New simulation profile, with two outcomes instead of one, for better …

…testing.
OHDSI · Nov 5, 2015 · 5b83db6 · 5b83db6
1 parent 797d10f
commit 5b83db6
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Showing 3 changed files with 14 additions and 10 deletions.
diff --git a/R/Simulation.R b/R/Simulation.R
@@ -43,18 +43,13 @@ createPlpSimulationProfile <- function(plpData) {
   outcomeModels <- vector("list", length(plpData$metaData$outcomeIds))
   for (i in 1:length(plpData$metaData$outcomeIds)) {
     outcomeId <- plpData$metaData$outcomeIds[i]
-    # model <- fitPredictiveModel(plpData = plpData, outcomeId = outcomeId, modelType = 'poisson', prior
-    # = Cyclops::createPrior('laplace', exclude = c(0), useCrossValidation = TRUE), control =
-    # Cyclops::createControl(noiseLevel = 'quiet', cvType = 'auto', startingVariance = 0.01, threads =
-    # 10))
     model <- fitPredictiveModel(plpData = plpData,
                                 outcomeId = outcomeId,
                                 modelType = "poisson",
                                 prior = Cyclops::createPrior("laplace",
                                                              exclude = c(0),
-                                                             variance = 0.01))
-    # model$coefficients[1] <- log(ffbase::sum.ff(plpData$outcomes$outcomeCount) /
-    # ffbase::sum.ff(plpData$cohorts$time))
+                                                             useCrossValidation = TRUE),
+                                control = Cyclops::createControl(noiseLevel = "quiet", cvType = "auto", startingVariance = 0.001, threads = 10))
     model$coefficients <- model$coefficients[model$coefficients != 0]
     outcomeModels[[i]] <- model$coefficients
   }

diff --git a/R/SimulationDataFetch.R b/R/SimulationDataFetch.R
@@ -73,7 +73,16 @@
   2 AS cohort_concept_id
   FROM  @cdmDatabaseSchema.condition_occurrence
   WHERE condition_concept_id IN (4108356, 4110189, 4110190, 4110192, 45767658, 45772786) /* Cerebral infarct */
-  AND condition_type_concept_id  = 38000183;
+  AND condition_type_concept_id  IN (38000183,38000199,44786627,38000184,38000200);
+
+  INSERT INTO @resultsDatabaseSchema.mschuemi_stroke
+  SELECT condition_occurrence.person_id AS subject_id,
+  condition_start_date AS cohort_start_date,
+  condition_end_date AS cohort_end_date,
+  3 AS cohort_concept_id
+  FROM  @cdmDatabaseSchema.condition_occurrence
+  WHERE condition_concept_id IN (312327, 434376, 436706, 438170, 438438, 438447, 439693, 441579, 444406) /* Myocardial infarction */
+  AND condition_type_concept_id IN (38000183,38000199,44786627,38000184,38000200);
   "
   sql <- SqlRender::renderSql(sql, 
                               cdmDatabaseSchema = cdmDatabaseSchema,
@@ -161,7 +170,7 @@
                           covariateSettings = covariateSettings,
                           outcomeDatabaseSchema = resultsDatabaseSchema,
                           outcomeTable = "mschuemi_stroke",
-                          outcomeIds = 2,
+                          outcomeIds = c(2,3),
                           firstOutcomeOnly = TRUE,
                           cdmVersion = cdmVersion)
   summary(plpData)
@@ -182,7 +191,7 @@
        file = "C:/Users/mschuemi/git/PatientLevelPrediction/data/plpDataSimulationProfile.rda",
        compress = "xz")
 
-  #plpDataSimulationProfile$outcomeModels[[1]][1]
+  #plpDataSimulationProfile$outcomeModels[[]][1]
 
 
   # load('C:/Users/mschuemi/git/PatientLevelPrediction/data/plpDataSimulationProfile.rda')

diff --git a/data/plpDataSimulationProfile.rda b/data/plpDataSimulationProfile.rda