unitTest_mod <- function(){
###################################################
### step 1: loadLibraries
###################################################
library(predictiveModeling)
library(BCC)
library(survival)
library(survcomp)
library(MASS)
library(federationPLoSRevision)
###### these are the utility functions to write #############
# Metabric training - Metabric testing
metabricTrainingData <- loadFederationMetabricTrainingData()
metabricTestData1 <- loadFederationMetabricTestData1()
metabricTestData2 <- loadFederationMetabricTestData2()
# Metabric training - MICMA testing
metabricTrainingData1 <- loadMetabricMicmaTrainingData()
micmaData <- loadFederationMicmaData()
# Metabric
coxTest<-CoxphModel$new()
coxTest$customTrain(metabricTrainingData$exprData, metabricTrainingData$copyData,
metabricTrainingData$clinicalFeaturesData, metabricTrainingData$clinicalSurvData)
metabricPredictions1 <- coxTest$customPredict(metabricTestData1$exprData, metabricTestData1$copyData,
metabricTestData1$clinicalFeaturesData)
metabricPredictions2 <- coxTest$customPredict(metabricTestData2$exprData, metabricTestData2$copyData,
metabricTestData2$clinicalFeaturesData)
# Metabric with MICMA
coxTest2<-CoxphModel$new()
coxTest2$customTrain(metabricTrainingData1$exprData, metabricTrainingData1$copyData,
metabricTrainingData1$clinicalFeaturesData, metabricTrainingData1$clinicalSurvData)
micmaPredictions <- coxTest2$customPredict(micmaData$exprData, micmaData$copyData,
micmaData$clinicalFeaturesData)
trainPerformance <- SurvivalModelPerformance$new(as.numeric(micmaPredictions), micmaData$clinicalSurvData)
cIndex_micma <- trainPerformance$getExactConcordanceIndex()
print(paste("cIndex_micma", cIndex_micma))
}
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