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Fix R check warnings/notes
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Gennadiy Anisimov committed Mar 21, 2024
1 parent 10349d4 commit bf47864
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Showing 3 changed files with 38 additions and 36 deletions.
1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -8,3 +8,4 @@ deploy.sh
_pkgdown.yml
^CRAN-SUBMISSION$
^cran-comments\.md$
^.lintr
1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -28,6 +28,7 @@ Depends:
R (>= 4.0.0)
Imports:
DBI,
duckdb,
SqlRender (>= 1.6.0),
dplyr,
jsonlite,
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72 changes: 36 additions & 36 deletions R/exportToAres.R
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Expand Up @@ -333,7 +333,7 @@ generateAOAchillesPerformanceReport <- function(connection, cdmDatabaseSchema, r

queryAchillesPerformance <- SqlRender::loadRenderTranslateSql(sqlFilename = "export/performance/sqlAchillesPerformance.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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warnOnMissingParameters = FALSE,
cdm_database_schema = cdmDatabaseSchema,
results_database_schema = resultsDatabaseSchema,
Expand All @@ -352,30 +352,30 @@ generateAODeathReport <- function(connection, cdmDatabaseSchema, resultsDatabase
queryPrevalenceByGenderAgeYear <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/death/sqlPrevalenceByGenderAgeYear.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)

queryPrevalenceByMonth <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/death/sqlPrevalenceByMonth.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)

queryDeathByType <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/death/sqlDeathByType.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)

queryAgeAtDeath <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/death/sqlAgeAtDeath.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -398,7 +398,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/ageatfirst.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
ageAtFirstObservationData <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -407,7 +407,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/agebygender.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -418,7 +418,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observationlength_stats.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
observationLengthStats <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -430,7 +430,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observationlength_data.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
observationLengthData <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -439,7 +439,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/cumulativeduration.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
cumulativeDurationData <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -451,7 +451,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observationlengthbygender.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -469,7 +469,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observationlengthbyage.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
opLengthByAgeData <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -486,7 +486,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observedbyyear_stats.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
observedByYearStats <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -498,7 +498,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observedbyyear_data.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
observedByYearData <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -509,7 +509,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/observedbymonth.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
observedByMonth <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -518,7 +518,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observationperiod/periodsperperson.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
personPeriodsData <- DatabaseConnector::querySql(connection, renderedSql)
Expand Down Expand Up @@ -793,7 +793,7 @@ generateAOMetadataReport <- function(connection, cdmDatabaseSchema, outputPath)
queryMetadata <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/metadata/sqlMetadata.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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cdm_database_schema = cdmDatabaseSchema
)
dataMetadata <- DatabaseConnector::querySql(connection, queryMetadata)
Expand Down Expand Up @@ -943,7 +943,7 @@ generateAOCdmSourceReport <- function(connection, cdmDatabaseSchema, outputPath)
queryCdmSource <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/metadata/sqlCdmSource.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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cdm_database_schema = cdmDatabaseSchema
)

Expand Down Expand Up @@ -1901,7 +1901,7 @@ generateDataDensityTotal <- function(connection, resultsDatabaseSchema) {
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/datadensity/totalrecords.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)

Expand All @@ -1919,7 +1919,7 @@ generateDataDensityRecordsPerPerson <- function(connection, resultsDatabaseSchem
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/datadensity/recordsperperson.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)

Expand All @@ -1934,7 +1934,7 @@ generateDataDensityConceptsPerPerson <- function(connection, resultsDatabaseSche
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/datadensity/conceptsperperson.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
conceptsPerPerson <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -1947,7 +1947,7 @@ generateDataDensityDomainsPerPerson <- function(connection, resultsDatabaseSchem
renderedSql <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/datadensity/domainsperperson.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
domainsPerPerson <- DatabaseConnector::querySql(connection, renderedSql)
Expand All @@ -1961,7 +1961,7 @@ generateDomainSummaryConditions <- function(connection, resultsDatabaseSchema, v
queryConditions <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/condition/sqlConditionTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -1979,7 +1979,7 @@ generateDomainSummaryConditionEras <- function(connection, resultsDatabaseSchema
queryConditionEra <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/conditionera/sqlConditionEraTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -1996,7 +1996,7 @@ generateDomainSummaryDrugs <- function(connection, resultsDatabaseSchema, vocabD
queryDrugs <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/drug/sqlDrugTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2013,7 +2013,7 @@ generateDomainDrugStratification <- function(connection, resultsDatabaseSchema,
queryDrugType <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/drug/sqlDomainDrugStratification.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2026,7 +2026,7 @@ generateDomainSummaryDrugEra <- function(connection, resultsDatabaseSchema, voca
queryDrugEra <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/drugera/sqlDrugEraTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2043,7 +2043,7 @@ generateDomainSummaryMeasurements <- function(connection, resultsDatabaseSchema,
queryMeasurements <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/measurement/sqlMeasurementTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2060,7 +2060,7 @@ generateDomainSummaryObservations <- function(connection, resultsDatabaseSchema,
queryObservations <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/observation/sqlObservationTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2077,7 +2077,7 @@ generateDomainSummaryVisitDetails <- function(connection, resultsDatabaseSchema,
queryVisitDetails <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/visitdetail/sqlVisitDetailTreemap.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2095,7 +2095,7 @@ generateDomainSummaryVisits <- function(connection, resultsDatabaseSchema, vocab
queryVisits <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/visit/sqlVisitTreemap.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2113,7 +2113,7 @@ generateDomainVisitStratification <- function(connection, resultsDatabaseSchema,
queryVisits <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/visit/sqlDomainVisitStratification.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2126,7 +2126,7 @@ generateDomainSummaryProcedures <- function(connection, resultsDatabaseSchema, v
queryProcedures <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/procedure/sqlProcedureTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2143,7 +2143,7 @@ generateDomainSummaryDevices <- function(connection, resultsDatabaseSchema, voca
queryDevices <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/device/sqlDeviceTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2160,7 +2160,7 @@ generateDomainSummaryProvider <- function(connection, resultsDatabaseSchema, voc
queryProviders <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/provider/sqlProviderSpecialty.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema,
vocab_database_schema = vocabDatabaseSchema
)
Expand All @@ -2176,7 +2176,7 @@ generateQualityCompleteness <- function(connection, resultsDatabaseSchema) {
queryCompleteness <- SqlRender::loadRenderTranslateSql(
sqlFilename = "export/quality/sqlCompletenessTable.sql",
packageName = "Achilles",
dbms = connectionDetails$dbms,
dbms = connection@dbms,

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results_database_schema = resultsDatabaseSchema
)
dataCompleteness <- DatabaseConnector::querySql(connection, queryCompleteness)
Expand Down

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