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ablack3ablack3
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Merge pull request #82 from darwin-eu-dev/issue_68
Issue 68
2 parents f109b62 + 910d774 commit 53d5f1c

31 files changed

+2767
-66
lines changed

‎CohortDiagnostics.Rproj

+1
Original file line numberDiff line numberDiff line change
@@ -13,5 +13,6 @@ RnwWeave: Sweave
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LaTeX: pdfLaTeX
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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PackageRoxygenize: rd,collate,namespace

‎R/hold/executeDiagnostics.R

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@@ -864,11 +864,11 @@ executeDiagnostics <- function(cohortDefinitionSet,
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if (runVisitContext) {
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timeExecution(
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exportFolder,
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"executeVisitContextDiagnostics",
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"runVisitContext",
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cohortIds,
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parent = "executeDiagnostics",
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expr = {
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executeVisitContextDiagnostics(
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runVisitContext(
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connection = connection,
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tempEmulationSchema = tempEmulationSchema,
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cdmDatabaseSchema = cdmDatabaseSchema,

‎R/runVisitContext.R

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@@ -14,8 +14,7 @@
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# See the License for the specific language governing permissions and
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# limitations under the License.
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17-
getVisitContext <- function(connectionDetails = NULL,
18-
connection = NULL,
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getVisitContext <- function(connection = NULL,
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cdmDatabaseSchema,
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tempEmulationSchema = NULL,
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cohortDatabaseSchema = cdmDatabaseSchema,
@@ -30,8 +29,7 @@ getVisitContext <- function(connectionDetails = NULL,
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start <- Sys.time()
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3231
if (is.null(connection)) {
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connection <- DatabaseConnector::connect(connectionDetails)
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on.exit(DatabaseConnector::disconnect(connection))
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stop("Connection cannot be null.")
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}
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sql <- SqlRender::loadRenderTranslateSql(
@@ -108,30 +106,66 @@ getVisitContext <- function(connectionDetails = NULL,
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return(visitContext)
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}
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runVisitContext <- function(connection,
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cohortDefinitionSet,
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exportFolder,
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databaseId,
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cohortDatabaseSchema,
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cdmDatabaseSchema,
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tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
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cohortTable = "cohort",
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cdmVersion = 5,
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minCellCount,
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incremental,
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incrementalFolder = file.path(exportFolder, "incremental")){
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112-
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executeVisitContextDiagnostics <- function(connection,
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tempEmulationSchema,
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cdmDatabaseSchema,
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cohortDatabaseSchema,
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cohortTable,
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cdmVersion,
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databaseId,
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exportFolder,
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minCellCount,
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cohorts,
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instantiatedCohorts,
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recordKeepingFile,
125-
incremental) {
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if (incremental && !file.exists(incrementalFolder)) {
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# Create the file if it doesn't exist
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file.create(incrementalFolder)
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ParallelLogger::logInfo(
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sprintf(
128+
"Created record keeping file %s.",
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incrementalFolder
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)
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)
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}
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134+
cohortCounts <- CohortGenerator::getCohortCounts(
135+
connection = connection,
136+
cohortDatabaseSchema = cohortDatabaseSchema,
137+
cohortTable = cohortTable,
138+
cohortIds = cohortDefinitionSet$cohortId,
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cohortDefinitionSet = cohortDefinitionSet,
140+
databaseId = databaseId
141+
)
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143+
if (nrow(cohortCounts) > 0) {
144+
instantiatedCohorts <- cohortCounts %>%
145+
dplyr::filter(.data$cohortEntries > 0) %>%
146+
dplyr::pull(.data$cohortId)
147+
ParallelLogger::logInfo(
148+
sprintf(
149+
"Found %s of %s (%1.2f%%) submitted cohorts instantiated. ",
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length(instantiatedCohorts),
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nrow(cohortDefinitionSet),
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100 * (length(instantiatedCohorts) / nrow(cohortDefinitionSet))
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),
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"Beginning cohort diagnostics for instantiated cohorts. "
155+
)
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} else {
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stop("All cohorts were either not instantiated or all have 0 records.")
158+
}
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126160
ParallelLogger::logInfo("Retrieving visit context for index dates")
127161
subset <- subsetToRequiredCohorts(
128-
cohorts = cohorts %>%
162+
cohorts = cohortDefinitionSet %>%
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dplyr::filter(.data$cohortId %in% instantiatedCohorts),
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task = "runVisitContext",
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incremental = incremental,
132-
recordKeepingFile = recordKeepingFile
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recordKeepingFile = incrementalFolder
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)
134-
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135169
if (incremental &&
136170
(length(instantiatedCohorts) - nrow(subset)) > 0) {
137171
ParallelLogger::logInfo(sprintf(
@@ -166,7 +200,7 @@ executeVisitContextDiagnostics <- function(connection,
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cohortId = subset$cohortId,
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task = "runVisitContext",
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checksum = subset$checksum,
169-
recordKeepingFile = recordKeepingFile,
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recordKeepingFile = incrementalFolder,
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incremental = incremental
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)
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}

‎inst/doc/RunningCohortDiagnostics.pdf

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‎inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf

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‎inst/doc/WhatIsCohortDiagnostics.pdf

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‎inst/test_cases/runVisitContext/testSubjectCounts/expectedResult.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_cohort.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_patientData.json

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{
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"visit_occurrence": [
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{
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"visit_occurrence_id": 1,
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"person_id": 1,
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"visit_concept_id": 9201,
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"visit_start_date": "2015-01-01",
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"visit_start_datetime": "2015-01-01 08:00:00",
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"visit_end_date": "2015-01-01",
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"visit_end_datetime": "2015-01-01 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 2,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-09",
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"visit_start_datetime": "2015-01-09 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 3,
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"person_id": 1,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-10",
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"visit_start_datetime": "2015-01-10 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 4,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-10",
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"visit_start_datetime": "2015-01-10 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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}
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]
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}

‎inst/test_cases/runVisitContext/testSubjectCounts/test_getVisitContext_patientData.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCountsDates/expectedResult.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCountsDates/test_getVisitContext_cohort.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCountsDates/test_getVisitContext_patientData.json

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{
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"visit_occurrence": [
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{
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"visit_occurrence_id": 1,
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"person_id": 1,
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"visit_concept_id": 9201,
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"visit_start_date": "2015-01-01",
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"visit_start_datetime": "2015-01-01 08:00:00",
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"visit_end_date": "2015-01-01",
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"visit_end_datetime": "2015-01-01 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
17+
"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
20+
"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 2,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-09",
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"visit_start_datetime": "2015-01-09 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 3,
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"person_id": 1,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-10",
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"visit_start_datetime": "2015-01-10 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
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"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
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"visit_occurrence_id": 4,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2015-01-10",
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"visit_start_datetime": "2015-01-10 08:00:00",
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"visit_end_date": "2015-01-10",
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"visit_end_datetime": "2015-01-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
75+
"discharge_to_concept_id": 581476,
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"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
80+
"visit_occurrence_id": 5,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2015-03-10",
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"visit_start_datetime": "2015-03-10 08:00:00",
85+
"visit_end_date": "2015-03-10",
86+
"visit_end_datetime": "2015-03-10 18:00:00",
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"visit_type_concept_id": 32817,
88+
"provider_id": 1,
89+
"care_site_id": 1,
90+
"visit_source_value": 0,
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"visit_source_concept_id": 0,
92+
"admitting_source_concept_id": 8870,
93+
"admitting_source_value": "TRANSFER FROM HOSPITAL",
94+
"discharge_to_concept_id": 581476,
95+
"discharge_to_source_value": "HOME HEALTH CARE",
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"preceding_visit_occurrence_id": 0
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},
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{
99+
"visit_occurrence_id": 6,
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"person_id": 2,
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"visit_concept_id": 262,
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"visit_start_date": "2014-03-10",
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"visit_start_datetime": "2014-03-10 08:00:00",
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"visit_end_date": "2014-03-10",
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"visit_end_datetime": "2014-03-10 18:00:00",
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"visit_type_concept_id": 32817,
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"provider_id": 1,
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"care_site_id": 1,
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"visit_source_value": 0,
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"visit_source_concept_id": 0,
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"admitting_source_concept_id": 8870,
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"admitting_source_value": "TRANSFER FROM HOSPITAL",
113+
"discharge_to_concept_id": 581476,
114+
"discharge_to_source_value": "HOME HEALTH CARE",
115+
"preceding_visit_occurrence_id": 0
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}
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]
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}

‎inst/test_cases/runVisitContext/testSubjectCountsDates/test_getVisitContext_patientData.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCountsNoVisits/expectedResult.xlsx

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‎inst/test_cases/runVisitContext/testSubjectCountsNoVisits/test_getVisitContext_cohort.xlsx

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