optional) The name of the table where the covariate reference will be stored. -#' +#' #' @param targetAnalysisRefTable (Optional) The name of the table where the analysis reference will be stored. #' @param targetTimeRefTable (Optional) The name of the table for the time reference #' @param minCharacterizationMean The minimum mean value for binary characterization output. Values below this will be cut off from output. This @@ -171,13 +171,11 @@ getDbCohortBasedCovariatesData <- function(connection, cdmVersion = cdmVersion, rowIdField = rowIdField, covariateSettings = detailledSettings, - targetCovariateTable = targetCovariateTable, targetCovariateContinuousTable = targetCovariateContinuousTable, targetCovariateRefTable = targetCovariateRefTable, targetAnalysisRefTable = targetAnalysisRefTable, targetTimeRefTable = targetTimeRefTable, - aggregated = aggregated, minCharacterizationMean = minCharacterizationMean ) diff --git a/R/GetDefaultCovariates.R b/R/GetDefaultCovariates.R index 6243635..849d227 100644 --- a/R/GetDefaultCovariates.R +++ b/R/GetDefaultCovariates.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # @@ -31,7 +31,7 @@ #' it is a temp table, do not specify \code{targetDatabaseSchema}. #' @param targetCovariateContinuousTable (Optional) The name of the table where the resulting continuous covariates should be stored. #' @param targetCovariateRefTable (Optional) The name of the table where the covariate reference will be stored. -#' +#' #' @param targetAnalysisRefTable (Optional) The name of the table where the analysis reference will be stored. #' @param targetTimeRefTable (Optional) The name of the table for the time reference #' @param minCharacterizationMean The minimum mean value for binary characterization output. Values below this will be cut off from output. This @@ -98,8 +98,8 @@ getDbDefaultCovariateData <- function(connection, minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE) checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, upper = 1, add = errorMessages) checkmate::reportAssertions(collection = errorMessages) - - + + targetTables <- list( covariates = targetCovariateTable, covariatesContinuous = targetCovariateContinuousTable, @@ -108,9 +108,9 @@ getDbDefaultCovariateData <- function(connection, timeRef = targetTimeRefTable ) # Is the target schema missing or are all the specified tables temp - allTempTables <- all(substr(targetTables,1,1) == "#") + allTempTables <- all(substr(targetTables, 1, 1) == "#") extractToAndromeda <- is.null(targetCovariateTable) - + settings <- .toJson(covariateSettings) rJava::J("org.ohdsi.featureExtraction.FeatureExtraction")$init(system.file("", package = "FeatureExtraction")) @@ -146,32 +146,32 @@ getDbDefaultCovariateData <- function(connection, ParallelLogger::logInfo("Fetching data from server") start <- Sys.time() covariateData <- Andromeda::andromeda() - + # Binary or non-aggregated features if (!is.null(todo$sqlQueryFeatures)) { - # etracting covariate table - if(extractToAndromeda){ - sql <- SqlRender::translate(sql = todo$sqlQueryFeatures, - targetDialect = attr(connection, "dbms"), - tempEmulationSchema = tempEmulationSchema) + if (extractToAndromeda) { + sql <- SqlRender::translate( + sql = todo$sqlQueryFeatures, + targetDialect = attr(connection, "dbms"), + tempEmulationSchema = tempEmulationSchema + ) DatabaseConnector::querySqlToAndromeda( connection = connection, sql = sql, andromeda = covariateData, andromedaTableName = "covariates", snakeCaseToCamelCase = TRUE - ) - } else{ - + ) + } else { # for testing to see column order - #print(todo$sqlQueryFeatures) - + # print(todo$sqlQueryFeatures) + sql <- " INSERT INTO @target_covariate_table( - + {@temporal | @temporal_sequence} ? {time_id,} - + {@aggregated}?{ cohort_definition_id, covariate_id, @@ -182,9 +182,9 @@ getDbDefaultCovariateData <- function(connection, row_id, covariate_value } - + ) @sub_query; " - + sql <- SqlRender::render( sql = sql, target_covariate_table = targetTables$covariates, @@ -193,7 +193,7 @@ getDbDefaultCovariateData <- function(connection, temporal_sequence = covariateSettings$temporalSequence, aggregated = aggregated ) - + sql <- SqlRender::translate( sql = sql, targetDialect = DatabaseConnector::dbms(connection), @@ -203,18 +203,17 @@ getDbDefaultCovariateData <- function(connection, connection = connection, sql = sql ) - } - } # Continuous aggregated features if (!is.null(todo$sqlQueryContinuousFeatures)) { - - if(extractToAndromeda){ - sql <- SqlRender::translate(sql = todo$sqlQueryContinuousFeatures, - targetDialect = attr(connection, "dbms"), - tempEmulationSchema = tempEmulationSchema) + if (extractToAndromeda) { + sql <- SqlRender::translate( + sql = todo$sqlQueryContinuousFeatures, + targetDialect = attr(connection, "dbms"), + tempEmulationSchema = tempEmulationSchema + ) DatabaseConnector::querySqlToAndromeda( connection = connection, sql = sql, @@ -222,11 +221,11 @@ getDbDefaultCovariateData <- function(connection, andromedaTableName = "covariatesContinuous", snakeCaseToCamelCase = TRUE ) - } else{ + } else { sql <- " INSERT INTO @target_covariate_continuous_table( {@aggregated}?{ - + cohort_definition_id, covariate_id, {@temporal | @temporal_sequence} ? {time_id,} @@ -236,22 +235,22 @@ getDbDefaultCovariateData <- function(connection, average_value, standard_deviation, median_value, - p10_value, - p25_value, - p75_value, + p10_value, + p25_value, + p75_value, p90_value - + }:{ - + covariate_id, {@temporal | @temporal_sequence} ? {time_id,} row_id, covariate_value - + } - + ) @sub_query;" - + sql <- SqlRender::render( sql = sql, target_covariate_continuous_table = targetTables$covariatesContinuous, @@ -260,7 +259,7 @@ getDbDefaultCovariateData <- function(connection, temporal_sequence = covariateSettings$temporalSequence, aggregated = aggregated ) - + sql <- SqlRender::translate( sql = sql, targetDialect = DatabaseConnector::dbms(connection), @@ -271,16 +270,16 @@ getDbDefaultCovariateData <- function(connection, sql = sql ) } - } # Covariate reference if (!is.null(todo$sqlQueryFeatureRef)) { - - if(extractToAndromeda){ - sql <- SqlRender::translate(sql = todo$sqlQueryFeatureRef, - targetDialect = attr(connection, "dbms"), - tempEmulationSchema = tempEmulationSchema) + if (extractToAndromeda) { + sql <- SqlRender::translate( + sql = todo$sqlQueryFeatureRef, + targetDialect = attr(connection, "dbms"), + tempEmulationSchema = tempEmulationSchema + ) DatabaseConnector::querySqlToAndromeda( connection = connection, sql = sql, @@ -290,32 +289,32 @@ getDbDefaultCovariateData <- function(connection, ) collisions <- covariateData$covariateRef %>% - dplyr::filter(collisions > 0) %>% - dplyr::collect() - + dplyr::filter(collisions > 0) %>% + dplyr::collect() + if (nrow(collisions) > 0) { warning(sprintf( "Collisions in covariate IDs detected for post-coordinated concepts with covariate IDs %s", paste(collisions$covariateId, paste = ", ") )) - } - } else{ + } + } else { sql <- " INSERT INTO @target_covariate_ref_table( covariate_id, covariate_name, analysis_id, concept_id, - value_as_concept_id, + value_as_concept_id, collisions ) @sub_query ;" - + sql <- SqlRender::render( sql = sql, target_covariate_ref_table = targetTables$covariateRef, sub_query = gsub(";", "", todo$sqlQueryFeatureRef) ) - + sql <- SqlRender::translate( sql = sql, targetDialect = DatabaseConnector::dbms(connection), @@ -326,17 +325,17 @@ getDbDefaultCovariateData <- function(connection, sql = sql ) } - } - + # Analysis reference if (!is.null(todo$sqlQueryAnalysisRef)) { - - if(extractToAndromeda){ - sql <- SqlRender::translate(sql = todo$sqlQueryAnalysisRef, - targetDialect = attr(connection, "dbms"), - tempEmulationSchema = tempEmulationSchema) + if (extractToAndromeda) { + sql <- SqlRender::translate( + sql = todo$sqlQueryAnalysisRef, + targetDialect = attr(connection, "dbms"), + tempEmulationSchema = tempEmulationSchema + ) DatabaseConnector::querySqlToAndromeda( connection = connection, sql = sql, @@ -344,7 +343,7 @@ getDbDefaultCovariateData <- function(connection, andromedaTableName = "analysisRef", snakeCaseToCamelCase = TRUE ) - } else{ + } else { sql <- " INSERT INTO @target_analysis_ref_table( analysis_id, @@ -357,14 +356,14 @@ getDbDefaultCovariateData <- function(connection, is_binary, missing_means_zero ) @sub_query ;" - + sql <- SqlRender::render( sql = sql, target_analysis_ref_table = targetTables$analysisRef, sub_query = gsub(";", "", todo$sqlQueryAnalysisRef), temporal = covariateSettings$temporal | covariateSettings$temporalSequence ) - + sql <- SqlRender::translate( sql = sql, targetDialect = DatabaseConnector::dbms(connection), @@ -375,17 +374,17 @@ getDbDefaultCovariateData <- function(connection, sql = sql ) } - } - + # Time reference if (!is.null(todo$sqlQueryTimeRef)) { - - if(extractToAndromeda){ - sql <- SqlRender::translate(sql = todo$sqlQueryTimeRef, - targetDialect = attr(connection, "dbms"), - tempEmulationSchema = tempEmulationSchema) + if (extractToAndromeda) { + sql <- SqlRender::translate( + sql = todo$sqlQueryTimeRef, + targetDialect = attr(connection, "dbms"), + tempEmulationSchema = tempEmulationSchema + ) DatabaseConnector::querySqlToAndromeda( connection = connection, sql = sql, @@ -393,7 +392,7 @@ getDbDefaultCovariateData <- function(connection, andromedaTableName = "timeRef", snakeCaseToCamelCase = TRUE ) - } else{ + } else { # TODO - what columns are in time ref table?! sql <- " INSERT INTO @target_time_ref_table( @@ -402,13 +401,13 @@ getDbDefaultCovariateData <- function(connection, sequence_start_day, sequence_end_day ) @sub_query;" - + sql <- SqlRender::render( sql = sql, target_covariate_ref_table = targetTables$timeRef, sub_query = gsub(";", "", todo$sqlQueryTimeRef) ) - + sql <- SqlRender::translate( sql = sql, targetDialect = DatabaseConnector::dbms(connection), @@ -419,7 +418,6 @@ getDbDefaultCovariateData <- function(connection, sql = sql ) } - } delta <- Sys.time() - start @@ -458,7 +456,7 @@ getDbDefaultCovariateData <- function(connection, class(covariateData) <- "CovariateData" attr(class(covariateData), "package") <- "FeatureExtraction" return(covariateData) - } else{ + } else { return(invisible(NULL)) } } diff --git a/R/HelperFunctions.R b/R/HelperFunctions.R index 1979107..b05da06 100644 --- a/R/HelperFunctions.R +++ b/R/HelperFunctions.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/Normalization.R b/R/Normalization.R index 45cace8..c0c6896 100644 --- a/R/Normalization.R +++ b/R/Normalization.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/Table1.R b/R/Table1.R index d1dab25..fb963a0 100644 --- a/R/Table1.R +++ b/R/Table1.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/R/UnitTestHelperFunctions.R b/R/UnitTestHelperFunctions.R index d2bce2b..bdf4499 100644 --- a/R/UnitTestHelperFunctions.R +++ b/R/UnitTestHelperFunctions.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/docs/404.html b/docs/404.html index 69a032d..ee1f49a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -118,7 +118,7 @@

Page not found (404)

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/CreatingCovariatesBasedOnOtherCohorts.html b/docs/articles/CreatingCovariatesBasedOnOtherCohorts.html index 3845ba9..57ee8d1 100644 --- a/docs/articles/CreatingCovariatesBasedOnOtherCohorts.html +++ b/docs/articles/CreatingCovariatesBasedOnOtherCohorts.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Creating covariates based on other cohorts

Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/CreatingCovariatesBasedOnOtherCohorts.Rmd @@ -390,7 +390,7 @@

Using the cohort as covariate

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/CreatingCovariatesUsingCohortAttributes.html b/docs/articles/CreatingCovariatesUsingCohortAttributes.html index f544dcb..57aef7b 100644 --- a/docs/articles/CreatingCovariatesUsingCohortAttributes.html +++ b/docs/articles/CreatingCovariatesUsingCohortAttributes.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Creating covariates using cohort attributes

Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/CreatingCovariatesUsingCohortAttributes.Rmd @@ -308,7 +308,7 @@

Using the attributes as covariates

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/CreatingCustomCovariateBuilders.html b/docs/articles/CreatingCustomCovariateBuilders.html index 61e963f..820a796 100644 --- a/docs/articles/CreatingCustomCovariateBuilders.html +++ b/docs/articles/CreatingCustomCovariateBuilders.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Creating custom covariate builders

Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/CreatingCustomCovariateBuilders.Rmd @@ -424,7 +424,7 @@

Using the custom covariate builder

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/CreatingCustomCovariateBuildersKorean.html b/docs/articles/CreatingCustomCovariateBuildersKorean.html index b38a499..ab9ea82 100644 --- a/docs/articles/CreatingCustomCovariateBuildersKorean.html +++ b/docs/articles/CreatingCustomCovariateBuildersKorean.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Creating custom covariate builders (Korean)

Jeon Ga Bin & Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/CreatingCustomCovariateBuildersKorean.Rmd @@ -374,7 +374,7 @@

사용자 지정 공변량 빌

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/UsingFeatureExtraction.html b/docs/articles/UsingFeatureExtraction.html index 90a18d0..aa1cd7d 100644 --- a/docs/articles/UsingFeatureExtraction.html +++ b/docs/articles/UsingFeatureExtraction.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Using FeatureExtraction

Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/UsingFeatureExtraction.Rmd @@ -807,7 +807,7 @@

Comparing two cohorts

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/UsingFeatureExtractionKorean.html b/docs/articles/UsingFeatureExtractionKorean.html index 8829312..2d07583 100644 --- a/docs/articles/UsingFeatureExtractionKorean.html +++ b/docs/articles/UsingFeatureExtractionKorean.html @@ -1,5 +1,5 @@ - + @@ -32,7 +32,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -99,8 +99,8 @@

Using FeatureExtraction (Korean)

Jeon Ga Bin & Martijn J. Schuemie

-

2025-10-28

- +

2026-03-05

+ Source: vignettes/UsingFeatureExtractionKorean.Rmd @@ -729,7 +729,7 @@

테이블 만들기 1

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/articles/index.html b/docs/articles/index.html index af982be..9a22c66 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,5 +1,5 @@ -Articles • FeatureExtractionArticles • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -100,7 +100,7 @@

All vignettes

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/authors.html b/docs/authors.html index 1f082e4..5e21d17 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -Authors and Citation • FeatureExtractionAuthors and Citation • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -113,15 +113,15 @@

Citation

-

Schuemie M, Suchard M, Ryan P, Reps J, Sena A, Inberg G (2025). +

Schuemie M, Suchard M, Ryan P, Reps J, Sena A, Inberg G (2026). FeatureExtraction: Generating Features for a Cohort. -R package version 3.12.0, https://github.com/OHDSI/FeatureExtraction. +R package version 3.13.0, https://github.com/OHDSI/FeatureExtraction. 

@Manual{,
   title = {FeatureExtraction: Generating Features for a Cohort},
   author = {Martijn Schuemie and Marc Suchard and Patrick Ryan and Jenna Reps and Anthony Sena and Ger Inberg},
-  year = {2025},
-  note = {R package version 3.12.0},
+  year = {2026},
+  note = {R package version 3.13.0},
   url = {https://github.com/OHDSI/FeatureExtraction},
 }
@@ -136,7 +136,7 @@

Citation

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/index.html b/docs/index.html index 3165562..a6bdac3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,5 +1,5 @@ - + @@ -33,7 +33,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -232,12 +232,12 @@

Citation

Developers

@@ -255,7 +255,7 @@

Developers

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/news/index.html b/docs/news/index.html index 0cf8594..355534f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • FeatureExtractionChangelog • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -76,7 +76,14 @@

Changelog

-

FeatureExtraction 3.12.0

+

FeatureExtraction 3.13.0

+

New Features:

+

Bugfixes:

+
+
+

FeatureExtraction 3.12.02025-10-28

@@ -284,7 +291,7 @@

Feature

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 2caf6c6..86d0a91 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: '3.4' -pkgdown: 2.1.0 +pandoc: 3.6.3 +pkgdown: 2.2.0 pkgdown_sha: ~ articles: CreatingCovariatesBasedOnOtherCohorts: CreatingCovariatesBasedOnOtherCohorts.html @@ -8,4 +8,4 @@ articles: CreatingCustomCovariateBuildersKorean: CreatingCustomCovariateBuildersKorean.html UsingFeatureExtraction: UsingFeatureExtraction.html UsingFeatureExtractionKorean: UsingFeatureExtractionKorean.html -last_built: 2025-10-28T06:29Z +last_built: 2026-03-05T19:00Z diff --git a/docs/reference/CovariateData-class.html b/docs/reference/CovariateData-class.html index 4993a01..c1e4b04 100644 --- a/docs/reference/CovariateData-class.html +++ b/docs/reference/CovariateData-class.html @@ -1,5 +1,5 @@ -Covariate Data — CovariateData-class • FeatureExtractionCovariate Data — CovariateData-class • FeatureExtraction FeatureExtraction - 3.12.0 + 3.13.0 @@ -129,7 +129,7 @@

See also

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/FeatureExtraction-package.html b/docs/reference/FeatureExtraction-package.html index 2394e46..1b67bc4 100644 --- a/docs/reference/FeatureExtraction-package.html +++ b/docs/reference/FeatureExtraction-package.html @@ -1,5 +1,5 @@ -FeatureExtraction: Generating Features for a Cohort — FeatureExtraction-package • FeatureExtractionFeatureExtraction: Generating Features for a Cohort — FeatureExtraction-package • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -110,7 +110,7 @@

Author

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/aggregateCovariates.html b/docs/reference/aggregateCovariates.html index 6ddaae9..b310f14 100644 --- a/docs/reference/aggregateCovariates.html +++ b/docs/reference/aggregateCovariates.html @@ -1,5 +1,5 @@ -Aggregate covariate data — aggregateCovariates • FeatureExtractionAggregate covariate data — aggregateCovariates • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -107,7 +107,7 @@

Examples

temporal = FALSE ) aggregatedCovariateData <- aggregateCovariates(covariateData) -#> Aggregating covariates took 0.441 secs +#> Aggregating covariates took 2.79 secs # } @@ -124,7 +124,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/computeStandardizedDifference.html b/docs/reference/computeStandardizedDifference.html index dd0739a..1e83d3d 100644 --- a/docs/reference/computeStandardizedDifference.html +++ b/docs/reference/computeStandardizedDifference.html @@ -1,5 +1,5 @@ -Compute standardized difference of mean for all covariates. — computeStandardizedDifference • FeatureExtractionCompute standardized difference of mean for all covariates. — computeStandardizedDifference • FeatureExtractionConvert prespecified covariate settings into detailed covariate settings — convertPrespecSettingsToDetailedSettings • FeatureExtractionConvert prespecified covariate settings into detailed covariate settings — convertPrespecSettingsToDetailedSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -123,7 +123,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createAnalysisDetails.html b/docs/reference/createAnalysisDetails.html index 23b158b..5389a79 100644 --- a/docs/reference/createAnalysisDetails.html +++ b/docs/reference/createAnalysisDetails.html @@ -1,5 +1,5 @@ -Create detailed covariate settings — createAnalysisDetails • FeatureExtractionCreate detailed covariate settings — createAnalysisDetails • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -178,7 +178,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createCohortAttrCovariateSettings.html b/docs/reference/createCohortAttrCovariateSettings.html index a3e7012..fb8c63a 100644 --- a/docs/reference/createCohortAttrCovariateSettings.html +++ b/docs/reference/createCohortAttrCovariateSettings.html @@ -1,5 +1,5 @@ -Create cohort attribute covariate settings — createCohortAttrCovariateSettings • FeatureExtractionCreate cohort attribute covariate settings — createCohortAttrCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -187,7 +187,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createCohortBasedCovariateSettings.html b/docs/reference/createCohortBasedCovariateSettings.html index 1a661af..3195f6b 100644 --- a/docs/reference/createCohortBasedCovariateSettings.html +++ b/docs/reference/createCohortBasedCovariateSettings.html @@ -1,5 +1,5 @@ -Create settings for covariates based on other cohorts — createCohortBasedCovariateSettings • FeatureExtractionCreate settings for covariates based on other cohorts — createCohortBasedCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -163,7 +163,7 @@

Details

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createCohortBasedTemporalCovariateSettings.html b/docs/reference/createCohortBasedTemporalCovariateSettings.html index ceb72b1..2b64586 100644 --- a/docs/reference/createCohortBasedTemporalCovariateSettings.html +++ b/docs/reference/createCohortBasedTemporalCovariateSettings.html @@ -1,5 +1,5 @@ -Create settings for temporal covariates based on other cohorts — createCohortBasedTemporalCovariateSettings • FeatureExtractionCreate settings for temporal covariates based on other cohorts — createCohortBasedTemporalCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -171,7 +171,7 @@

Details

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createCovariateSettings.html b/docs/reference/createCovariateSettings.html index a41f408..3001849 100644 --- a/docs/reference/createCovariateSettings.html +++ b/docs/reference/createCovariateSettings.html @@ -1,5 +1,5 @@ -Create covariate settings — createCovariateSettings • FeatureExtractionCreate covariate settings — createCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -1109,7 +1109,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createDefaultCovariateSettings.html b/docs/reference/createDefaultCovariateSettings.html index 84be26e..7c0e7c4 100644 --- a/docs/reference/createDefaultCovariateSettings.html +++ b/docs/reference/createDefaultCovariateSettings.html @@ -1,5 +1,5 @@ -Create default covariate settings — createDefaultCovariateSettings • FeatureExtractionCreate default covariate settings — createDefaultCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -149,7 +149,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createDefaultTemporalCovariateSettings.html b/docs/reference/createDefaultTemporalCovariateSettings.html index ad650b6..24de983 100644 --- a/docs/reference/createDefaultTemporalCovariateSettings.html +++ b/docs/reference/createDefaultTemporalCovariateSettings.html @@ -1,5 +1,5 @@ -Create default covariate settings — createDefaultTemporalCovariateSettings • FeatureExtractionCreate default covariate settings — createDefaultTemporalCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -149,7 +149,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createDetailedCovariateSettings.html b/docs/reference/createDetailedCovariateSettings.html index 2cfe61c..8348d9d 100644 --- a/docs/reference/createDetailedCovariateSettings.html +++ b/docs/reference/createDetailedCovariateSettings.html @@ -1,5 +1,5 @@ -Create detailed covariate settings — createDetailedCovariateSettings • FeatureExtractionCreate detailed covariate settings — createDetailedCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -137,7 +137,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createDetailedTemporalCovariateSettings.html b/docs/reference/createDetailedTemporalCovariateSettings.html index ab49f27..7b92782 100644 --- a/docs/reference/createDetailedTemporalCovariateSettings.html +++ b/docs/reference/createDetailedTemporalCovariateSettings.html @@ -1,5 +1,5 @@ -Create detailed temporal covariate settings — createDetailedTemporalCovariateSettings • FeatureExtractionCreate detailed temporal covariate settings — createDetailedTemporalCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -157,7 +157,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createEmptyCovariateData.html b/docs/reference/createEmptyCovariateData.html index 0fc5be0..a028f71 100644 --- a/docs/reference/createEmptyCovariateData.html +++ b/docs/reference/createEmptyCovariateData.html @@ -1,5 +1,5 @@ -Creates an empty covariate data object — createEmptyCovariateData • FeatureExtractionCreates an empty covariate data object — createEmptyCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -128,7 +128,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createTable1.html b/docs/reference/createTable1.html index 29e30e0..5fc475a 100644 --- a/docs/reference/createTable1.html +++ b/docs/reference/createTable1.html @@ -1,5 +1,5 @@ -Create a table 1 — createTable1 • FeatureExtractionCreate a table 1 — createTable1 • FeatureExtractionCreate covariate settings for a table 1 — createTable1CovariateSettings • FeatureExtractionCreate covariate settings for a table 1 — createTable1CovariateSettings • FeatureExtractionCreate covariate settings — createTemporalCovariateSettings • FeatureExtractionCreate covariate settings — createTemporalCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -486,7 +486,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/createTemporalSequenceCovariateSettings.html b/docs/reference/createTemporalSequenceCovariateSettings.html index 24b275f..9ac900c 100644 --- a/docs/reference/createTemporalSequenceCovariateSettings.html +++ b/docs/reference/createTemporalSequenceCovariateSettings.html @@ -1,5 +1,5 @@ -Create covariate settings — createTemporalSequenceCovariateSettings • FeatureExtractionCreate covariate settings — createTemporalSequenceCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -315,7 +315,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dot-createLooCovariateSettings.html b/docs/reference/dot-createLooCovariateSettings.html index d12b599..c766307 100644 --- a/docs/reference/dot-createLooCovariateSettings.html +++ b/docs/reference/dot-createLooCovariateSettings.html @@ -1,5 +1,5 @@ -Get covariate settings — .createLooCovariateSettings • FeatureExtractionGet covariate settings — .createLooCovariateSettings • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -109,7 +109,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/dot-getDbLooCovariateData.html b/docs/reference/dot-getDbLooCovariateData.html index d1eef43..458d0bf 100644 --- a/docs/reference/dot-getDbLooCovariateData.html +++ b/docs/reference/dot-getDbLooCovariateData.html @@ -1,5 +1,5 @@ -Get covariate information from the database — .getDbLooCovariateData • FeatureExtractionGet covariate information from the database — .getDbLooCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -91,7 +91,8 @@

Get covariate information from the database

rowIdField = "subject_id", covariateSettings, aggregated = FALSE, - minCharacterizationMean = 0 + minCharacterizationMean = 0, + ... ) @@ -155,6 +156,10 @@

Arguments

will help reduce the file size of the characterization output, but will remove information on covariates that have very low values. The default is 0.

+ +
...
+

Additional arguments, not used.

+

Value

@@ -173,7 +178,7 @@

Value

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/filterByCohortDefinitionId.html b/docs/reference/filterByCohortDefinitionId.html index 471589b..b0d52d2 100644 --- a/docs/reference/filterByCohortDefinitionId.html +++ b/docs/reference/filterByCohortDefinitionId.html @@ -1,5 +1,5 @@ -Filter covariates by cohort definition IDs — filterByCohortDefinitionId • FeatureExtractionFilter covariates by cohort definition IDs — filterByCohortDefinitionId • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -134,7 +134,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/filterByRowId.html b/docs/reference/filterByRowId.html index 5535bdd..930738f 100644 --- a/docs/reference/filterByRowId.html +++ b/docs/reference/filterByRowId.html @@ -1,5 +1,5 @@ -Filter covariates by row ID — filterByRowId • FeatureExtractionFilter covariates by row ID — filterByRowId • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -130,7 +130,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/getDbCohortAttrCovariatesData.html b/docs/reference/getDbCohortAttrCovariatesData.html index db2c462..e23f9a9 100644 --- a/docs/reference/getDbCohortAttrCovariatesData.html +++ b/docs/reference/getDbCohortAttrCovariatesData.html @@ -1,5 +1,5 @@ -Getcovariate information from the database through the cohort_attribute table — getDbCohortAttrCovariatesData • FeatureExtractionGetcovariate information from the database through the cohort_attribute table — getDbCohortAttrCovariatesData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -191,8 +191,8 @@

Details

Examples

# \donttest{
-connectionDetails <- Eunomia::getEunomiaConnectionDetails()
-Eunomia::createCohorts(
+connectionDetails <- Eunomia::getEunomiaConnectionDetails()
+Eunomia::createCohorts(
   connectionDetails = connectionDetails,
   cdmDatabaseSchema = "main",
   cohortDatabaseSchema = "main",
@@ -237,8 +237,8 @@ 
Examples

   aggregated = FALSE
 )
 #> Constructing covariates from cohort attributes table
-#> Inserting data took 0.00588 secs
-#> Loading took 0.0269 secs
+#> Inserting data took 0.0172 secs
+#> Loading took 0.0838 secs
 # }
@@ -255,7 +255,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/getDbCohortBasedCovariatesData.html b/docs/reference/getDbCohortBasedCovariatesData.html index 2f33870..16cd0ed 100644 --- a/docs/reference/getDbCohortBasedCovariatesData.html +++ b/docs/reference/getDbCohortBasedCovariatesData.html @@ -1,5 +1,5 @@ -Get covariate information from the database based on other cohorts — getDbCohortBasedCovariatesData • FeatureExtractionGet covariate information from the database based on other cohorts — getDbCohortBasedCovariatesData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -91,6 +91,12 @@

Get covariate information from the database based on other cohorts

cdmVersion = "5", rowIdField = "subject_id", covariateSettings, + targetDatabaseSchema = NULL, + targetCovariateTable = NULL, + targetCovariateContinuousTable = NULL, + targetCovariateRefTable = NULL, + targetAnalysisRefTable = NULL, + targetTimeRefTable = NULL, aggregated = FALSE, minCharacterizationMean = 0, tempEmulationSchema = getOption("sqlRenderTempEmulationSchema") @@ -153,6 +159,34 @@

Arguments

createCohortBasedTemporalCovariateSettings functions.

+
targetDatabaseSchema
+

(Optional) The name of the database schema where the resulting covariates +should be stored. If not provided, results will be fetched to R.

+ + +
targetCovariateTable
+

(Optional) The name of the table where the resulting covariates will +be stored. If not provided, results will be fetched to R. The table can be +a permanent table in the targetDatabaseSchema or a temp table. If +it is a temp table, do not specify targetDatabaseSchema.

+ + +
targetCovariateContinuousTable
+

(Optional) The name of the table where the resulting continuous covariates should be stored.

+ + +
targetCovariateRefTable
+

(Optional) The name of the table where the covariate reference will be stored.

+ + +
targetAnalysisRefTable
+

(Optional) The name of the table where the analysis reference will be stored.

+ + +
targetTimeRefTable
+

(Optional) The name of the table for the time reference

+ +
aggregated

Should aggregate statistics be computed instead of covariates per cohort entry?

@@ -208,7 +242,7 @@

Details

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/getDbCovariateData.html b/docs/reference/getDbCovariateData.html index ac14aa1..3063818 100644 --- a/docs/reference/getDbCovariateData.html +++ b/docs/reference/getDbCovariateData.html @@ -1,5 +1,5 @@ -Get covariate information from the database — getDbCovariateData • FeatureExtractionGet covariate information from the database — getDbCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -94,6 +94,15 @@

Get covariate information from the database

cohortIds = c(-1), rowIdField = "subject_id", covariateSettings, + exportToTable = FALSE, + createTable = exportToTable, + dropTableIfExists = exportToTable, + targetDatabaseSchema = NULL, + targetCovariateTable = NULL, + targetCovariateContinuousTable = NULL, + targetCovariateRefTable = NULL, + targetAnalysisRefTable = NULL, + targetTimeRefTable = NULL, aggregated = FALSE, minCharacterizationMean = 0, tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"), @@ -174,6 +183,53 @@

Arguments

of the createCovariate functions, or a list of such objects.

+
exportToTable
+

Whether to export to a table rather than Andromeda object

+ + +
createTable
+

Run sql to create table? Code does not check if table exists.

+ + +
dropTableIfExists
+

If targetDatabaseSchema, drop any existing tables. Otherwise, results are merged +into existing table data. Overides createTable.

+ + +
targetDatabaseSchema
+

(Optional) The name of the database schema where the resulting covariates +should be stored as a table. If not provided, results will be fetched to R.

+ + +
targetCovariateTable
+

(Optional) The name of the table where the resulting covariates will +be stored. If not provided, results will be fetched to R. The table can be +a permanent table in the targetDatabaseSchema or a temp table. If +it is a temp table, do not specify targetDatabaseSchema.

+ + +
targetCovariateContinuousTable
+

(Optional) The name of the table where the resulting continuous covariates will +be stored. If not provided, results will be fetched to R. The table can be +a permanent table in the targetDatabaseSchema or a temp table. If +it is a temp table, do not specify targetDatabaseSchema.

+ + +
targetCovariateRefTable
+

(Optional) The name of the table where the covariate reference will be stored. If +it is a temp table, do not specify targetDatabaseSchema.

+ + +
targetAnalysisRefTable
+

(Optional) The name of the table where the analysis reference will be stored. If +it is a temp table, do not specify targetDatabaseSchema.

+ + +
targetTimeRefTable
+

(Optional) The name of the table for the time reference. If +it is a temp table, do not specify targetDatabaseSchema.

+ +
aggregated

Should aggregate statistics be computed instead of covariates per cohort entry? If aggregated is set to FALSE, the results returned will be based @@ -218,9 +274,9 @@

Details

Examples

# \donttest{
-eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
+eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
 covSettings <- createDefaultCovariateSettings()
-Eunomia::createCohorts(
+Eunomia::createCohorts(
   connectionDetails = eunomiaConnectionDetails,
   cdmDatabaseSchema = "main",
   cohortDatabaseSchema = "main",
@@ -258,9 +314,9 @@ 
Examples

 #> Connecting using SQLite driver
 #> Constructing features on server
 #>   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                              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-#> Executing SQL took 1.41 secs
+#> Executing SQL took 2.06 secs
 #> Fetching data from server
-#> Fetching data took 0.158 secs
+#> Fetching data took 0.671 secs
 # }
@@ -277,7 +333,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/getDbDefaultCovariateData.html b/docs/reference/getDbDefaultCovariateData.html index 0f3f1f1..1cb21fe 100644 --- a/docs/reference/getDbDefaultCovariateData.html +++ b/docs/reference/getDbDefaultCovariateData.html @@ -1,5 +1,5 @@ -Get default covariate information from the database — getDbDefaultCovariateData • FeatureExtractionGet default covariate information from the database — getDbDefaultCovariateData • FeatureExtractionGet the default table 1 specifications — getDefaultTable1Specifications • FeatureExtractionGet the default table 1 specifications — getDefaultTable1Specifications • FeatureExtractionPackage index • FeatureExtractionPackage index • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -79,10 +79,6 @@

All functions

-

show(<CovariateData>) summary(<CovariateData>)

- -

Covariate Data

-

aggregateCovariates()

Aggregate covariate data

@@ -94,6 +90,10 @@

All functions convertPrespecSettingsToDetailedSettings()

Convert prespecified covariate settings into detailed covariate settings

+ +

show(<CovariateData>) summary(<CovariateData>)

+ +

Covariate Data

createAnalysisDetails()

@@ -227,7 +227,7 @@

All functions
-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/isAggregatedCovariateData.html b/docs/reference/isAggregatedCovariateData.html index 9a91c38..0653b3e 100644 --- a/docs/reference/isAggregatedCovariateData.html +++ b/docs/reference/isAggregatedCovariateData.html @@ -1,5 +1,5 @@ -Check whether covariate data is aggregated — isAggregatedCovariateData • FeatureExtractionCheck whether covariate data is aggregated — isAggregatedCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -122,7 +122,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/isCovariateData.html b/docs/reference/isCovariateData.html index ba0b904..ea8ae33 100644 --- a/docs/reference/isCovariateData.html +++ b/docs/reference/isCovariateData.html @@ -1,5 +1,5 @@ -Check whether an object is a CovariateData object — isCovariateData • FeatureExtractionCheck whether an object is a CovariateData object — isCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -121,7 +121,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/isTemporalCovariateData.html b/docs/reference/isTemporalCovariateData.html index 8c483c6..1b2f9a6 100644 --- a/docs/reference/isTemporalCovariateData.html +++ b/docs/reference/isTemporalCovariateData.html @@ -1,5 +1,5 @@ -Check whether covariate data is temporal — isTemporalCovariateData • FeatureExtractionCheck whether covariate data is temporal — isTemporalCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -122,7 +122,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/loadCovariateData.html b/docs/reference/loadCovariateData.html index 66943f4..b8c658a 100644 --- a/docs/reference/loadCovariateData.html +++ b/docs/reference/loadCovariateData.html @@ -1,5 +1,5 @@ -Load the covariate data from a folder — loadCovariateData • FeatureExtractionLoad the covariate data from a folder — loadCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -128,7 +128,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/replaceCovariateSettingsCohortSchemaTable.html b/docs/reference/replaceCovariateSettingsCohortSchemaTable.html index 4d5867a..3fca53e 100644 --- a/docs/reference/replaceCovariateSettingsCohortSchemaTable.html +++ b/docs/reference/replaceCovariateSettingsCohortSchemaTable.html @@ -1,5 +1,5 @@ -Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings — replaceCovariateSettingsCohortSchemaTable • FeatureExtractionUtility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings — replaceCovariateSettingsCohortSchemaTable • FeatureExtractionSave the covariate data to folder — saveCovariateData • FeatureExtractionSave the covariate data to folder — saveCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -137,7 +137,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/reference/tidyCovariateData.html b/docs/reference/tidyCovariateData.html index 0eeb6e8..f5e2b6b 100644 --- a/docs/reference/tidyCovariateData.html +++ b/docs/reference/tidyCovariateData.html @@ -1,5 +1,5 @@ -Tidy covariate data — tidyCovariateData • FeatureExtractionTidy covariate data — tidyCovariateData • FeatureExtraction @@ -17,7 +17,7 @@ FeatureExtraction - 3.12.0 + 3.13.0 @@ -137,7 +137,7 @@

Examples

normalize = TRUE, removeRedundancy = TRUE ) -#> Tidying covariates took 0.22 secs +#> Tidying covariates took 1.71 secs # } @@ -154,7 +154,7 @@

Examples

-

Site built with pkgdown 2.1.0.

+

Site built with pkgdown 2.2.0.

diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 2986c72..ed7afbb 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,20 +4,19 @@ /articles/CreatingCovariatesUsingCohortAttributes.html /articles/CreatingCustomCovariateBuilders.html /articles/CreatingCustomCovariateBuildersKorean.html +/articles/index.html /articles/UsingFeatureExtraction.html /articles/UsingFeatureExtractionKorean.html -/articles/index.html /authors.html /index.html /news/index.html /pull_request_template.html -/reference/CovariateData-class.html -/reference/FeatureExtraction-package.html /reference/aggregateCovariates.html /reference/byMaxFf.html /reference/bySumFf.html /reference/computeStandardizedDifference.html /reference/convertPrespecSettingsToDetailedSettings.html +/reference/CovariateData-class.html /reference/createAnalysisDetails.html /reference/createCohortAttrCovariateSettings.html /reference/createCohortBasedCovariateSettings.html @@ -35,6 +34,7 @@ /reference/createTemporalSequenceCovariateSettings.html /reference/dot-createLooCovariateSettings.html /reference/dot-getDbLooCovariateData.html +/reference/FeatureExtraction-package.html /reference/filterByCohortDefinitionId.html /reference/filterByRowId.html /reference/filterCovariateDataCovariates.html diff --git a/extras/CohortBasedCovariatesVignetteDataFetch.R b/extras/CohortBasedCovariatesVignetteDataFetch.R index f9fd175..ce62771 100644 --- a/extras/CohortBasedCovariatesVignetteDataFetch.R +++ b/extras/CohortBasedCovariatesVignetteDataFetch.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/extras/DefaultCovariateSettingsTemplate.R b/extras/DefaultCovariateSettingsTemplate.R index b7210f8..40ed0de 100644 --- a/extras/DefaultCovariateSettingsTemplate.R +++ b/extras/DefaultCovariateSettingsTemplate.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/extras/DetailedCovariateSettingsTemplate.R b/extras/DetailedCovariateSettingsTemplate.R index 61a6e61..88677a9 100644 --- a/extras/DetailedCovariateSettingsTemplate.R +++ b/extras/DetailedCovariateSettingsTemplate.R @@ -1,4 +1,4 @@ -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/extras/FeatureExtraction.pdf b/extras/FeatureExtraction.pdf index c2e45b0..ea6e9eb 100644 Binary files a/extras/FeatureExtraction.pdf and b/extras/FeatureExtraction.pdf differ diff --git a/extras/GetHdpsCovariates.R b/extras/GetHdpsCovariates.R index 150cf1d..098f099 100644 --- a/extras/GetHdpsCovariates.R +++ b/extras/GetHdpsCovariates.R @@ -1,6 +1,6 @@ # @file GetHdpsCovariates.R # -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R index a17d432..c44b82f 100644 --- a/extras/PackageMaintenance.R +++ b/extras/PackageMaintenance.R @@ -1,6 +1,6 @@ # @file PackageMaintenance # -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/extras/VignetteDataFetch.R b/extras/VignetteDataFetch.R index 13e63d0..a6d029e 100644 --- a/extras/VignetteDataFetch.R +++ b/extras/VignetteDataFetch.R @@ -1,6 +1,6 @@ # @file VignetteDataFetch.R # -# Copyright 2025 Observational Health Data Sciences and Informatics +# Copyright 2026 Observational Health Data Sciences and Informatics # # This file is part of FeatureExtraction # diff --git a/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf b/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf index 70ad1ce..f19c604 100644 Binary files a/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf and b/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf differ diff --git a/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf b/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf index b123d17..7c65014 100644 Binary files a/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf and b/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf differ diff --git a/inst/doc/CreatingCustomCovariateBuilders.pdf b/inst/doc/CreatingCustomCovariateBuilders.pdf index 113e9bc..209ccfd 100644 Binary files a/inst/doc/CreatingCustomCovariateBuilders.pdf and b/inst/doc/CreatingCustomCovariateBuilders.pdf differ diff --git a/inst/doc/CreatingCustomCovariateBuildersKorean.pdf b/inst/doc/CreatingCustomCovariateBuildersKorean.pdf index d70b37e..0cd129b 100644 Binary files a/inst/doc/CreatingCustomCovariateBuildersKorean.pdf and b/inst/doc/CreatingCustomCovariateBuildersKorean.pdf differ diff --git a/inst/doc/UsingFeatureExtraction.pdf b/inst/doc/UsingFeatureExtraction.pdf index 02bddec..2aa9268 100644 Binary files a/inst/doc/UsingFeatureExtraction.pdf and b/inst/doc/UsingFeatureExtraction.pdf differ diff --git a/inst/doc/UsingFeatureExtractionKorean.pdf b/inst/doc/UsingFeatureExtractionKorean.pdf index 1cc8fef..147fc6f 100644 Binary files a/inst/doc/UsingFeatureExtractionKorean.pdf and b/inst/doc/UsingFeatureExtractionKorean.pdf differ diff --git a/inst/sql/sql_server/CreateExportTables.sql b/inst/sql/sql_server/CreateExportTables.sql index 7065214..4dc2fd2 100644 --- a/inst/sql/sql_server/CreateExportTables.sql +++ b/inst/sql/sql_server/CreateExportTables.sql @@ -59,4 +59,4 @@ CREATE TABLE @time_ref_table ( time_interval BIGINT, sequence_start_day BIGINT, sequence_end_day BIGINT - ); \ No newline at end of file + ); diff --git a/inst/sql/sql_server/GetAttrCovariates.sql b/inst/sql/sql_server/GetAttrCovariates.sql index 7a71b66..908d539 100644 --- a/inst/sql/sql_server/GetAttrCovariates.sql +++ b/inst/sql/sql_server/GetAttrCovariates.sql @@ -1,7 +1,7 @@ /************************************************************************ @file GetAttrCovariates.sql -Copyright 2025 Observational Health Data Sciences and Informatics +Copyright 2026 Observational Health Data Sciences and Informatics This file is part of FeatureExtraction diff --git a/inst/sql/sql_server/GetHdpsCovariates.sql b/inst/sql/sql_server/GetHdpsCovariates.sql index 52450bf..57a44f3 100644 --- a/inst/sql/sql_server/GetHdpsCovariates.sql +++ b/inst/sql/sql_server/GetHdpsCovariates.sql @@ -1,5 +1,5 @@ /************************************************************************ -Copyright 2025 Observational Health Data Sciences and Informatics +Copyright 2026 Observational Health Data Sciences and Informatics This file is part of FeatureExtraction diff --git a/inst/sql/sql_server/IncludeDescendants.sql b/inst/sql/sql_server/IncludeDescendants.sql index e97e6d5..5ca458a 100644 --- a/inst/sql/sql_server/IncludeDescendants.sql +++ b/inst/sql/sql_server/IncludeDescendants.sql @@ -1,5 +1,5 @@ /************************************************************************ -Copyright 2025 Observational Health Data Sciences and Informatics +Copyright 2026 Observational Health Data Sciences and Informatics This file is part of FeatureExtraction diff --git a/inst/sql/sql_server/RemoveCovariateTempTables.sql b/inst/sql/sql_server/RemoveCovariateTempTables.sql index aaf3fb1..daad97b 100644 --- a/inst/sql/sql_server/RemoveCovariateTempTables.sql +++ b/inst/sql/sql_server/RemoveCovariateTempTables.sql @@ -1,5 +1,5 @@ /************************************************************************ -Copyright 2025 Observational Health Data Sciences and Informatics +Copyright 2026 Observational Health Data Sciences and Informatics This file is part of FeatureExtraction diff --git a/java/org/ohdsi/featureExtraction/FeatureExtraction.java b/java/org/ohdsi/featureExtraction/FeatureExtraction.java index 7e0de8c..d403e82 100644 --- a/java/org/ohdsi/featureExtraction/FeatureExtraction.java +++ b/java/org/ohdsi/featureExtraction/FeatureExtraction.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright 2025 Observational Health Data Sciences and Informatics + * Copyright 2026 Observational Health Data Sciences and Informatics * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/java/org/ohdsi/featureExtraction/ReadCSVFile.java b/java/org/ohdsi/featureExtraction/ReadCSVFile.java index 6e423b4..29652fb 100644 --- a/java/org/ohdsi/featureExtraction/ReadCSVFile.java +++ b/java/org/ohdsi/featureExtraction/ReadCSVFile.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright 2025 Observational Health Data Sciences and Informatics + * Copyright 2026 Observational Health Data Sciences and Informatics * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java b/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java index 028d3d0..ae8ac5a 100644 --- a/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java +++ b/java/org/ohdsi/featureExtraction/ReadCSVFileWithHeader.java @@ -1,5 +1,5 @@ /******************************************************************************* - * Copyright 2025 Observational Health Data Sciences and Informatics + * Copyright 2026 Observational Health Data Sciences and Informatics * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/tests/testthat/test-GetDefaultCovariates.R b/tests/testthat/test-GetDefaultCovariates.R index 4411827..c832a4c 100644 --- a/tests/testthat/test-GetDefaultCovariates.R +++ b/tests/testthat/test-GetDefaultCovariates.R @@ -41,4 +41,3 @@ test_that("Test exit conditions", { aggregated = TRUE )) }) - diff --git a/tests/testthat/test-Table1.R b/tests/testthat/test-Table1.R index ad169f8..3300adc 100644 --- a/tests/testthat/test-Table1.R +++ b/tests/testthat/test-Table1.R @@ -80,7 +80,6 @@ test_that("createTable1 works with categorical covariates", { }) - test_that("createTable1 works with continuous covariates", { skip_on_cran() skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))