Bumped version to 1.0.0. Updated and reran vignette.

OHDSI · Nov 2, 2015 · 7562fa2 · 7562fa2
1 parent bf44eea
commit 7562fa2
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Showing 5 changed files with 9 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PatientLevelPrediction
 Type: Package
 Title: Package for patient level prediction using data in the OMOP Common Data Model
-Version: 0.0.4
+Version: 1.0.0
 Date: 2015-10-7
 Author: Martijn J. Schuemie [aut, cre],
   Marc A. Suchard [aut],
@@ -11,8 +11,8 @@ Description: A package for creating patient level prediction models. Given a coh
 License: Apache License 2.0
 Depends:
     R (>= 3.1.0),
-    DatabaseConnector (>= 1.1.2),
-    Cyclops (>= 1.0.0)
+    DatabaseConnector (>= 1.3.0),
+    Cyclops (>= 1.2.0)
 Imports:     
     ggplot2,
     bit,

diff --git a/R/VignetteDataFetch.R b/R/VignetteDataFetch.R
@@ -1,6 +1,6 @@
 # @file VignetteDataFetch.R
 #
-# Copyright 2014 Observational Health Data Sciences and Informatics
+# Copyright 2015 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 # 
@@ -129,6 +129,7 @@
                           cohortDatabaseSchema = resultsDatabaseSchema,
                           cohortTable = "rehospitalization",
                           cohortIds = 1,
+                          washoutWindow = 183,
                           useCohortEndDate = TRUE,
                           windowPersistence = 0,
                           covariateSettings = covariateSettings,
@@ -150,6 +151,8 @@
 
   parts <- splitData(plpData, c(0.75, 0.25))
 
+  savePlpData(parts[[1]], "s:/temp/PlpVignette/plpData_train")
+
   savePlpData(parts[[2]], "s:/temp/PlpVignette/plpData_test")
 
   model <- fitPredictiveModel(parts[[1]],
@@ -159,7 +162,7 @@
                                                   useCrossValidation = TRUE),
                               control = createControl(noiseLevel = "quiet",
                                                       cvType = "auto",
-                                                      startingVariance = 0.01,
+                                                      startingVariance = 0.001,
                                                       threads = 10))
 
   saveRDS(model, file = "s:/temp/PlpVignette/model.rds")

diff --git a/inst/doc/BuildingPredictiveModels.pdf b/inst/doc/BuildingPredictiveModels.pdf
diff --git a/man/PatientLevelPrediction.pdf b/man/PatientLevelPrediction.pdf
diff --git a/vignettes/BuildingPredictiveModels.Rmd b/vignettes/BuildingPredictiveModels.Rmd
@@ -15,7 +15,7 @@ output:
 %\VignetteIndexEntry{Building patient-level predictive models}
 -->
 
-```{r echo=FALSE,message=FALSE,eval=TRUE}
+```{r echo=FALSE,message=FALSE,warning=FALSE,eval=TRUE}
 library(PatientLevelPrediction)
 # Load all needed data if it exists on this computer:
 if (file.exists("s:/temp/PlpVignette")){