merge with master branch

ohdsi-studies · Nov 14, 2023 · a6a5108 · a6a5108
2 parents 0e1e39e + 3eca1eb
commit a6a5108
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diff --git a/extra/CodeToRunRedShift.R b/extra/CodeToRunRedShift.R
@@ -35,7 +35,7 @@ outputFolder <- "E:/LegendT2dmOutput_optum_ehr_drug2"
 # databaseName <- "IBM Health MarketScan Medicare Supplemental and Coordination of Benefits Database"
 # databaseDescription <- "IBM Health MarketScan® Medicare Supplemental and Coordination of Benefits Database (MDCR) represents health services of retirees in the United States with primary or Medicare supplemental coverage through privately insured fee-for-service, point-of-service, or capitated health plans. These data include adjudicated health insurance claims (e.g. inpatient, outpatient, and outpatient pharmacy). Additionally, it captures laboratory tests for a subset of the covered lives."
 # tablePrefix <- "legend_t2dm_mdcr"
-# outputFolder <- "E:/LegendT2dmOutput_mdcr_continuousAge_test"
+# outputFolder <- "E:/LegendT2dmOutput_mdcr_drug2"
 
 # # Feb 2023: fast forward data version to the latest accessible
 # TBD: run drug-level study on MDCD
@@ -49,14 +49,14 @@ outputFolder <- "E:/LegendT2dmOutput_optum_ehr_drug2"
 # outputFolder <- "E:/LegendT2dmOutput_mdcd_drug2"
 
 # # Feb 2023: fast forward data version to the latest accessible
-# cdmDatabaseSchema <- "cdm_optum_extended_dod_v2323" #v2228 #v2134
-# serverSuffix <- "optum_extended_dod"
-# cohortDatabaseSchema <- "scratch_fbu2"
-# databaseId <- "OptumDod"
-# databaseName <- "Optum Clinformatics Extended Data Mart - Date of Death (DOD)"
-# databaseDescription <- "Optum Clinformatics Extended DataMart is an adjudicated US administrative health claims database for members of private health insurance, who are fully insured in commercial plans or in administrative services only (ASOs), Legacy Medicare Choice Lives (prior to January 2006), and Medicare Advantage (Medicare Advantage Prescription Drug coverage starting January 2006).  The population is primarily representative of commercial claims patients (0-65 years old) with some Medicare (65+ years old) however ages are capped at 90 years.  It includes data captured from administrative claims processed from inpatient and outpatient medical services and prescriptions as dispensed, as well as results for outpatient lab tests processed by large national lab vendors who participate in data exchange with Optum.  This dataset also provides date of death (month and year only) for members with both medical and pharmacy coverage from the Social Security Death Master File (however after 2011 reporting frequency changed due to changes in reporting requirements) and location information for patients is at the US state level."
-# tablePrefix <- "legend_t2dm_optum_dod"
-# outputFolder <- "E:/LegendT2dmOutput_optum_dod_drug2"
+cdmDatabaseSchema <- "cdm_optum_extended_dod_v2323" #v2228 #v2134
+serverSuffix <- "optum_extended_dod"
+cohortDatabaseSchema <- "scratch_fbu2"
+databaseId <- "OptumDod"
+databaseName <- "Optum Clinformatics Extended Data Mart - Date of Death (DOD)"
+databaseDescription <- "Optum Clinformatics Extended DataMart is an adjudicated US administrative health claims database for members of private health insurance, who are fully insured in commercial plans or in administrative services only (ASOs), Legacy Medicare Choice Lives (prior to January 2006), and Medicare Advantage (Medicare Advantage Prescription Drug coverage starting January 2006).  The population is primarily representative of commercial claims patients (0-65 years old) with some Medicare (65+ years old) however ages are capped at 90 years.  It includes data captured from administrative claims processed from inpatient and outpatient medical services and prescriptions as dispensed, as well as results for outpatient lab tests processed by large national lab vendors who participate in data exchange with Optum.  This dataset also provides date of death (month and year only) for members with both medical and pharmacy coverage from the Social Security Death Master File (however after 2011 reporting frequency changed due to changes in reporting requirements) and location information for patients is at the US state level."
+tablePrefix <- "legend_t2dm_optum_dod"
+outputFolder <- "E:/LegendT2dmOutput_optum_dod_drug2"
 
 
 conn <- DatabaseConnector::createConnectionDetails(
@@ -88,15 +88,15 @@ assessPhenotypes(connectionDetails = conn,
                  createOutcomeCohorts = TRUE,
                  runOutcomeCohortDiagnostics = FALSE) #TRUE)
 
-# assessPropensityModels(connectionDetails = conn,
-#                        cdmDatabaseSchema = cdmDatabaseSchema,
-#                        tablePrefix = tablePrefix,
-#                        indicationId = 'drug',
-#                        oracleTempSchema = oracleTempSchema,
-#                        cohortDatabaseSchema = cohortDatabaseSchema,
-#                        outputFolder = outputFolder,
-#                        databaseId = databaseId,
-#                        maxCores = 16)
+assessPropensityModels(connectionDetails = conn,
+                       cdmDatabaseSchema = cdmDatabaseSchema,
+                       tablePrefix = tablePrefix,
+                       indicationId = 'drug',
+                       oracleTempSchema = oracleTempSchema,
+                       cohortDatabaseSchema = cohortDatabaseSchema,
+                       outputFolder = outputFolder,
+                       databaseId = databaseId,
+                       maxCores = 16)
 
 
 # Cohort Explorer
@@ -157,30 +157,31 @@ execute(connectionDetails = conn,
         runSections = c(1:6),
         computeCovariateBalance = TRUE,
         exportToCsv = TRUE,
-        maxCores = 16)
+        maxCores = 10)
+
+# # try re-packaging OptumEHR result files
+# execute(
+#   connectionDetails = conn,
+#   cdmDatabaseSchema = cdmDatabaseSchema,
+#   oracleTempSchema = oracleTempSchema,
+#   cohortDatabaseSchema = cohortDatabaseSchema,
+#   outputFolder = outputFolder,
+#   indicationId = "drug",
+#   databaseId = databaseId,
+#   databaseName = databaseName,
+#   databaseDescription = databaseDescription,
+#   tablePrefix = tablePrefix,
+#   createExposureCohorts = FALSE,
+#   createOutcomeCohorts = FALSE,
+#   fetchAllDataFromServer = FALSE,
+#   generateAllCohortMethodDataObjects = FALSE,
+#   runCohortMethod = FALSE,
+#   runSections = c(1:6),
+#   computeCovariateBalance = FALSE,
+#   exportToCsv = TRUE,
+#   maxCores = 4
+# )
 
-# quick bug-fix to re-package results (likelihood profile re-extraction)
-# re-run SGLT2i with OT2 only
-# execute(connectionDetails = conn,
-#         cdmDatabaseSchema = cdmDatabaseSchema,
-#         oracleTempSchema = oracleTempSchema,
-#         cohortDatabaseSchema = cohortDatabaseSchema,
-#         outputFolder = outputFolder,
-#         indicationId = "sglt2i",
-#         databaseId = databaseId,
-#         databaseName = databaseName,
-#         databaseDescription = databaseDescription,
-#         tablePrefix = tablePrefix,
-#         createExposureCohorts = FALSE,
-#         createOutcomeCohorts = TRUE,
-#         fetchAllDataFromServer = TRUE,
-#         generateAllCohortMethodDataObjects = TRUE,
-#         runCohortMethod = TRUE,
-#         runSections = c(3,6),
-#         computeCovariateBalance = TRUE,
-#         exportToCsv = TRUE,
-#         maxCores = 16)
-#
 
 #### test staged execution code on a big JnJ data source ----
 # prepareStagedExecution(originalOutputFolder = outputFolder,

diff --git a/extra/ManageDrugDiagnostics.R b/extra/ManageDrugDiagnostics.R
@@ -40,12 +40,25 @@ drugSchema <- "legendt2dm_drug_diagnostics"
 
 
 ## grant user read permission
-LegendT2dm::grantPermissionOnServer(connectionDetails = connectionDetails,
-                                    user = "legend", schema = drugSchema)
+# LegendT2dm::grantPermissionOnServer(connectionDetails = connectionDetails,
+#                                     user = "legend", schema = drugSchema)
+#
+# ## grant user read permission
+# LegendT2dm::grantPermissionOnServer(connectionDetails = connectionDetails,
+#                                     user = "legendt2dm_readonly", schema = drugSchema)
+
+# uploaded, Oct 2023
+CohortDiagnostics::uploadResults(
+  connectionDetails = connectionDetails,
+  schema = drugSchema,
+  zipFileName = "E:/LegendT2dmOutput_optum_ehr_drug2/drug/cohortDiagnosticsExport/Results_drug_exposures_OptumEHR.zip")
+
+# uploaded, Oct 2023
+CohortDiagnostics::uploadResults(
+  connectionDetails = connectionDetails,
+  schema = drugSchema,
+  zipFileName = "C:/Users/Admin_FBu2/Downloads/b9ps8anh_Results_drug_exposures_CUIMC.zip")
 
-## grant user read permission
-LegendT2dm::grantPermissionOnServer(connectionDetails = connectionDetails,
-                                    user = "legendt2dm_readonly", schema = drugSchema)
 
 # uploaded, Feb 28 2023
 CohortDiagnostics::uploadResults(
@@ -71,12 +84,6 @@ CohortDiagnostics::uploadResults(
   zipFileName = "E:/LegendT2dmOutput_mdcd_new/sglt2i/cohortDiagnosticsExport/Results_sglt2i_exposures_MDCD.zip")
 
 
-# # uploaded for dpp4i too, Feb 6 2023
-# CohortDiagnostics::uploadResults(
-#   connectionDetails = connectionDetails,
-#   schema = drugSchema,
-#   zipFileName = "E:/LegendT2dmOutput_mdcr_DPP4I_2/DPP4I/cohortDiagnosticsExport/Results_DPP4I_exposures_MDCR.zip")
-
 # uploaded, Feb 8 2023
 CohortDiagnostics::uploadResults(
   connectionDetails = connectionDetails,
@@ -96,6 +103,18 @@ CohortDiagnostics::uploadResults(
   zipFileName = "E:/Results_sglt2i_exposures_CUIMC.zip")
 
 
+# Sept 2023: upload IQVIA data sources' exposure diagnostics
+CohortDiagnostics::uploadResults(
+  connectionDetails = connectionDetails,
+  schema = drugSchema,
+  zipFileName = "E:/Results_drug_exposures_DA_GERMANY.zip")
+
+CohortDiagnostics::uploadResults(
+  connectionDetails = connectionDetails,
+  schema = drugSchema,
+  zipFileName = "E:/Results_drug_exposures_LPD_FRANCE.zip")
+
+
 
 # CohortDiagnostics::uploadResults(
 #   connectionDetails = connectionDetails,

diff --git a/extra/ManageDrugResults.R b/extra/ManageDrugResults.R
@@ -45,26 +45,39 @@ LegendT2dm::grantPermissionOnServer(connectionDetails = connectionDetails,
 
 
 # July 2023 drug-vs-drug CES results upload ----
-# Results uploaded for newer data versions!
-# March 2023: uploaded DA Germany & US Open Claims
+# Results after for newer data version & package de-bug
 LegendT2dm::uploadResultsToDatabase(
   connectionDetails = connectionDetails,
   schema = resultsSchema,
-  purgeSiteDataBeforeUploading = FALSE,
+  purgeSiteDataBeforeUploading =TRUE,
   zipFileName = c(
     #"E:/LegendT2dmOutput_mdcr_drug/drug/export/Results_drug_study_MDCR.zip",
     #"E:/LegendT2dmOutput_ccae_drug/drug/export/Results_drug_study_CCAE.zip"
     #"E:/LegendT2dmOutput_optum_ehr_new/sglt2i/export/Results_sglt2i_study_OptumEHR.zip",
     #"E:/LegendT2dmOutput_optum_dod_new/sglt2i/export/Results_sglt2i_study_OptumDod.zip",
     #"E:/LegendT2dmOutput_mdcd_drug2/drug/export/Results_drug_study_MDCD.zip",
-    "E:/LegendT2dmOutput_mdcr_continuousAge_test/sglt2i/export/Results_sglt2i_study_MDCR.zip",
-    #"E:/LegendT2dmOutput_ccae_sglt2i_new/sglt2i/export/Results_sglt2i_study_CCAE.zip"
+    #"E:/LegendT2dmOutput_mdcr_continuousAge_test/sglt2i/export/Results_sglt2i_study_MDCR.zip",
+    #"E:/LegendT2dmOutput_ccae_sglt2i_new/sglt2i/export/Results_sglt2i_study_CCAE.zip",
+    #"C:/Users/Admin_FBu2/Downloads/Results_drug_study_DA_GERMANY.zip",
+    #"C:/Users/Admin_FBu2/Downloads/Results_drug_study_LPD_FRANCE.zip",
+    # "E:/Results_drug_study_LPD_FRANCE.zip",
+    # "E:/Results_drug_study_DA_GERMANY.zip",
+    # "E:/LegendT2dmOutput_mdcr_drug2/drug/export/Results_drug_study_MDCR.zip",
+    # "E:/LegendT2dmOutput_mdcd_drug2/drug/export/Results_drug_study_MDCD.zip",
+    "E:/LegendT2dmOutput_optum_ehr_drug2/drug/export/Results_drug_study_OptumEHR.zip",
+    #"C:/Users/Admin_FBu2/Downloads/rzbxa8v1_Results_drug_study_IMRD.zip",
     NULL
     ),
-  specifications = tibble::tibble(read.csv("inst/settings/ResultsModelSpecs.csv"))
+  specifications = tibble::tibble(read.csv("inst/settings/ResultsModelSpecs.csv")),
+  tempFolder = "E:/uploadTemp/"
 )
 
 
+# locally examine OptumEHR drug-v-drug results
+optumEHRZipFile =  "E:/LegendT2dmOutput_optum_ehr_drug2/drug/export/Results_drug_study_OptumEHR.zip"
+LegendT2dm::prepareForEvidenceExplorer(resultsZipFile = optumEHRZipFile,
+                                       dataFolder = "E:/LegendT2dmOutput_optum_ehr_drug2/EvidenceExplorer/")
+
 
 
 imrdZipFile <- "/Users/msuchard/Dropbox/Projects/LegendT2dm_Results/class_ces/5w17o2h3_Results_class_study_UK-IMRD.zip"