diff --git a/DESCRIPTION b/DESCRIPTION index fddffaee2..81daa817c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CohortDiagnostics Type: Package Title: Diagnostics for OHDSI Cohorts -Version: 3.2.4 +Version: 3.3.0 Date: 2022-12-19 Authors@R: c( person("Jamie", "Gilbert", email = "gilbert@ohdsi.org", role = c("aut", "cre")), @@ -25,7 +25,7 @@ Depends: R (>= 4.1.0) Imports: Andromeda (>= 0.6.0), - ResultModelManager, + ResultModelManager (>= 0.5.2), checkmate, clock, digest, @@ -50,14 +50,16 @@ Suggests: zip, knitr, shiny, - OhdsiShinyModules + OhdsiShinyModules, + rsconnect, + yaml Remotes: ohdsi/Eunomia, ohdsi/FeatureExtraction, ohdsi/ResultModelManager, ohdsi/ROhdsiWebApi, ohdsi/CirceR, - ohdsi/CohortGenerator, + ohdsi/CohortGenerator@random_sample, ohdsi/OhdsiShinyModules License: Apache License VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index 2626704ae..883dc22a9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,6 +3,7 @@ export(createDiagnosticsExplorerZip) export(createMergedResultsFile) export(createResultsDataModel) +export(deployPositConnectApp) export(executeDiagnostics) export(getCdmDataSourceInformation) export(getCohortCounts) diff --git a/NEWS.md b/NEWS.md index 92ea27cad..67404baf1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,22 @@ +CohortDiagnostics 3.3.0 +======================= + +Changes: + +1. Resolved issues with package creating build errors + +2. Added function to make deployment to posit connect servers easier + +3. Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very +large cohort definitions + +Bug fix: + +1. Fixes to loading shiny app in OHDSI shiny modules + +2. Bug fixes to prevent null value issues with included source concept diagnostics + + CohortDiagnostics 3.2.4 ======================= Bug Fix: diff --git a/R/CohortCharacterizationDiagnostics.R b/R/CohortCharacterizationDiagnostics.R index 2878ab9c0..030e0c765 100644 --- a/R/CohortCharacterizationDiagnostics.R +++ b/R/CohortCharacterizationDiagnostics.R @@ -82,11 +82,11 @@ getCohortCharacteristics <- function(connectionDetails = NULL, covariates <- featureExtractionOutput$covariates %>% dplyr::rename("cohortId" = "cohortDefinitionId") %>% dplyr::left_join(populationSize, by = "cohortId", copy = TRUE) %>% - dplyr::mutate(p = sumValue / populationSize) + dplyr::mutate(p = .data$sumValue / populationSize) if (nrow(covariates %>% - dplyr::filter(p > 1) %>% - dplyr::collect()) > 0) { + dplyr::filter(.data$p > 1) %>% + dplyr::collect()) > 0) { stop( paste0( "During characterization, population size (denominator) was found to be smaller than features Value (numerator).", @@ -96,10 +96,10 @@ getCohortCharacteristics <- function(connectionDetails = NULL, } covariates <- covariates %>% - dplyr::mutate(sd = sqrt(p * (1 - p))) %>% - dplyr::select(-p) %>% + dplyr::mutate(sd = sqrt(.data$p * (1 - .data$p))) %>% + dplyr::select(-"p") %>% dplyr::rename("mean" = "averageValue") %>% - dplyr::select(-populationSize) + dplyr::select(-"populationSize") if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) { covariates <- covariates %>% @@ -113,13 +113,13 @@ getCohortCharacteristics <- function(connectionDetails = NULL, ) tidNaCount <- covariates %>% - dplyr::filter(is.na(timeId)) %>% + dplyr::filter(is.na(.data$timeId)) %>% dplyr::count() %>% dplyr::pull() if (tidNaCount > 0) { covariates <- covariates %>% - dplyr::mutate(timeId = if_else(is.na(.data$timeId), -1, .data$timeId)) + dplyr::mutate(timeId = dplyr::if_else(is.na(.data$timeId), -1, .data$timeId)) } } else { covariates <- covariates %>% @@ -144,9 +144,9 @@ getCohortCharacteristics <- function(connectionDetails = NULL, dplyr::pull(dplyr::count(featureExtractionOutput$covariatesContinuous)) > 0) { covariates <- featureExtractionOutput$covariatesContinuous %>% dplyr::rename( - mean = averageValue, - sd = standardDeviation, - cohortId = cohortDefinitionId + mean = "averageValue", + sd = "standardDeviation", + cohortId = "cohortDefinitionId" ) covariatesContinuous <- covariates if (FeatureExtraction::isTemporalCovariateData(featureExtractionOutput)) { @@ -162,13 +162,13 @@ getCohortCharacteristics <- function(connectionDetails = NULL, ) tidNaCount <- covariates %>% - dplyr::filter(is.na(timeId)) %>% + dplyr::filter(is.na(.data$timeId)) %>% dplyr::count() %>% dplyr::pull() if (tidNaCount > 0) { covariates <- covariates %>% - dplyr::mutate(timeId = if_else(is.na(.data$timeId), -1, .data$timeId)) + dplyr::mutate(timeId = dplyr::if_else(is.na(.data$timeId), -1, .data$timeId)) } } else { covariates <- covariates %>% @@ -235,7 +235,7 @@ executeCohortCharacterization <- function(connection, startCohortCharacterization <- Sys.time() subset <- subsetToRequiredCohorts( cohorts = cohorts %>% - dplyr::filter(cohortId %in% instantiatedCohorts), + dplyr::filter(.data$cohortId %in% instantiatedCohorts), task = task, incremental = incremental, recordKeepingFile = recordKeepingFile @@ -286,7 +286,7 @@ executeCohortCharacterization <- function(connection, tempEmulationSchema = tempEmulationSchema, cohortDatabaseSchema = cohortDatabaseSchema, cohortTable = cohortTable, - cohortIds = subset[start:end,]$cohortId, + cohortIds = subset[start:end, ]$cohortId, covariateSettings = covariateSettings, cdmVersion = cdmVersion, exportFolder = exportFolder @@ -308,9 +308,9 @@ executeCohortCharacterization <- function(connection, ) recordTasksDone( - cohortId = subset[start:end,]$cohortId, + cohortId = subset[start:end, ]$cohortId, task = task, - checksum = subset[start:end,]$checksum, + checksum = subset[start:end, ]$checksum, recordKeepingFile = recordKeepingFile, incremental = incremental ) diff --git a/R/CohortRelationship.R b/R/CohortRelationship.R index ed56c1f01..b7b3ee194 100644 --- a/R/CohortRelationship.R +++ b/R/CohortRelationship.R @@ -85,7 +85,7 @@ runCohortRelationshipDiagnostics <- timePeriods <- relationshipDays %>% dplyr::distinct() %>% - dplyr::arrange(startDay, endDay) %>% + dplyr::arrange(.data$startDay, .data$endDay) %>% dplyr::mutate(timeId = dplyr::row_number()) ParallelLogger::logTrace(" - Creating Andromeda object to collect results") @@ -161,12 +161,12 @@ runCohortRelationshipDiagnostics <- resultsInAndromeda$cohortRelationships <- resultsInAndromeda$cohortRelationships %>% dplyr::inner_join(resultsInAndromeda$timePeriods, by = "timeId") %>% - dplyr::select(-timeId) %>% + dplyr::select(-"timeId") %>% dplyr::arrange( - cohortId, - comparatorCohortId, - startDay, - endDay + .data$cohortId, + .data$comparatorCohortId, + .data$startDay, + .data$endDay ) resultsInAndromeda$timePeriods <- NULL @@ -209,21 +209,21 @@ executeCohortRelationshipDiagnostics <- function(connection, startCohortRelationship <- Sys.time() allCohortIds <- cohortDefinitionSet %>% - dplyr::select(cohortId, checksum) %>% + dplyr::select("cohortId", "checksum") %>% dplyr::rename( - targetCohortId = cohortId, - targetChecksum = checksum + targetCohortId = "cohortId", + targetChecksum = "checksum" ) %>% dplyr::distinct() combinationsOfPossibleCohortRelationships <- allCohortIds %>% tidyr::crossing(allCohortIds %>% dplyr::rename( - comparatorCohortId = targetCohortId, - comparatorChecksum = targetChecksum + comparatorCohortId = "targetCohortId", + comparatorChecksum = "targetChecksum" )) %>% - dplyr::filter(targetCohortId != comparatorCohortId) %>% - dplyr::arrange(targetCohortId, comparatorCohortId) %>% - dplyr::mutate(checksum = paste0(targetChecksum, comparatorChecksum)) + dplyr::filter(.data$targetCohortId != .data$comparatorCohortId) %>% + dplyr::arrange(.data$targetCohortId, .data$comparatorCohortId) %>% + dplyr::mutate(checksum = paste0(.data$targetChecksum, .data$comparatorChecksum)) subset <- subsetToRequiredCombis( combis = combinationsOfPossibleCohortRelationships, @@ -247,7 +247,7 @@ executeCohortRelationshipDiagnostics <- function(connection, (nrow(combinationsOfPossibleCohortRelationships) - ( nrow( combinationsOfPossibleCohortRelationships %>% - dplyr::filter(targetCohortId %in% c(subset$targetCohortId)) + dplyr::filter(.data$targetCohortId %in% c(subset$targetCohortId)) ) )) > 0) { ParallelLogger::logInfo( @@ -255,7 +255,7 @@ executeCohortRelationshipDiagnostics <- function(connection, " - Skipping %s combinations in incremental mode because these were previously computed.", nrow(combinationsOfPossibleCohortRelationships) - nrow( combinationsOfPossibleCohortRelationships %>% - dplyr::filter(targetCohortId %in% c(subset$targetCohortId)) + dplyr::filter(.data$targetCohortId %in% c(subset$targetCohortId)) ) ) ) diff --git a/R/ConceptSets.R b/R/ConceptSets.R index 141a1e89c..95f1991e3 100644 --- a/R/ConceptSets.R +++ b/R/ConceptSets.R @@ -20,6 +20,9 @@ extractConceptSetsSqlFromCohortSql <- function(cohortSql) { } sql <- gsub("with primary_events.*", "", cohortSql) + if (is.null(sql) || length(nchar(sql)) == 0 || is.na(nchar(sql)) || is.nan(nchar(sql))) { + return(tidyr::tibble()) + } # Find opening and closing parentheses: starts <- stringr::str_locate_all(sql, "\\(")[[1]][, 1] ends <- stringr::str_locate_all(sql, "\\)")[[1]][, 1] @@ -71,8 +74,14 @@ extractConceptSetsSqlFromCohortSql <- function(cohortSql) { extractConceptSetsJsonFromCohortJson <- function(cohortJson) { - cohortDefinition <- - RJSONIO::fromJSON(content = cohortJson, digits = 23) + cohortDefinition <- tryCatch( + { + RJSONIO::fromJSON(content = cohortJson, digits = 23) + }, + error = function(msg) { + return(list()) + } + ) if ("expression" %in% names(cohortDefinition)) { expression <- cohortDefinition$expression } else { @@ -121,10 +130,10 @@ combineConceptSetsFromCohorts <- function(cohorts) { checkmate::reportAssertions(errorMessage) checkmate::assertDataFrame( x = cohorts %>% dplyr::select( - cohortId, - sql, - json, - cohortName + "cohortId", + "sql", + "json", + "cohortName" ), any.missing = FALSE, min.cols = 4, @@ -176,7 +185,7 @@ combineConceptSetsFromCohorts <- function(cohorts) { } } if (length(conceptSets) == 0) { - return(NULL) + return(data.frame()) } conceptSets <- dplyr::bind_rows(conceptSets) %>% dplyr::arrange(.data$cohortId, .data$conceptSetId) @@ -187,7 +196,10 @@ combineConceptSetsFromCohorts <- function(cohorts) { dplyr::distinct() conceptSets <- conceptSets %>% - dplyr::inner_join(uniqueConceptSets, by = "conceptSetExpression") %>% + dplyr::inner_join(uniqueConceptSets, + by = "conceptSetExpression", + relationship = "many-to-many" + ) %>% dplyr::distinct() %>% dplyr::relocate( "uniqueConceptSetId", @@ -321,7 +333,7 @@ getCodeSetIds <- function(criterionList) { return(NULL) } else { return(dplyr::tibble(domain = names(criterionList), codeSetIds = codeSetIds) - %>% dplyr::filter(!is.na(codeSetIds))) + %>% dplyr::filter(!is.na(.data$codeSetIds))) } } @@ -330,11 +342,17 @@ exportConceptSets <- function(cohortDefinitionSet, exportFolder, minCellCount, d # We need to get concept sets from all cohorts in case subsets are present and # Added incrementally after cohort generation conceptSets <- combineConceptSetsFromCohorts(cohortDefinitionSet) + + if (!hasData(conceptSets)) { + return(invisible(NULL)) + } + + conceptSets <- conceptSets %>% + dplyr::select(-"uniqueConceptSetId") %>% + dplyr::distinct() # Save concept set metadata --------------------------------------- conceptSetsExport <- makeDataExportable( - x = conceptSets %>% - dplyr::select(-uniqueConceptSetId) %>% - dplyr::distinct(), + x = conceptSets, tableName = "concept_sets", minCellCount = minCellCount, databaseId = databaseId @@ -404,7 +422,7 @@ runConceptSetDiagnostics <- function(connection, subset <- dplyr::distinct(subset) if (nrow(subset) == 0) { - return() + return(NULL) } # We need to get concept sets from all cohorts in case subsets are present and @@ -514,7 +532,8 @@ runConceptSetDiagnostics <- function(connection, "cohortId", "conceptSetId" ) %>% dplyr::distinct(), - by = "uniqueConceptSetId" + by = "uniqueConceptSetId", + relationship = "many-to-many" ) %>% dplyr::select(-"uniqueConceptSetId") %>% dplyr::mutate(databaseId = !!databaseId) %>% @@ -664,7 +683,7 @@ runConceptSetDiagnostics <- function(connection, ) return(tidyr::tibble()) } - primaryCodesetIds <- primaryCodesetIds %>% dplyr::filter(domain %in% + primaryCodesetIds <- primaryCodesetIds %>% dplyr::filter(.data$domain %in% c(domains$domain %>% unique())) if (nrow(primaryCodesetIds) == 0) { warning( @@ -927,7 +946,8 @@ runConceptSetDiagnostics <- function(connection, "cohortId", "conceptSetId" ) %>% dplyr::distinct(), - by = "uniqueConceptSetId" + by = "uniqueConceptSetId", + relationship = "many-to-many" ) %>% dplyr::select(-"uniqueConceptSetId") %>% dplyr::select( @@ -943,8 +963,8 @@ runConceptSetDiagnostics <- function(connection, .data$conceptId ) %>% dplyr::summarise( - conceptCount = max(conceptCount), - conceptSubjects = max(conceptSubjects) + conceptCount = max(.data$conceptCount), + conceptSubjects = max(.data$conceptSubjects) ) %>% dplyr::ungroup() data <- makeDataExportable( @@ -1012,7 +1032,8 @@ runConceptSetDiagnostics <- function(connection, dplyr::tibble() %>% dplyr::rename("uniqueConceptSetId" = "codesetId") %>% dplyr::inner_join(conceptSets %>% dplyr::distinct(), - by = "uniqueConceptSetId" + by = "uniqueConceptSetId", + relationship = "many-to-many" ) %>% dplyr::select( "cohortId", diff --git a/R/ExportCharacterization.R b/R/ExportCharacterization.R index c82a1f9bb..62ffe1d94 100644 --- a/R/ExportCharacterization.R +++ b/R/ExportCharacterization.R @@ -31,7 +31,7 @@ exportCharacterization <- function(characteristics, } else if (dplyr::pull(dplyr::count(characteristics$covariateRef)) > 0) { characteristics$filteredCovariates <- characteristics$covariates %>% - dplyr::filter(mean >= minCharacterizationMean) %>% + dplyr::filter(.data$mean >= minCharacterizationMean) %>% dplyr::mutate(databaseId = !!databaseId) %>% dplyr::left_join(counts, by = c("cohortId", "databaseId"), @@ -39,22 +39,22 @@ exportCharacterization <- function(characteristics, ) %>% dplyr::mutate( mean = dplyr::if_else( - mean != 0 & mean < minCellCount / as.numeric(cohortEntries), - -minCellCount / as.numeric(cohortEntries), - mean + .data$mean != 0 & .data$mean < minCellCount / as.numeric(.data$cohortEntries), + -minCellCount / as.numeric(.data$cohortEntries), + .data$mean ), sumValue = dplyr::if_else( - sumValue != 0 & sumValue < minCellCount, + .data$sumValue != 0 & .data$sumValue < minCellCount, -minCellCount, - sumValue + .data$sumValue ) ) %>% - dplyr::mutate(sd = dplyr::if_else(mean >= 0, sd, 0)) %>% + dplyr::mutate(sd = dplyr::if_else(mean >= 0, .data$sd, 0)) %>% dplyr::mutate( - mean = round(mean, digits = 4), - sd = round(sd, digits = 4) + mean = round(.data$mean, digits = 4), + sd = round(.data$sd, digits = 4) ) %>% - dplyr::select(-cohortEntries, -cohortSubjects) %>% + dplyr::select(-"cohortEntries", -"cohortSubjects") %>% dplyr::distinct() %>% makeDataExportable( tableName = "temporal_covariate_value", diff --git a/R/IncidenceRates.R b/R/IncidenceRates.R index 345421f3e..1a081c779 100644 --- a/R/IncidenceRates.R +++ b/R/IncidenceRates.R @@ -218,7 +218,7 @@ computeIncidenceRates <- function(connection, startIncidenceRate <- Sys.time() subset <- subsetToRequiredCohorts( cohorts = cohorts %>% - dplyr::filter(cohortId %in% instantiatedCohorts), + dplyr::filter(.data$cohortId %in% instantiatedCohorts), task = "runIncidenceRate", incremental = incremental, recordKeepingFile = recordKeepingFile diff --git a/R/InclusionRules.R b/R/InclusionRules.R index 8648f10f9..70214a44f 100644 --- a/R/InclusionRules.R +++ b/R/InclusionRules.R @@ -27,7 +27,7 @@ getInclusionStats <- function(connection, ParallelLogger::logInfo("Fetching inclusion statistics from files") subset <- subsetToRequiredCohorts( cohorts = cohortDefinitionSet %>% - dplyr::filter(cohortId %in% instantiatedCohorts), + dplyr::filter(.data$cohortId %in% instantiatedCohorts), task = "runInclusionStatistics", incremental = incremental, recordKeepingFile = recordKeepingFile diff --git a/R/Incremental.R b/R/Incremental.R index b49dfb199..99fb64a19 100644 --- a/R/Incremental.R +++ b/R/Incremental.R @@ -125,11 +125,11 @@ recordTasksDone <- as.character(recordKeeping$timeStamp) if ("cohortId" %in% colnames(recordKeeping)) { recordKeeping <- recordKeeping %>% - dplyr::mutate(cohortId = as.double(cohortId)) + dplyr::mutate(cohortId = as.double(.data$cohortId)) } if ("comparatorId" %in% colnames(recordKeeping)) { recordKeeping <- recordKeeping %>% - dplyr::mutate(comparatorId = as.double(comparatorId)) + dplyr::mutate(comparatorId = as.double(.data$comparatorId)) } idx <- getKeyIndex(list(...), recordKeeping) if (length(idx) > 0) { diff --git a/R/Private.R b/R/Private.R index c8381f1a9..f7317affe 100644 --- a/R/Private.R +++ b/R/Private.R @@ -56,9 +56,11 @@ swapColumnContents <- enforceMinCellValue <- function(data, columnName, minValues, silent = FALSE) { + data <- as.data.frame(data) toCensor <- !is.na(data[, columnName]) & - data[, columnName] < minValues & data[, columnName] != 0 + data[, columnName] < minValues & data[, columnName] > 0 + if (!silent) { percent <- round(100 * sum(toCensor) / nrow(data), 1) ParallelLogger::logInfo( @@ -71,6 +73,7 @@ enforceMinCellValue <- " because value below minimum" ) } + if (length(minValues) == 1) { data[toCensor, columnName] <- -minValues } else { @@ -141,28 +144,28 @@ makeDataExportable <- function(x, fieldsInDataModel <- resultsDataModel %>% dplyr::filter(.data$tableName == !!tableName) %>% - dplyr::pull(columnName) %>% + dplyr::pull(.data$columnName) %>% SqlRender::snakeCaseToCamelCase() %>% unique() requiredFieldsInDataModel <- resultsDataModel %>% dplyr::filter(.data$tableName == !!tableName) %>% - dplyr::filter(isRequired == "Yes") %>% - dplyr::pull(columnName) %>% + dplyr::filter(.data$isRequired == "Yes") %>% + dplyr::pull(.data$columnName) %>% SqlRender::snakeCaseToCamelCase() %>% unique() primaryKeyInDataModel <- resultsDataModel %>% dplyr::filter(.data$tableName == !!tableName) %>% - dplyr::filter(primaryKey == "Yes") %>% - dplyr::pull(columnName) %>% + dplyr::filter(.data$primaryKey == "Yes") %>% + dplyr::pull(.data$columnName) %>% SqlRender::snakeCaseToCamelCase() %>% unique() columnsToApplyMinCellValue <- resultsDataModel %>% dplyr::filter(.data$tableName == !!tableName) %>% - dplyr::filter(minCellCount == "Yes") %>% - dplyr::pull(columnName) %>% + dplyr::filter(.data$minCellCount == "Yes") %>% + dplyr::pull(.data$columnName) %>% SqlRender::snakeCaseToCamelCase() %>% unique() @@ -244,7 +247,9 @@ makeDataExportable <- function(x, # Ensure that timeId is never NA if ("timeId" %in% colnames(x)) { - x[is.na(x$timeId), ]$timeId <- 0 + if (any(is.na(x$timeId))) { + x[is.na(x$timeId), "timeId"] <- 0 + } } return(x) } @@ -310,7 +315,7 @@ getPrefixedTableNames <- function(tablePrefix) { return(resultList) } -#' Internal utility function for logging execution of variables +# Internal utility function for logging execution of variables timeExecution <- function(exportFolder, taskName, cohortIds = NULL, diff --git a/R/RunDiagnostics.R b/R/RunDiagnostics.R index 6c7d9a483..02c5e43d4 100644 --- a/R/RunDiagnostics.R +++ b/R/RunDiagnostics.R @@ -136,7 +136,23 @@ getDefaultCovariateSettings <- function() { #' @param incremental Create only cohort diagnostics that haven't been created before? #' @param incrementalFolder If \code{incremental = TRUE}, specify a folder where records are kept #' of which cohort diagnostics has been executed. +#' @param runOnSample Logical. If TRUE, the function will operate on a sample of the data. +#' Default is FALSE, meaning the function will operate on the full data set. #' +#' @param sampleN Integer. The number of records to include in the sample if runOnSample is TRUE. +#' Default is 1000. Ignored if runOnSample is FALSE. +#' +#' @param seed Integer. The seed for the random number generator used to create the sample. +#' This ensures that the same sample can be drawn again in future runs. Default is 64374. +#' +#' @param seedArgs List. Additional arguments to pass to the sampling function. +#' This can be used to control aspects of the sampling process beyond the seed and sample size. +#' +#' @param sampleIdentifierExpression Character. An expression that generates unique identifiers for each sample. +#' This expression can use the variables 'cohortId' and 'seed'. +#' Default is "cohortId * 1000 + seed", which ensures unique identifiers +#' as long as there are fewer than 1000 cohorts. + #' @examples #' \dontrun{ #' # Load cohorts (assumes that they have already been instantiated) @@ -211,7 +227,12 @@ executeDiagnostics <- function(cohortDefinitionSet, minCharacterizationMean = 0.01, irWashoutPeriod = 0, incremental = FALSE, - incrementalFolder = file.path(exportFolder, "incremental")) { + incrementalFolder = file.path(exportFolder, "incremental"), + runOnSample = FALSE, + sampleN = 1000, + seed = 64374, + seedArgs = NULL, + sampleIdentifierExpression = "cohortId * 1000 + seed") { # collect arguments that were passed to cohort diagnostics at initiation callingArgs <- formals(executeDiagnostics) callingArgsJson <- @@ -288,7 +309,7 @@ executeDiagnostics <- function(cohortDefinitionSet, add = errorMessage ) minCellCount <- utils::type.convert(minCellCount, as.is = TRUE) - checkmate::assertInteger(x = minCellCount, lower = 0, add = errorMessage) + checkmate::assertInteger(x = minCellCount, len = 1, lower = 0, add = errorMessage) minCharacterizationMean <- utils::type.convert(minCharacterizationMean, as.is = TRUE) checkmate::assertNumeric(x = minCharacterizationMean, lower = 0, add = errorMessage) checkmate::assertLogical(incremental, add = errorMessage) @@ -443,7 +464,7 @@ executeDiagnostics <- function(cohortDefinitionSet, checkmate::reportAssertions(collection = errorMessage) if (!is.null(cohortIds)) { - cohortDefinitionSet <- cohortDefinitionSet %>% dplyr::filter(cohortId %in% cohortIds) + cohortDefinitionSet <- cohortDefinitionSet %>% dplyr::filter(.data$cohortId %in% cohortIds) } if (nrow(cohortDefinitionSet) == 0) { @@ -528,6 +549,23 @@ executeDiagnostics <- function(cohortDefinitionSet, } } + if (runOnSample & !isTRUE(attr(cohortDefinitionSet, "isSampledCohortDefinition"))) { + cohortDefinitionSet <- + CohortGenerator::sampleCohortDefinitionSet( + connection = connection, + cohortDefinitionSet = cohortDefinitionSet, + tempEmulationSchema = tempEmulationSchema, + cohortDatabaseSchema = cohortDatabaseSchema, + cohortTableNames = cohortTableNames, + n = sampleN, + seed = seed, + seedArgs = seedArgs, + identifierExpression = sampleIdentifierExpression, + incremental = incremental, + incrementalFolder = incrementalFolder + ) + } + ## CDM source information---- timeExecution( exportFolder, @@ -631,8 +669,8 @@ executeDiagnostics <- function(cohortDefinitionSet, if (nrow(cohortCounts) > 0) { instantiatedCohorts <- cohortCounts %>% - dplyr::filter(cohortEntries > 0) %>% - dplyr::pull(cohortId) + dplyr::filter(.data$cohortEntries > 0) %>% + dplyr::pull(.data$cohortId) ParallelLogger::logInfo( sprintf( "Found %s of %s (%1.2f%%) submitted cohorts instantiated. ", @@ -646,6 +684,9 @@ executeDiagnostics <- function(cohortDefinitionSet, stop("All cohorts were either not instantiated or all have 0 records.") } + cohortDefinitionSet <- cohortDefinitionSet %>% + dplyr::filter(.data$cohortId %in% instantiatedCohorts) + # Inclusion statistics ----------------------------------------------------------------------- if (runInclusionStatistics) { timeExecution( diff --git a/R/Shiny.R b/R/Shiny.R index 0e357c875..867072bbf 100644 --- a/R/Shiny.R +++ b/R/Shiny.R @@ -33,7 +33,6 @@ #' @param port (optional) Only used if \code{runOverNetwork} = TRUE. #' @param launch.browser Should the app be launched in your default browser, or in a Shiny window. #' Note: copying to clipboard will not work in a Shiny window. -#' @param enableAnnotation Enable annotation functionality in shiny app #' @param aboutText Text (using HTML markup) that will be displayed in an About tab in the Shiny app. #' If not provided, no About tab will be shown. #' @param tablePrefix (Optional) string to insert before table names (e.g. "cd_") for database table names @@ -63,8 +62,7 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat makePublishable = FALSE, publishDir = file.path(getwd(), "DiagnosticsExplorer"), overwritePublishDir = FALSE, - launch.browser = FALSE, - enableAnnotation = TRUE) { + launch.browser = FALSE) { useShinyPublishFile <- FALSE if (is.null(shinyConfigPath)) { if (is.null(connectionDetails)) { @@ -106,11 +104,8 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat tablePrefix = tablePrefix, cohortTableName = cohortTableName, databaseTableName = databaseTableName, - enableAnnotation = enableAnnotation, enableAuthorization = FALSE ) - - options("enableCdAnnotation" = enableAnnotation) on.exit(rm("shinySettings", envir = .GlobalEnv)) } else { checkmate::assertFileExists(shinyConfigPath) @@ -118,7 +113,7 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat on.exit(options("CD-shiny-config" = NULL)) } - if (!"OhdsiShinyModules" %in% as.data.frame(installed.packages())$Package) { + if (!"OhdsiShinyModules" %in% as.data.frame(utils::installed.packages())$Package) { remotes::install_github("OHDSI/OhdsiShinyModules") } @@ -134,7 +129,7 @@ launchDiagnosticsExplorer <- function(sqliteDbPath = "MergedCohortDiagnosticsDat } dir.create(publishDir, showWarnings = FALSE) - filesToCopy <- file.path(appDir, list.files(appDir)) + filesToCopy <- list.files(appDir, all.files = TRUE, full.names = TRUE) file.copy(filesToCopy, publishDir, recursive = TRUE, overwrite = TRUE) if (useShinyPublishFile) { file.copy(sqliteDbPath, file.path(publishDir, "data", "MergedCohortDiagnosticsData.sqlite"), overwrite = TRUE) @@ -198,6 +193,7 @@ createMergedResultsFile <- list.files( path = dataFolder, pattern = ".zip", + all.files = TRUE, full.names = TRUE, recursive = TRUE ) @@ -251,8 +247,103 @@ createDiagnosticsExplorerZip <- function(outputZipfile = file.path(getwd(), "Dia on.exit(unlink(tmpDir, recursive = TRUE, force = TRUE), add = TRUE) file.copy(shinyDirectory, tmpDir, recursive = TRUE) - dir.create(file.path(tmpDir, "DiagnosticsExplorer", "data")) + dir.create(file.path(tmpDir, "DiagnosticsExplorer", "data"), showWarnings = FALSE) file.copy(sqliteDbPath, file.path(tmpDir, "DiagnosticsExplorer", "data", "MergedCohortDiagnosticsData.sqlite")) DatabaseConnector::createZipFile(outputZipfile, file.path(tmpDir, "DiagnosticsExplorer"), rootFolder = tmpDir) } + + +#' Rsconnect deploy +#' @description +#' Deploy your application to an posit connect platform or shinyapps.io server +#' +#' @export +#' @inheritParams launchDiagnosticsExplorer +#' @param appName string name to call app - should be unique on posit connect server +#' @param appDir optional - directory to use to copy files for deployment. If you use a consistent dir +#' other internal options can change. +#' @param useRenvironFile logical - not recommended, store db credentials in .Renviron file +#' @param shinyDirectory (optional) Directyory shiny app code lives. Use this if you wish to modify the explorer +#' @param ... other parameters passed to rsconnect::deployApp +deployPositConnectApp <- function(appName, + appDir = tempfile(), + sqliteDbPath = "MergedCohortDiagnosticsData.sqlite", + shinyDirectory = system.file(file.path("shiny", "DiagnosticsExplorer"), + package = "CohortDiagnostics" + ), + connectionDetails = NULL, + shinyConfigPath = NULL, + resultsDatabaseSchema = NULL, + vocabularyDatabaseSchemas = resultsDatabaseSchema, + tablePrefix = "", + cohortTableName = "cohort", + databaseTableName = "database", + port = 80, + useRenvironFile = FALSE, + ...) { + if (!"rsconnect" %in% as.data.frame(utils::installed.packages())$Package) { + install.packages("rsconnect") + } + + if (!"yaml" %in% as.data.frame(utils::installed.packages())$Package) { + install.packages("yaml") + } + + if (!"OhdsiShinyModules" %in% as.data.frame(utils::installed.packages())$Package) { + remotes::install_github("OHDSI/OhdsiShinyModules") + } + + checkmate::assertDirectory(appDir, access = "w") + + args <- rlang::dots_list(...) + args$envVars <- c(args$envVars, DATABASECONNECTOR_JAR_FOLDER = "./") + + dir.create(appDir, showWarnings = FALSE) + filesToCopy <- list.files(shinyDirectory, all.files = TRUE, full.names = TRUE) + file.copy(filesToCopy, appDir, recursive = TRUE, overwrite = TRUE) + + if (is.null(connectionDetails) && is.null(shinyConfigPath)) { + checkmate::assertFileExists(sqliteDbPath) + file.copy(sqliteDbPath, file.path(appDir, "data", "MergedCohortDiagnosticsData.sqlite"), overwrite = TRUE) + } else if (!is.null(shinyConfigPath)) { + DatabaseConnector::downloadJdbcDrivers(connectionDetails$dbms, appDir) + file.copy(shinyConfigPath, file.path(appDir, "config.yml")) + } else { + DatabaseConnector::downloadJdbcDrivers(connectionDetails$dbms, appDir) + if (useRenvironFile) { + outputText <- "# Edit credentials here to set on remote server +# Using an renviron file will store plaintext variables and is not reccomended. +# A local copy of this will be created and deleted following app deployment +shinyDbServer='' +shinydbPw='' +shinydbUser='' +shinydbPort=5432 +DATABASECONNECTOR_JAR_FOLDER='.' +" + writeLines(outputText, file.path(appDir, ".Renviron")) + res <- utils::edit(file = file.path(appDir, ".Renviron")) + # File should always be deleted + on.exit(unlink(file.path(appDir, ".Renviron"), force = TRUE)) + } else { + args$envVars <- c(args$envVars, + shinyDbServer = connectionDetails$server(), + shinydbPw = connectionDetails$password(), + shinydbUser = connectionDetails$user(), + shinydbPort = connectionDetails$port() + ) + } + + configOpts <- yaml::read_yaml(file.path(appDir, "config-ohdsi-shiny.yml")) + configOpts$tablePrefix <- tablePrefix + configOpts$resultsDatabaseSchema <- resultsDatabaseSchema + configOpts$vocabularyDatabaseSchemas <- vocabularyDatabaseSchemas + configOpts$cohortTableName <- cohortTableName + configOpts$databaseTableName <- databaseTableName + yaml::write_yaml(configOpts, file.path(appDir, "config.yml")) + } + + args$appDir <- appDir + args$appName <- appName + do.call(rsconnect::deployApp, args) +} diff --git a/R/TimeSeries.R b/R/TimeSeries.R index ab4d3a48e..33841dda7 100644 --- a/R/TimeSeries.R +++ b/R/TimeSeries.R @@ -98,7 +98,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, ) if (resultsInAndromeda$cohortCount %>% dplyr::summarise(n = dplyr::n()) %>% - dplyr::pull(n) == 0) { + dplyr::pull(.data$n) == 0) { warning("Please check if cohorts are instantiated. Exiting cohort time series.") return(NULL) } @@ -123,7 +123,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, by = clock::duration_months(3) ) ) %>% - dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 3) - 1) %>% + dplyr::mutate(periodEnd = clock::add_months(x = .data$periodBegin, n = 3) - 1) %>% dplyr::mutate(calendarInterval = "q") calendarMonth <- @@ -134,7 +134,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, by = clock::duration_months(1) ) ) %>% - dplyr::mutate(periodEnd = clock::add_months(x = periodBegin, n = 1) - 1) %>% + dplyr::mutate(periodEnd = clock::add_months(x = .data$periodBegin, n = 1) - 1) %>% dplyr::mutate(calendarInterval = "m") calendarYear <- @@ -145,7 +145,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, by = clock::duration_years(1) ) ) %>% - dplyr::mutate(periodEnd = clock::add_years(x = periodBegin, n = 1) - 1) %>% + dplyr::mutate(periodEnd = clock::add_years(x = .data$periodBegin, n = 1) - 1) %>% dplyr::mutate(calendarInterval = "y") timeSeriesDateRange <- dplyr::tibble( @@ -162,7 +162,7 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, timeSeriesDateRange ) %>% # calendarWeek dplyr::distinct() %>% - dplyr::arrange(periodBegin, periodEnd, calendarInterval) %>% + dplyr::arrange(.data$periodBegin, .data$periodEnd, .data$calendarInterval) %>% dplyr::mutate(timeId = dplyr::row_number()) ParallelLogger::logTrace(" - Inserting calendar periods") @@ -454,11 +454,11 @@ runCohortTimeSeriesDiagnostics <- function(connectionDetails = NULL, by = c("timeId") ) %>% dplyr::arrange( - cohortId, - periodBegin, - calendarInterval, - seriesType, - periodBegin + .data$cohortId, + .data$periodBegin, + .data$calendarInterval, + .data$seriesType, + .data$periodBegin ) %>% dplyr::select(-"timeId") %>% dplyr::mutate(ageGroup = dplyr::if_else( @@ -533,7 +533,7 @@ executeTimeSeriesDiagnostics <- function(connection, incremental = incremental, recordKeepingFile = recordKeepingFile ) %>% - dplyr::arrange(cohortId) + dplyr::arrange(.data$cohortId) if (nrow(subset) > 0) { if (incremental && diff --git a/R/VisitContext.R b/R/VisitContext.R index 668b728ac..3ecd4ed89 100644 --- a/R/VisitContext.R +++ b/R/VisitContext.R @@ -107,7 +107,7 @@ executeVisitContextDiagnostics <- function(connection, ParallelLogger::logInfo("Retrieving visit context for index dates") subset <- subsetToRequiredCohorts( cohorts = cohorts %>% - dplyr::filter(cohortId %in% instantiatedCohorts), + dplyr::filter(.data$cohortId %in% instantiatedCohorts), task = "runVisitContext", incremental = incremental, recordKeepingFile = recordKeepingFile diff --git a/docs/404.html b/docs/404.html index 5e7a49d8d..55e65e878 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html index 01773dc89..baf9d5f53 100644 --- a/docs/articles/CreatingAStudyPackage.html +++ b/docs/articles/CreatingAStudyPackage.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -97,7 +97,7 @@

Creating a study package

Gowtham A. Rao

-

2023-09-19

+

2023-11-16

Source: vignettes/CreatingAStudyPackage.Rmd diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html index 23cfe96cc..611755608 100644 --- a/docs/articles/DatabaseModeInDiagnosticsExplorer.html +++ b/docs/articles/DatabaseModeInDiagnosticsExplorer.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -97,7 +97,7 @@

Database mode in Diagnostics Explorer

Gowtham Rao

-

2023-09-19

+

2023-11-16

Source: vignettes/DatabaseModeInDiagnosticsExplorer.Rmd diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html index 2d1af9433..deb2425b2 100644 --- a/docs/articles/RunningCohortDiagnostics.html +++ b/docs/articles/RunningCohortDiagnostics.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -97,7 +97,7 @@

Running Cohort Diagnostics

Gowtham Rao and James P. Gilbert

-

2023-09-19

+

2023-11-16

Source: vignettes/RunningCohortDiagnostics.Rmd @@ -148,7 +148,7 @@

Configuring the connection to

For the purposes of this example, we will use the Eunomia test CDM package that is in an Sqlite database stored locally.

-connectionDetails <- Eunomia::getEunomiaConnectionDetails()
+connectionDetails <- Eunomia::getEunomiaConnectionDetails()
 
 cdmDatabaseSchema <- "main"
 tempEmulationSchema <- NULL
diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
index 515d223a2..272798bd4 100644
--- a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
+++ b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
@@ -33,7 +33,7 @@
       
       
         CohortDiagnostics
-        3.2.4
+        3.3.0
@@ -97,7 +97,7 @@

Viewing results using Diagnostics Explorer

Gowtham Rao

-

2023-09-19

+

2023-11-16

Source: vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html index 22ad3cc37..4f6b2f40b 100644 --- a/docs/articles/WhatIsCohortDiagnostics.html +++ b/docs/articles/WhatIsCohortDiagnostics.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -97,7 +97,7 @@

What is Cohort Diagnostics?

Gowtham Rao

-

2023-09-19

+

2023-11-16

Source: vignettes/WhatIsCohortDiagnostics.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 2043de551..ef8f0d07c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/authors.html b/docs/authors.html index 478196a77..e3c520238 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -108,13 +108,14 @@

Citation

Gilbert J, Rao G, Schuemie M, Ryan P, Weaver J (2023). CohortDiagnostics: Diagnostics for OHDSI Cohorts. -https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics. +R package version 3.3.0, https://github.com/OHDSI/CohortDiagnostics, https://ohdsi.github.io/CohortDiagnostics. 

@Manual{,
   title = {CohortDiagnostics: Diagnostics for OHDSI Cohorts},
   author = {Jamie Gilbert and Gowtham Rao and Martijn Schuemie and Patrick Ryan and James Weaver},
   year = {2023},
-  note = {https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics},
+  note = {R package version 3.3.0, https://github.com/OHDSI/CohortDiagnostics},
+  url = {https://ohdsi.github.io/CohortDiagnostics},
 }
diff --git a/docs/index.html b/docs/index.html index c7d82f7d1..4ad9974f1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -157,13 +157,13 @@

User Documentationpackage website.

PDF versions of the documentation are also available:

diff --git a/docs/news/index.html b/docs/news/index.html index 1a39727f8..4151c18c1 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -72,6 +72,16 @@

Changelog

Source: NEWS.md +
+

CohortDiagnostics 3.3.0

+

Changes:

+

  1. Resolved issues with package creating build errors

    2. +

  2. Added function to make deployment to posit connect servers easier

    3. +

  3. Added ability to use CohortGenerator sample functionality to executeDiagnostics which speeds up execution for very large cohort definitions

    4. +

Bug fix:

+

  1. Fixes to loading shiny app in OHDSI shiny modules

    2. +

  2. Bug fixes to prevent null value issues with included source concept diagnostics

    3. +

CohortDiagnostics 3.2.4

Bug Fix:

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b615b8513..ed8784ce6 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,5 +7,5 @@ articles: RunningCohortDiagnostics: RunningCohortDiagnostics.html ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html -last_built: 2023-09-19T21:26Z +last_built: 2023-11-16T15:11Z diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html index 790dcf7d4..2c51c79d7 100644 --- a/docs/reference/CohortDiagnostics-package.html +++ b/docs/reference/CohortDiagnostics-package.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html index 853a42554..5cb44ed1b 100644 --- a/docs/reference/checkInputFileEncoding.html +++ b/docs/reference/checkInputFileEncoding.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html index ac9d8ea7d..79caf9a59 100644 --- a/docs/reference/createDiagnosticsExplorerZip.html +++ b/docs/reference/createDiagnosticsExplorerZip.html @@ -20,7 +20,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html index a7ca7393f..cb2d55fda 100644 --- a/docs/reference/createMergedResultsFile.html +++ b/docs/reference/createMergedResultsFile.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html index ad99e2687..2c93876a1 100644 --- a/docs/reference/createResultsDataModel.html +++ b/docs/reference/createResultsDataModel.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/deployPositConnectApp.html b/docs/reference/deployPositConnectApp.html new file mode 100644 index 000000000..8aa40f0f5 --- /dev/null +++ b/docs/reference/deployPositConnectApp.html @@ -0,0 +1,191 @@ + +Rsconnect deploy — deployPositConnectApp • CohortDiagnostics + + +
+
+ + + +
+
+
+

Rsconnect deploy

+ Source: R/Shiny.R + +
+ +
+

Deploy your application to an posit connect platform or shinyapps.io server

+
+ +
+ 
deployPositConnectApp(
+  appName,
+  appDir = tempfile(),
+  sqliteDbPath = "MergedCohortDiagnosticsData.sqlite",
+  shinyDirectory = system.file(file.path("shiny", "DiagnosticsExplorer"), package =
+    "CohortDiagnostics"),
+  connectionDetails = NULL,
+  shinyConfigPath = NULL,
+  resultsDatabaseSchema = NULL,
+  vocabularyDatabaseSchemas = resultsDatabaseSchema,
+  tablePrefix = "",
+  cohortTableName = "cohort",
+  databaseTableName = "database",
+  port = 80,
+  useRenvironFile = FALSE,
+  ...
+)
+
+ +
+

Arguments

+
appName
+

string name to call app - should be unique on posit connect server

+ + +
appDir
+

optional - directory to use to copy files for deployment. If you use a consistent dir +other internal options can change.

+ + +
sqliteDbPath
+

Path to merged sqlite file. See createMergedResultsFile to create file.

+ + +
shinyDirectory
+

(optional) Directyory shiny app code lives. Use this if you wish to modify the explorer

+ + +
connectionDetails
+

An object of type connectionDetails as created using the +createConnectionDetails function in the +DatabaseConnector package, specifying how to connect to the server where +the CohortDiagnostics results have been uploaded using the +uploadResults function.

+ + +
shinyConfigPath
+

Path to shiny yml configuration file (use instead of sqliteDbPath or connectionDetails object)

+ + +
resultsDatabaseSchema
+

The schema on the database server where the CohortDiagnostics results +have been uploaded.

+ + +
vocabularyDatabaseSchemas
+

(optional) A list of one or more schemas on the database server where the vocabulary tables are located. +The default value is the value of the resultsDatabaseSchema. We can provide a list of vocabulary schema +that might represent different versions of the OMOP vocabulary tables. It allows us to compare the impact +of vocabulary changes on Diagnostics. Not supported with an sqlite database.

+ + +
tablePrefix
+

(Optional) string to insert before table names (e.g. "cd_") for database table names

+ + +
cohortTableName
+

(Optional) if cohort table name differs from the standard - cohort (ignores prefix if set)

+ + +
databaseTableName
+

(Optional) if database table name differs from the standard - database (ignores prefix if set)

+ + +
port
+

(optional) Only used if runOverNetwork = TRUE.

+ + +
useRenvironFile
+

logical - not recommended, store db credentials in .Renviron file

+ + +
...
+

other parameters passed to rsconnect::deployApp

+ +
+ +
+ +
+ + +
+

Developed by Jamie Gilbert, Gowtham Rao, Martijn Schuemie, Patrick Ryan, James Weaver.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/reference/deployShinyApp.html b/docs/reference/deployShinyApp.html new file mode 100644 index 000000000..1a725c5a5 --- /dev/null +++ b/docs/reference/deployShinyApp.html @@ -0,0 +1,110 @@ + +Deploy shiny app to rsconnect platform — deployShinyApp • CohortDiagnostics + + +
+
+ + + +
+
+
+

Deploy shiny app to rsconnect platform

+ Source: R/Shiny.R + +
+ +
+

Uses the rsconnect package to create a bundle suitable for deployment on a posit connect server. +For example, shinyApps.io

+
+ +
+ 
deployShinyApp(...)
+
+ + +
+ +
+ + +
+

Developed by Jamie Gilbert, Gowtham Rao, Martijn Schuemie, Patrick Ryan, James Weaver.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html index 693ab6b4a..eaaf64010 100644 --- a/docs/reference/executeDiagnostics.html +++ b/docs/reference/executeDiagnostics.html @@ -22,7 +22,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -118,7 +118,12 @@

Execute cohort diagnostics

minCharacterizationMean = 0.01, irWashoutPeriod = 0, incremental = FALSE, - incrementalFolder = file.path(exportFolder, "incremental") + incrementalFolder = file.path(exportFolder, "incremental"), + runOnSample = FALSE, + sampleN = 1000, + seed = 64374, + seedArgs = NULL, + sampleIdentifierExpression = "cohortId * 1000 + seed" ) @@ -267,6 +272,33 @@

Arguments

If incremental = TRUE, specify a folder where records are kept of which cohort diagnostics has been executed.

+ +
runOnSample
+

Logical. If TRUE, the function will operate on a sample of the data. +Default is FALSE, meaning the function will operate on the full data set.

+ + +
sampleN
+

Integer. The number of records to include in the sample if runOnSample is TRUE. +Default is 1000. Ignored if runOnSample is FALSE.

+ + +
seed
+

Integer. The seed for the random number generator used to create the sample. +This ensures that the same sample can be drawn again in future runs. Default is 64374.

+ + +
seedArgs
+

List. Additional arguments to pass to the sampling function. +This can be used to control aspects of the sampling process beyond the seed and sample size.

+ + +
sampleIdentifierExpression
+

Character. An expression that generates unique identifiers for each sample. +This expression can use the variables 'cohortId' and 'seed'. +Default is "cohortId * 1000 + seed", which ensures unique identifiers +as long as there are fewer than 1000 cohorts.

+

Details

diff --git a/docs/reference/getCdmDataSourceInformation.html b/docs/reference/getCdmDataSourceInformation.html index e39eecb97..bab245cf7 100644 --- a/docs/reference/getCdmDataSourceInformation.html +++ b/docs/reference/getCdmDataSourceInformation.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0
diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html index 96357a4b8..7a42574c2 100644 --- a/docs/reference/getCohortCounts.html +++ b/docs/reference/getCohortCounts.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html index 61c802b3f..4150efab4 100644 --- a/docs/reference/getDataMigrator.html +++ b/docs/reference/getDataMigrator.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/getDefaultCovariateSettings.html b/docs/reference/getDefaultCovariateSettings.html index 7853cc908..2ff90f622 100644 --- a/docs/reference/getDefaultCovariateSettings.html +++ b/docs/reference/getDefaultCovariateSettings.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/getDefaultVocabularyTableNames.html b/docs/reference/getDefaultVocabularyTableNames.html index 1f40bfd3a..617b07b49 100644 --- a/docs/reference/getDefaultVocabularyTableNames.html +++ b/docs/reference/getDefaultVocabularyTableNames.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html index 7f8eef6cf..3d60d272e 100644 --- a/docs/reference/getResultsDataModelSpecifications.html +++ b/docs/reference/getResultsDataModelSpecifications.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 1bbee13f5..4f51cb11a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -92,9 +92,9 @@

All functions

Create the results data model tables on a database server.

-

deployShinyApp()

+

deployPositConnectApp()

-

Deploy shiny app to rsconnect platform

+

Rsconnect deploy

executeDiagnostics()

@@ -139,10 +139,6 @@

All functions runCohortTimeSeriesDiagnostics()

Given a set of instantiated cohorts get time series for the cohorts.

- -

timeExecution()

- -

Internal utility function for logging execution of variables

uploadResults()

diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html index 57b08053a..8564d945a 100644 --- a/docs/reference/launchDiagnosticsExplorer.html +++ b/docs/reference/launchDiagnosticsExplorer.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 @@ -94,8 +94,7 @@

Launch the Diagnostics Explorer Shiny app

makePublishable = FALSE, publishDir = file.path(getwd(), "DiagnosticsExplorer"), overwritePublishDir = FALSE, - launch.browser = FALSE, - enableAnnotation = TRUE + launch.browser = FALSE ) @@ -174,10 +173,6 @@

Arguments

Should the app be launched in your default browser, or in a Shiny window. Note: copying to clipboard will not work in a Shiny window.

- -
enableAnnotation
-

Enable annotation functionality in shiny app

-

Details

diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html index a72bf29d2..493a76414 100644 --- a/docs/reference/migrateDataModel.html +++ b/docs/reference/migrateDataModel.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0
diff --git a/docs/reference/runCohortRelationshipDiagnostics.html b/docs/reference/runCohortRelationshipDiagnostics.html index c0f9c2f9e..c8a57a736 100644 --- a/docs/reference/runCohortRelationshipDiagnostics.html +++ b/docs/reference/runCohortRelationshipDiagnostics.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/runCohortTimeSeriesDiagnostics.html b/docs/reference/runCohortTimeSeriesDiagnostics.html index 1bd102b8c..148a5ecd3 100644 --- a/docs/reference/runCohortTimeSeriesDiagnostics.html +++ b/docs/reference/runCohortTimeSeriesDiagnostics.html @@ -25,7 +25,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html index 5eb3a6514..a8c7bc34e 100644 --- a/docs/reference/uploadResults.html +++ b/docs/reference/uploadResults.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.4 + 3.3.0 diff --git a/docs/sitemap.xml b/docs/sitemap.xml index f9a99ba7b..f7ac2a523 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -87,6 +87,9 @@ /reference/createResultsDataModel.html + + /reference/deployPositConnectApp.html + /reference/deployShinyApp.html diff --git a/extras/EditIncrementalLogDiagnostics.R b/extras/EditIncrementalLogDiagnostics.R index b8e183126..e01e56a74 100644 --- a/extras/EditIncrementalLogDiagnostics.R +++ b/extras/EditIncrementalLogDiagnostics.R @@ -31,7 +31,7 @@ for (i in (1:length(listFiles))) { col_types = readr::cols(), guess_max = min(1e7) ) %>% - dplyr::filter(!task %in% tasksToRemove) %>% + dplyr::filter(!.data$task %in% tasksToRemove) %>% readr::write_excel_csv(file = listFiles[[i]]) } diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R index f8229d68e..6424161b3 100644 --- a/extras/PackageMaintenance.R +++ b/extras/PackageMaintenance.R @@ -68,10 +68,4 @@ filePath <- file.path("inst", "sql", "sql_server", "UpdateVersionNumber.sql") text <- readChar(filePath, file.info(filePath)$size) patternRep <- "\\{DEFAULT @version_number = '(\\d+\\.\\d+\\.\\d+)'\\}" text <- gsub(patternRep, paste0("\\{DEFAULT @version_number = '", version, "'\\}"), text) -writeLines(text, con = file(filePath)) - - -# Copy data model specs to Shiny app -file.copy(from = "inst/settings/resultsDataModelSpecification.csv", - to = "inst/shiny/DiagnosticsExplorer/data/resultsDataModelSpecification.csv", - overwrite = TRUE) +writeLines(text, con = file(filePath)) \ No newline at end of file diff --git a/inst/doc/RunningCohortDiagnostics.pdf b/inst/doc/RunningCohortDiagnostics.pdf index ac855cd4a..666dc0c65 100644 Binary files a/inst/doc/RunningCohortDiagnostics.pdf and b/inst/doc/RunningCohortDiagnostics.pdf differ diff --git a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf index 46ab0568e..fbeb0fed6 100644 Binary files a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf and b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf differ diff --git a/inst/doc/WhatIsCohortDiagnostics.pdf b/inst/doc/WhatIsCohortDiagnostics.pdf index 23ea367e6..eeaabfeda 100644 Binary files a/inst/doc/WhatIsCohortDiagnostics.pdf and b/inst/doc/WhatIsCohortDiagnostics.pdf differ diff --git a/inst/shiny/DiagnosticsExplorer/config-ohdsi-shiny.yml b/inst/shiny/DiagnosticsExplorer/config-ohdsi-shiny.yml index 046e6e066..5557dafd1 100644 --- a/inst/shiny/DiagnosticsExplorer/config-ohdsi-shiny.yml +++ b/inst/shiny/DiagnosticsExplorer/config-ohdsi-shiny.yml @@ -23,12 +23,3 @@ resultsDatabaseSchema: "some_schema" vocabularyDatabaseSchemas: ["some_schema"] cohortTableName: "cohort" databaseTableName: "database" - -enableAnnotation: TRUE -enableAuthorization: TRUE - -### if you need a way to authorize users -### generate hash using code like digest::digest("diagnostics",algo = "sha512") -### store in external file called UserCredentials.csv - with fields userId, hashCode -### place the file in the root folder -userCredentialsFile: UserCredentials.csv diff --git a/inst/shiny/DiagnosticsExplorer/global.R b/inst/shiny/DiagnosticsExplorer/global.R index c3895f518..03fe5208e 100644 --- a/inst/shiny/DiagnosticsExplorer/global.R +++ b/inst/shiny/DiagnosticsExplorer/global.R @@ -78,30 +78,29 @@ if (FALSE) { connectionHandler <- ResultModelManager::PooledConnectionHandler$new(shinySettings$connectionDetails) +if (!shinySettings$connectionDetails$dbms %in% c("duckdb", "sqlite")) { + DatabaseConnector::downloadJdbcDrivers(dbms = shinySettings$connectionDetails, + pathToDriver = shinySettings$connectionDetails$pathToDriver) -if (packageVersion("OhdsiShinyModules") >= as.numeric_version("1.2.0")) { - resultDatabaseSettings <- list( - schema = shinySettings$resultsDatabaseSchema, - vocabularyDatabaseSchema = shinySettings$vocabularyDatabaseSchema, - cdTablePrefix = shinySettings$tablePrefix, - cgTable = shinySettings$cohortTableName, - databaseTable = shinySettings$databaseTableName - ) - - dataSource <- - OhdsiShinyModules::createCdDatabaseDataSource(connectionHandler = connectionHandler, - resultDatabaseSettings = resultDatabaseSettings) -} else { - dataSource <- - OhdsiShinyModules::createCdDatabaseDataSource( - connectionHandler = connectionHandler, - schema = shinySettings$resultsDatabaseSchema, - vocabularyDatabaseSchema = shinySettings$vocabularyDatabaseSchema, - tablePrefix = shinySettings$tablePrefix, - cohortTableName = shinySettings$cohortTableName, - databaseTableName = shinySettings$databaseTableName - ) +} +if (packageVersion("OhdsiShinyModules") <= as.numeric_version("2.0.0")) { + stop("OhdsiShinyModules version no longer supported. + Update to a newer version with remotes::install_github('OhdsiShinyModules')") } +resultDatabaseSettings <- list( + schema = shinySettings$resultsDatabaseSchema, + vocabularyDatabaseSchema = shinySettings$vocabularyDatabaseSchema, + cdTablePrefix = shinySettings$tablePrefix, + cgTable = shinySettings$cohortTableName, + databaseTable = shinySettings$databaseTableName +) + +dataSource <- + OhdsiShinyModules::createCdDatabaseDataSource(connectionHandler = connectionHandler, + resultDatabaseSettings = resultDatabaseSettings) + + + diff --git a/inst/shiny/DiagnosticsExplorer/renv.lock b/inst/shiny/DiagnosticsExplorer/renv.lock deleted file mode 100644 index 46f050bb5..000000000 --- a/inst/shiny/DiagnosticsExplorer/renv.lock +++ /dev/null @@ -1,1721 +0,0 @@ -{ - 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"utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.7", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" - }, - "zip": { - "Package": "zip", - "Version": "2.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d98c94dacb7e0efcf83b0a133a705504" - } - } -} diff --git a/inst/sql/sql_server/CohortSourceCodes.sql b/inst/sql/sql_server/CohortSourceCodes.sql index cc45ab8f1..03ac9ba55 100644 --- a/inst/sql/sql_server/CohortSourceCodes.sql +++ b/inst/sql/sql_server/CohortSourceCodes.sql @@ -13,7 +13,7 @@ IF OBJECT_ID('tempdb..@include_source_concept_table', 'U') IS NOT NULL SELECT codeset_id AS concept_set_id, concept_sets.concept_id, - source_concept_id, + COALESCE(source_concept_id, concept_sets.concept_id) as source_concept_id, {@by_month} ? { event_year, event_month, diff --git a/inst/sql/sql_server/UpdateVersionNumber.sql b/inst/sql/sql_server/UpdateVersionNumber.sql index b9b3bcdbf..2cb68a1e0 100644 --- a/inst/sql/sql_server/UpdateVersionNumber.sql +++ b/inst/sql/sql_server/UpdateVersionNumber.sql @@ -1,5 +1,5 @@ {DEFAULT @package_version = package_version} -{DEFAULT @version_number = '3.2.4'} +{DEFAULT @version_number = '3.3.0'} DELETE FROM @database_schema.@table_prefix@package_version; INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALUES ('@version_number'); @@ -10,3 +10,4 @@ INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALU + diff --git a/man/deployPositConnectApp.Rd b/man/deployPositConnectApp.Rd new file mode 100644 index 000000000..71b2659e4 --- /dev/null +++ b/man/deployPositConnectApp.Rd @@ -0,0 +1,65 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/Shiny.R +\name{deployPositConnectApp} +\alias{deployPositConnectApp} +\title{Rsconnect deploy} +\usage{ +deployPositConnectApp( + appName, + appDir = tempfile(), + sqliteDbPath = "MergedCohortDiagnosticsData.sqlite", + shinyDirectory = system.file(file.path("shiny", "DiagnosticsExplorer"), package = + "CohortDiagnostics"), + connectionDetails = NULL, + shinyConfigPath = NULL, + resultsDatabaseSchema = NULL, + vocabularyDatabaseSchemas = resultsDatabaseSchema, + tablePrefix = "", + cohortTableName = "cohort", + databaseTableName = "database", + port = 80, + useRenvironFile = FALSE, + ... +) +} +\arguments{ +\item{appName}{string name to call app - should be unique on posit connect server} + +\item{appDir}{optional - directory to use to copy files for deployment. If you use a consistent dir +other internal options can change.} + +\item{sqliteDbPath}{Path to merged sqlite file. See \code{\link{createMergedResultsFile}} to create file.} + +\item{shinyDirectory}{(optional) Directyory shiny app code lives. Use this if you wish to modify the explorer} + +\item{connectionDetails}{An object of type \code{connectionDetails} as created using the +\code{\link[DatabaseConnector]{createConnectionDetails}} function in the +DatabaseConnector package, specifying how to connect to the server where +the CohortDiagnostics results have been uploaded using the +\code{\link{uploadResults}} function.} + +\item{shinyConfigPath}{Path to shiny yml configuration file (use instead of sqliteDbPath or connectionDetails object)} + +\item{resultsDatabaseSchema}{The schema on the database server where the CohortDiagnostics results +have been uploaded.} + +\item{vocabularyDatabaseSchemas}{(optional) A list of one or more schemas on the database server where the vocabulary tables are located. +The default value is the value of the resultsDatabaseSchema. We can provide a list of vocabulary schema +that might represent different versions of the OMOP vocabulary tables. It allows us to compare the impact +of vocabulary changes on Diagnostics. Not supported with an sqlite database.} + +\item{tablePrefix}{(Optional) string to insert before table names (e.g. "cd_") for database table names} + +\item{cohortTableName}{(Optional) if cohort table name differs from the standard - cohort (ignores prefix if set)} + +\item{databaseTableName}{(Optional) if database table name differs from the standard - database (ignores prefix if set)} + +\item{port}{(optional) Only used if \code{runOverNetwork} = TRUE.} + +\item{useRenvironFile}{logical - not recommended, store db credentials in .Renviron file} + +\item{...}{other parameters passed to rsconnect::deployApp} +} +\description{ +Deploy your application to an posit connect platform or shinyapps.io server +} diff --git a/man/executeDiagnostics.Rd b/man/executeDiagnostics.Rd index 836c50549..9884c5824 100644 --- a/man/executeDiagnostics.Rd +++ b/man/executeDiagnostics.Rd @@ -34,7 +34,12 @@ executeDiagnostics( minCharacterizationMean = 0.01, irWashoutPeriod = 0, incremental = FALSE, - incrementalFolder = file.path(exportFolder, "incremental") + incrementalFolder = file.path(exportFolder, "incremental"), + runOnSample = FALSE, + sampleN = 1000, + seed = 64374, + seedArgs = NULL, + sampleIdentifierExpression = "cohortId * 1000 + seed" ) } \arguments{ @@ -121,6 +126,23 @@ on covariates that have very low values. The default is 0.001 (i.e. 0.1 percent) \item{incrementalFolder}{If \code{incremental = TRUE}, specify a folder where records are kept of which cohort diagnostics has been executed.} + +\item{runOnSample}{Logical. If TRUE, the function will operate on a sample of the data. +Default is FALSE, meaning the function will operate on the full data set.} + +\item{sampleN}{Integer. The number of records to include in the sample if runOnSample is TRUE. +Default is 1000. Ignored if runOnSample is FALSE.} + +\item{seed}{Integer. The seed for the random number generator used to create the sample. +This ensures that the same sample can be drawn again in future runs. Default is 64374.} + +\item{seedArgs}{List. Additional arguments to pass to the sampling function. +This can be used to control aspects of the sampling process beyond the seed and sample size.} + +\item{sampleIdentifierExpression}{Character. An expression that generates unique identifiers for each sample. +This expression can use the variables 'cohortId' and 'seed'. +Default is "cohortId * 1000 + seed", which ensures unique identifiers +as long as there are fewer than 1000 cohorts.} } \description{ Runs the cohort diagnostics on all (or a subset of) the cohorts instantiated using the diff --git a/man/launchDiagnosticsExplorer.Rd b/man/launchDiagnosticsExplorer.Rd index 33eeb8fb3..390e7f6af 100644 --- a/man/launchDiagnosticsExplorer.Rd +++ b/man/launchDiagnosticsExplorer.Rd @@ -20,8 +20,7 @@ launchDiagnosticsExplorer( makePublishable = FALSE, publishDir = file.path(getwd(), "DiagnosticsExplorer"), overwritePublishDir = FALSE, - launch.browser = FALSE, - enableAnnotation = TRUE + launch.browser = FALSE ) } \arguments{ @@ -66,8 +65,6 @@ If not provided, no About tab will be shown.} \item{launch.browser}{Should the app be launched in your default browser, or in a Shiny window. Note: copying to clipboard will not work in a Shiny window.} - -\item{enableAnnotation}{Enable annotation functionality in shiny app} } \description{ Launch the Diagnostics Explorer Shiny app diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R index 75ba366cf..276c61fdb 100644 --- a/tests/testthat/helper.R +++ b/tests/testthat/helper.R @@ -67,7 +67,7 @@ loadTestCohortDefinitionSet <- function(cohortIds = NULL, useSubsets = TRUE) { cohortFileNameValue = c("cohortId") ) if (!is.null(cohortIds)) { - cohortDefinitionSet <- cohortDefinitionSet %>% dplyr::filter(cohortId %in% cohortIds) + cohortDefinitionSet <- cohortDefinitionSet %>% dplyr::filter(.data$cohortId %in% cohortIds) } if (useSubsets) { diff --git a/tests/testthat/test-1-ResultsDataModel.R b/tests/testthat/test-1-ResultsDataModel.R index 01b448192..07d71a30e 100644 --- a/tests/testthat/test-1-ResultsDataModel.R +++ b/tests/testthat/test-1-ResultsDataModel.R @@ -122,7 +122,8 @@ VALUES ('Synthea','Synthea','OHDSI Community','SyntheaTM is a Synthetic Patient runOrphanConcepts = TRUE, incremental = TRUE, incrementalFolder = file.path(folder, "incremental"), - temporalCovariateSettings = temporalCovariateSettings + temporalCovariateSettings = temporalCovariateSettings, + runOnSample = TRUE ) }, "CDM Source table has more than one record while only one is expected." @@ -147,7 +148,8 @@ VALUES ('Synthea','Synthea','OHDSI Community','SyntheaTM is a Synthetic Patient runOrphanConcepts = TRUE, incremental = TRUE, incrementalFolder = file.path(folder, "incremental"), - temporalCovariateSettings = temporalCovariateSettings + temporalCovariateSettings = temporalCovariateSettings, + runOnSample = TRUE ) } @@ -175,7 +177,7 @@ VALUES ('Synthea','Synthea','OHDSI Community','SyntheaTM is a Synthetic Patient primaryKey <- specifications %>% dplyr::filter(tableName == !!tableName & primaryKey == "Yes") %>% - dplyr::select(columnName) %>% + dplyr::select("columnName") %>% dplyr::pull() if ("database_id" %in% primaryKey) { @@ -211,7 +213,7 @@ test_that("Sqlite results data model", { primaryKey <- specifications %>% dplyr::filter(tableName == !!tableName & primaryKey == "Yes") %>% - dplyr::select(columnName) %>% + dplyr::select("columnName") %>% dplyr::pull() if ("database_id" %in% primaryKey) { diff --git a/tests/testthat/test-2-againstCdm.R b/tests/testthat/test-2-againstCdm.R index 54a2107ba..fa2ffeb15 100644 --- a/tests/testthat/test-2-againstCdm.R +++ b/tests/testthat/test-2-againstCdm.R @@ -44,7 +44,8 @@ test_that("Cohort diagnostics in incremental mode", { minCellCount = minCellCountValue, incremental = TRUE, incrementalFolder = file.path(folder, "incremental"), - temporalCovariateSettings = temporalCovariateSettings + temporalCovariateSettings = temporalCovariateSettings, + runOnSample = TRUE ) ) @@ -74,7 +75,8 @@ test_that("Cohort diagnostics in incremental mode", { minCellCount = minCellCountValue, incremental = TRUE, incrementalFolder = file.path(folder, "incremental"), - temporalCovariateSettings = temporalCovariateSettings + temporalCovariateSettings = temporalCovariateSettings, + runOnSample = TRUE ) ) # generate sqlite file @@ -120,7 +122,8 @@ test_that("Cohort diagnostics in incremental mode", { minCellCount = minCellCountValue, incremental = FALSE, incrementalFolder = file.path(folder, "incremental"), - temporalCovariateSettings = temporalCovariateSettings + temporalCovariateSettings = temporalCovariateSettings, + runOnSample = TRUE ) }) diff --git a/tests/testthat/test-5-moduleTimeSeries.R b/tests/testthat/test-5-moduleTimeSeries.R index e2e857a77..b8b5feee2 100644 --- a/tests/testthat/test-5-moduleTimeSeries.R +++ b/tests/testthat/test-5-moduleTimeSeries.R @@ -232,9 +232,9 @@ test_that("Testing time series logic", { # testing if values returned for cohort 1 is as expected timeSeriesCohort <- timeSeries %>% - dplyr::filter(cohortId == 1) %>% - dplyr::filter(seriesType == "T1") %>% - dplyr::filter(calendarInterval == "m") + dplyr::filter(.data$cohortId == 1) %>% + dplyr::filter(.data$seriesType == "T1") %>% + dplyr::filter(.data$calendarInterval == "m") # there should be 8 records in this data frame, representing 8 months for the one subject in the cohort id = 1 testthat::expect_equal( @@ -244,13 +244,13 @@ test_that("Testing time series logic", { # there should be 2 records in this data frame, representing the 2 starts for the one subject in the cohort id = 1 testthat::expect_equal( - object = nrow(timeSeriesCohort %>% dplyr::filter(recordsStart == 1)), + object = nrow(timeSeriesCohort %>% dplyr::filter(.data$recordsStart == 1)), expected = 2 ) # there should be 1 records in this data frame, representing the 1 incident start for the one subject in the cohort id = 1 testthat::expect_equal( - object = nrow(timeSeriesCohort %>% dplyr::filter(subjectsStartIn == 1)), + object = nrow(timeSeriesCohort %>% dplyr::filter(.data$subjectsStartIn == 1)), expected = 1 ) }) diff --git a/tests/testthat/test-other.R b/tests/testthat/test-other.R index cf57588c3..475f17b18 100644 --- a/tests/testthat/test-other.R +++ b/tests/testthat/test-other.R @@ -124,3 +124,35 @@ test_that("timeExecutions function", { checkmate::expect_data_frame(result, nrows = 5, ncols = 5) expect_false(all(is.na(result$startTime))) }) + +test_that("enforceMinCellValue replaces values below minimum with negative of minimum", { + data <- data.frame(a = c(1, 2, 3, 4, 5)) + minValues <- 3 + result <- enforceMinCellValue(data, "a", minValues, silent = TRUE) + + expect_equal(result$a, c(-3, -3, 3, 4, 5)) +}) + +test_that("enforceMinCellValue does not replace NA values", { + data <- data.frame(a = c(1, 2, NA, 4, 5)) + minValues <- 3 + result <- enforceMinCellValue(data, "a", minValues, silent = TRUE) + + expect_equal(result$a, c(-3, -3, NA, 4, 5)) +}) + +test_that("enforceMinCellValue does not replace zero values", { + data <- data.frame(a = c(0, 2, 3, 4, 5)) + minValues <- 3 + result <- enforceMinCellValue(data, "a", minValues, silent = TRUE) + + expect_equal(result$a, c(0, -3, 3, 4, 5)) +}) + +test_that("enforceMinCellValue works with vector of minimum values", { + data <- data.frame(a = c(1, 2, 3, 4, 5)) + minValues <- c(1, 2, 3, 4, 5) + result <- enforceMinCellValue(data, "a", minValues, silent = TRUE) + + expect_equal(result$a, c(1, 2, 3, 4, 5)) +})