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Merge pull request #266 from OHDSI/develop
Release v3.6.0
2 parents f4536fb + 8e70152 commit a0bbc9b

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‎.github/workflows/R_CMD_check_Hades.yaml‎

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- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
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CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
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CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
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CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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CDM_SNOWFLAKE_CDM53_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_CDM53_SCHEMA }}
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CDM_SNOWFLAKE_OHDSI_SCHEMA: ${{ secrets.CDM_SNOWFLAKE_OHDSI_SCHEMA }}
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CDM_SNOWFLAKE_PASSWORD: ${{ secrets.CDM_SNOWFLAKE_PASSWORD }}
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CDM_SNOWFLAKE_CONNECTION_STRING: ${{ secrets.CDM_SNOWFLAKE_CONNECTION_STRING }}
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CDM_SNOWFLAKE_USER: ${{ secrets.CDM_SNOWFLAKE_USER }}
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CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
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CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
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CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
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CDM5_SPARK_CDM_SCHEMA: ${{ secrets.CDM5_SPARK_CDM_SCHEMA }}
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CDM5_SPARK_OHDSI_SCHEMA: ${{ secrets.CDM5_SPARK_OHDSI_SCHEMA }}
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CDM_BIG_QUERY_CONNECTION_STRING: ${{ secrets.CDM_BIG_QUERY_CONNECTION_STRING }}
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CDM_BIG_QUERY_KEY_FILE: ${{ secrets.CDM_BIG_QUERY_KEY_FILE }}
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CDM_BIG_QUERY_CDM_SCHEMA: ${{ secrets.CDM_BIG_QUERY_CDM_SCHEMA }}
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CDM_BIG_QUERY_OHDSI_SCHEMA: ${{ secrets.CDM_BIG_QUERY_OHDSI_SCHEMA }}
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steps:
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- uses: actions/checkout@v2

‎DESCRIPTION‎

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Package: FeatureExtraction
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Type: Package
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Title: Generating Features for a Cohort
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Version: 3.5.2
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Date: 2024-05-01
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Version: 3.6.0
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Date: 2024-07-15
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Authors@R: c(
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person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
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person("Marc", "Suchard", role = c("aut")),
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dplyr,
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rJava,
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jsonlite,
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SqlRender (>= 1.6.0),
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SqlRender (>= 1.18.0),
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ParallelLogger (>= 2.0.2),
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cli,
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pillar,

‎NEWS.md‎

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FeatureExtraction 3.6.0
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=======================
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New Features:
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- Support for observation / measurement values (#67)
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- Add additional DB testing servers github action: Spark, Snowflake, BigQuery (#247)
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Bug fixes:
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- Inconsistent Handling of cohortIds in getDbCovariateData Depending on aggregated Setting (#229)
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- minor typo in specification file (#260)
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- Update custom covariate builder vignette (#258)
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FeatureExtraction 3.5.2
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=======================
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‎R/DefaultCovariateSettings.R‎

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#' medium term window. (analysis ID 403)
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#' @param useDrugEraShortTerm One covariate per drug in the drug_era
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#' table overlapping with any part of the
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#' short window. (analysis ID 404)
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#' short term window. (analysis ID 404)
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#' @param useDrugEraOverlapping One covariate per drug in the drug_era
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#' table overlapping with the end of the
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#' risk window. (analysis ID 405)
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#' table starting in the medium term
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#' window. (analysis ID 407)
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#' @param useDrugEraStartShortTerm One covariate per drug in the drug_era
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#' table starting in the long short window.
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#' table starting in the short term window.
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#' (analysis ID 408)
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#' @param useDrugGroupEraAnyTimePrior One covariate per drug rolled up to ATC
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#' groups in the drug_era table overlapping
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#' measurements are below, within, or above
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#' normal range in the short term window.
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#' (analysis ID 712)
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#' @param useMeasurementValueAsConceptAnyTimePrior One covariate per measurement-value
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#' concept combination any time prior to
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#' index. (analysis ID 713)
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#' @param useMeasurementValueAsConceptLongTerm One covariate per measurement-value
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#' concept combination in the long term
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#' window. (analysis ID 714)
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#' @param useMeasurementValueAsConceptMediumTerm One covariate per measurement-value
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#' concept combination in the medium term
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#' window. (analysis ID 715)
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#' @param useMeasurementValueAsConceptShortTerm One covariate per measurement-value
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#' concept combination in the short term
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#' window. (analysis ID 716)
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#' @param useObservationAnyTimePrior One covariate per observation in the
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#' observation table any time prior to
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#' index. (analysis ID 801)
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#' @param useObservationShortTerm One covariate per observation in the
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#' observation table in the short term
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#' window. (analysis ID 804)
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#' @param useObservationValueAsConceptAnyTimePrior One covariate per observation-value
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#' concept combination any time prior to
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#' index. (analysis ID 805)
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#' @param useObservationValueAsConceptLongTerm One covariate per observation-value
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#' concept combination in the long term
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#' window. (analysis ID 806)
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#' @param useObservationValueAsConceptMediumTerm One covariate per observation-value
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#' concept combination in the medium term
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#' window. (analysis ID 807)
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#' @param useObservationValueAsConceptShortTerm One covariate per observation-value
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#' concept combination in the short term
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#' window. (analysis ID 808)
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#' @param useCharlsonIndex The Charlson comorbidity index (Romano
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#' adaptation) using all conditions prior
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#' to the window end. (analysis ID 901)
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#' useMeasurementRangeGroupAnyTimePrior = FALSE,
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#' useMeasurementRangeGroupLongTerm = TRUE,
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#' useMeasurementRangeGroupMediumTerm = FALSE,
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#' useMeasurementRangeGroupShortTerm = FALSE,
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#' useMeasurementRangeGroupShortTerm = TRUE,
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#' useMeasurementValueAsConceptAnyTimePrior = FALSE,
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#' useMeasurementValueAsConceptLongTerm = TRUE,
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#' useMeasurementValueAsConceptMediumTerm = FALSE,
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#' useMeasurementValueAsConceptShortTerm = TRUE,
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#' useObservationAnyTimePrior = FALSE,
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#' useObservationLongTerm = TRUE,
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#' useObservationMediumTerm = FALSE,
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#' useObservationShortTerm = TRUE,
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#' useObservationValueAsConceptAnyTimePrior = FALSE,
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#' useObservationValueAsConceptLongTerm = TRUE,
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#' useObservationValueAsConceptMediumTerm = FALSE,
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#' useObservationValueAsConceptShortTerm = TRUE,
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#' useCharlsonIndex = TRUE,
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#' useDcsi = TRUE,
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#' useChads2 = TRUE,
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useMeasurementRangeGroupLongTerm = FALSE,
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useMeasurementRangeGroupMediumTerm = FALSE,
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useMeasurementRangeGroupShortTerm = FALSE,
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useMeasurementValueAsConceptAnyTimePrior = FALSE,
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useMeasurementValueAsConceptLongTerm = FALSE,
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useMeasurementValueAsConceptMediumTerm = FALSE,
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useMeasurementValueAsConceptShortTerm = FALSE,
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useObservationAnyTimePrior = FALSE,
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useObservationLongTerm = FALSE,
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useObservationMediumTerm = FALSE,
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useObservationShortTerm = FALSE,
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useObservationValueAsConceptAnyTimePrior = FALSE,
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useObservationValueAsConceptLongTerm = FALSE,
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useObservationValueAsConceptMediumTerm = FALSE,
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useObservationValueAsConceptShortTerm = FALSE,
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useCharlsonIndex = FALSE,
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useDcsi = FALSE,
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useChads2 = FALSE,

‎R/DefaultTemporalCovariateSettings.R‎

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#' the drug_era table starting in the time window.
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#' (analysis ID 403)
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#' @param useDrugEraGroupOverlap One covariate per drug rolled up to ATC groups in
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#' the drug_era table overlapping with any part of
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#' the time window. (analysis ID 404)
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#' the drug_era table overlapping with any part of the
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#' time window. (analysis ID 404)
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#' @param useProcedureOccurrence One covariate per procedure in the
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#' procedure_occurrence table in the time window.
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#' (analysis ID 501)
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#' @param useMeasurementRangeGroup Covariates indicating whether measurements are
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#' below, within, or above normal range within the time
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#' period. (analysis ID 703)
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#' @param useMeasurementValueAsConcept One covariate per measurement-value concept
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#' combination within the time period. (analysis ID
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#' 704)
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#' @param useObservation One covariate per observation in the observation
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#' table in the time window. (analysis ID 801)
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#' @param useObservationValueAsConcept One covariate per observation-value concept
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#' combination within the time period. (analysis ID
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#' 802)
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#' @param useCharlsonIndex The Charlson comorbidity index (Romano adaptation)
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#' using all conditions prior to the window end.
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#' (analysis ID 901)
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#' useMeasurement = TRUE,
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#' useMeasurementValue = FALSE,
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#' useMeasurementRangeGroup = TRUE,
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#' useMeasurementValueAsConcept = TRUE,
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#' useObservation = TRUE,
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#' useObservationValueAsConcept = TRUE,
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#' useCharlsonIndex = TRUE,
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#' useDcsi = TRUE,
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#' useChads2 = TRUE,
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useMeasurement = FALSE,
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useMeasurementValue = FALSE,
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useMeasurementRangeGroup = FALSE,
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useMeasurementValueAsConcept = FALSE,
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useObservation = FALSE,
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useObservationValueAsConcept = FALSE,
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useCharlsonIndex = FALSE,
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useDcsi = FALSE,
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useChads2 = FALSE,

‎R/GetCovariates.R‎

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#' @param covariateSettings Either an object of type \code{covariateSettings} as created using one
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#' of the createCovariate functions, or a list of such objects.
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#' @param aggregated Should aggregate statistics be computed instead of covariates per
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#' cohort entry?
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#' cohort entry? If aggregated is set to FALSE, the results returned will be based
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#' on each subject_id and cohort_start_date in your cohort table. If your cohort
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#' contains multiple entries for the same subject_id (due to different cohort_start_date values),
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#' you must carefully set the rowIdField so you can identify the patients properly.
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#' See issue #229 for more discussion on this parameter.
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#' @param minCharacterizationMean The minimum mean value for characterization output. Values below this will be cut off from output. This
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#' will help reduce the file size of the characterization output, but will remove information
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#' on covariates that have very low values. The default is 0.

‎R/GetDefaultCovariates.R‎

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andromedaTableName = "covariateRef",
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snakeCaseToCamelCase = TRUE
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)
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collisions <- covariateData$covariateRef %>%
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filter(collisions > 0) %>%
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collect()
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if (nrow(collisions) > 0) {
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warning(sprintf(
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"Collisions in covariate IDs detected for post-coordinated concepts with covariate IDs %s",
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paste(collisions$covariateId, paste = ", ")
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))
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}
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# Analysis reference
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sql <- SqlRender::translate(

‎docs/404.html‎

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‎docs/articles/CreatingCovariatesBasedOnOtherCohorts.html‎

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‎docs/articles/CreatingCovariatesUsingCohortAttributes.html‎

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