diff --git a/vignettes/Installing.Rmd b/vignettes/Installing.Rmd
index f816977..2a60857 100644
--- a/vignettes/Installing.Rmd
+++ b/vignettes/Installing.Rmd
@@ -44,7 +44,7 @@ This vignette describes how you need to install the Observational Health Data Sc
Under Windows the OHDSI Deep Patient Level Prediction (DeepPLP) package requires installing:
-- R ( ) - (R \>= 3.5.0, but latest is recommended)
+- R ( ) - (R \>= 3.3.0, but latest is recommended)
- Rstudio ( )
- Java ( )
- RTools ()
@@ -53,7 +53,7 @@ Under Windows the OHDSI Deep Patient Level Prediction (DeepPLP) package requires
Under Mac and Linux the OHDSI deepPLP package requires installing:
-- R ( ) - (R \>= 3.5.0, but latest is recommended)
+- R ( ) - (R \>= 3.3.0, but latest is recommended)
- Rstudio ( )
- Java ( )
- Xcode command line tools(run in terminal: xcode-select --install) [MAC USERS ONLY]
@@ -85,22 +85,63 @@ library(torch)
This will download the required libtorch and lantern binaries for your operating system and copy them to the required locations for torch to use.
-If you are using DeepPLP in an offline environment the function `torch::install_torch_from_file()` can be used. See [torch installation guide](https://torch.mlverse.org/docs/articles/installation.html) for more detailed instructions.
+If you are using DeepPLP in an offline environment the function `torch::install_torch_from_file()` can be used. This will first require to download and move the correct binaries to the offline environment. See [torch installation guide](https://torch.mlverse.org/docs/articles/installation.html) for more detailed instructions.
When installing make sure to close any other Rstudio sessions that are using `DeepPatientLevelPrediction` or any dependency. Keeping Rstudio sessions open can cause locks that prevent the package installing.
# Testing Installation
--add simple test code
-
-# Acknowledgments
-
-Considerable work has been dedicated to provide the `DeepPatientLevelPrediction` package.
-
-```{r tidy=TRUE,eval=TRUE}
-citation("PatientLevelPrediction")
+```{r, echo = TRUE, message = FALSE, warning = FALSE,tidy=FALSE,eval=FALSE}
+library(PatientLevelPrediction)
+library(DeepPatientLevelPrediction)
+
+data(plpDataSimulationProfile)
+sampleSize <- 1e4
+plpData <- simulatePlpData(
+ plpDataSimulationProfile,
+ n = sampleSize
+)
+
+populationSettings <- PatientLevelPrediction::createStudyPopulationSettings(
+ requireTimeAtRisk = F,
+ riskWindowStart = 1,
+ riskWindowEnd = 365)
+# a very simple resnet
+modelSettings <- setResNet(numLayers = 2,
+ sizeHidden = 64,
+ hiddenFactor = 1,
+ residualDropout = 0,
+ hiddenDropout = 0.2,
+ normalization = 'BatchNorm',
+ activation = 'RelU',
+ sizeEmbedding = 64,
+ weightDecay = 1e-6,
+ learningRate = 3e-4,
+ seed = 42,
+ hyperParamSearch = 'random',
+ randomSample = 1, device = 'cpu',batchSize = 128,
+ epochs = 3)
+
+plpResults <- PatientLevelPrediction::runPlp(plpData = plpData,
+ outcomeId = 3,
+ modelSettings = modelSettings,
+ analysisId = 'Test',
+ analysisName = 'Testing DeepPlp',
+ populationSettings = populationSettings,
+ splitSettings = createDefaultSplitSetting(),
+ sampleSettings = createSampleSettings(), # none
+ featureEngineeringSettings = createFeatureEngineeringSettings(), # none
+ preprocessSettings = createPreprocessSettings(),
+ logSettings = createLogSettings(),
+ executeSettings = createExecuteSettings(runSplitData = T,
+ runSampleData = F,
+ runfeatureEngineering = F,
+ runPreprocessData = T,
+ runModelDevelopment = T,
+ runCovariateSummary = T
+ ))
```
-**Please reference this paper if you use the DeepPLP Package in your work:**
+# Acknowledgments
-[Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek PR. Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. J Am Med Inform Assoc. 2018;25(8):969-975.](http://dx.doi.org/10.1093/jamia/ocy032)
+Considerable work has been dedicated to provide the `DeepPatientLevelPrediction` package.
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