changes for data model

OHDSI · Jan 7, 2025 · 7dcbebd · 7dcbebd
1 parent c5a32f6
commit 7dcbebd
Show file tree

Hide file tree

Showing 9 changed files with 25 additions and 18 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,6 +35,8 @@ Suggests:
     DiagrammeR,
     tidyr,
     R.utils
+Remotes:
+    OHDSI/ResultModelManager@big_int_type_check
 License: Apache License 2.0
 RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/R/RunAnalyses.R b/R/RunAnalyses.R
@@ -44,6 +44,7 @@ runSccAnalyses <- function(connectionDetails,
                            outputFolder = "./SelfControlledCohortOutput",
                            sccAnalysisList,
                            exposureOutcomeList,
+                           databaseId,
                            controlType = "outcome",
                            analysisThreads = 1,
                            computeThreads = 1) {
@@ -116,6 +117,7 @@ runSccAnalyses <- function(connectionDetails,
                  cdmVersion = cdmVersion,
                  exposureIds = exposureIds,
                  outcomeIds = outcomeId,
+                 databaseId = databaseId,
                  controlType = controlType,
                  analysisId = refRow$analysisId,
                  tempEmulationSchema = tempEmulationSchema,

diff --git a/R/SelfControlledCohort.R b/R/SelfControlledCohort.R
@@ -44,13 +44,13 @@ computeIrrs <- function(estimates) {
                  timeAtRiskExposed = estimates$time_at_risk_exposed,
                  timeAtRiskUnexposed = estimates$time_at_risk_unexposed)
 
-  estimates$irr <- irrs[1,]
-  estimates$irrLb95 <- irrs[2,]
-  estimates$irrUb95 <- irrs[3,]
+  estimates$rr <- irrs[1,]
+  estimates$irr_lb_95 <- irrs[2,]
+  estimates$irr_ub_95 <- irrs[3,]
 
-  estimates$logRr <- log(estimates$irr)
-  estimates$seLogRr <- (log(estimates$irrUb95) - log(estimates$irrLb95)) / (2 * qnorm(0.975))
-  zTest <- stats::pnorm(estimates$logRr / estimates$seLogRr)
+  estimates$log_rr <- log(estimates$rr)
+  estimates$se_log_rr <- (log(estimates$irr_ub_95) - log(estimates$irr_lb_95)) / (2 * qnorm(0.975))
+  zTest <- stats::pnorm(estimates$log_rr / estimates$se_log_rr)
   estimates$p <- 2 * pmin(zTest, 1 - zTest)
   return(estimates)
 }
@@ -135,7 +135,6 @@ batchComputeEstimates <- function(connection,
       ncPairsDf |>
         dplyr::group_by(.data$outcomeCohortId) |>
         dplyr::group_map(function(data, outcomeCohortId) {
-          browser()
           estimates <- andromeda$estimates |>
             dplyr::filter(.data$outcomeCohortId == outcomeCohortId)
 
@@ -266,7 +265,7 @@ batchComputeEstimates <- function(connection,
 #'                                         confidence intervals.
 #' @param resultExportPath                 Folder where result files are exported
 #' @param outputFolder                     Folder where intermediate files are stored
-#' @param databaseId                       Unique identifier for database
+#' @param databaseId                       Unique identifier for database - required
 #' @param resultExportManager              ResultModelManager::ResultExportManager instance - customize this to implement
 #'                                         an alternative mechanism for exporting results
 #'
@@ -325,7 +324,7 @@ runSelfControlledCohort <- function(connectionDetails = NULL,
                                     resultsDatabaseSchema = NULL,
                                     resultExportPath = "scc_result",
                                     outputFolder = "scc_work",
-                                    databaseId = NULL,
+                                    databaseId,
                                     analysisId = 1,
                                     resultExportManager = ResultModelManager::createResultExportManager(
                                       tableSpecification = getResultsDataModelSpecifications(),

diff --git a/inst/resultsDataModelSpecification.csv b/inst/resultsDataModelSpecification.csv
@@ -19,12 +19,11 @@ scc_result,calibrated_lb_95,float,0,0,0,Lower bound of the 95% confidence interv
 scc_result,calibrated_ub_95,float,0,0,0,Upper bound of the 95% confidence interval for calibrated results
 scc_result,calibrated_p_value,float,0,0,0,P-value for calibrated results
 scc_result,exposure_calibrated,int,0,0,0,Is the result calibrated with exposure negative controls or outcomes?
-scc_result,c_pt,float,0,0,0,Unexposed pt
-scc_result,t_pt,float,0,0,0,Exposed pt
-scc_result,t_at_risk,float,0,0,0,Time at risk exposed
-scc_result,c_at_risk,float,0,0,0,Time at risk unexposed
-scc_result,t_cases,float,0,0,1,Cases while exposed
-scc_result,c_cases,float,0,0,1,Cases while unexposed
+scc_result,num_persons,float,0,0,0,person count
+scc_result,time_at_risk_exposed,float,0,0,0,Time at risk exposed
+scc_result,time_at_risk_unexposed,float,0,0,0,Time at risk unexposed
+scc_result,num_outcomes_exposed,float,0,0,1,Cases while exposed
+scc_result,num_outcomes_unexposed,float,0,0,1,Cases while unexposed
 scc_result,num_exposures,float,0,0,1,Number of exposures
 scc_result,i_2,float,0,0,0,I² statistic for heterogeneity
 scc_stat,database_id,int,1,1,0,Unique identifier for the database

diff --git a/man/getSccRiskWindowStats.Rd b/man/getSccRiskWindowStats.Rd
diff --git a/man/runSccAnalyses.Rd b/man/runSccAnalyses.Rd
diff --git a/man/runSelfControlledCohort.Rd b/man/runSelfControlledCohort.Rd
diff --git a/tests/testthat/test-RunAnalyses.R b/tests/testthat/test-RunAnalyses.R
@@ -21,6 +21,7 @@ test_that("multiple analyses", {
                          sccAnalysisList = sccAnalysisList,
                          exposureOutcomeList = exposureOutcomeList,
                          outputFolder = outputFolder,
+                         databaseId = 1,
                          computeThreads = 1)
 
     expect_s3_class(rr, "data.frame")

diff --git a/tests/testthat/test-SelfControlledCohort.R b/tests/testthat/test-SelfControlledCohort.R
@@ -18,6 +18,7 @@ test_that("SCC method runs on Eunomia", {
                                        cdmDatabaseSchema = "main",
                                        exposureIds = '',
                                        outcomeIds = '',
+                                       databaseId = 1,
                                        riskWindowEndExposed = 1,
                                        riskWindowStartExposed = 30,
                                        addLengthOfExposureExposed = F),