library(Prova1)
### Data files
GrowDataFile<-"data/1864dataset.xls"
AnnotationFile <-"data/1864info.txt"
### Merge curves and target file
CONNECTORList <- DataImport(GrowDataFile,AnnotationFile)
### Visualization
DataVisualization(CONNECTORList,feature="Progeny",labels = c("time","volume","Tumor Growth"),save=TRUE,path="~/Desktop/ImagesPerFrancesca/")
CONNECTORList<- DataTruncation(CONNECTORList,feature="Progeny",truncTime=60,save=TRUE,path="~/Desktop/ImagesPerFrancesca/",labels = c("time","volume","Tumor Growth"))
### PCA
pca <- PCA.Analysis(data.tr$Dataset,save=TRUE,path="~/Desktop/ImagesPerFrancesca/")
pca$plot
k <- c(2:6)
CONNECTORList.FCM <- Cluster_choice(CONNECTORList,K=c(2:6),h=2)
CONNECTORList.FCM.k4.h2<- CONNECTORList.FCM$FCM_all$`k= 4`$`h= 2`
FCMplots <- ClusterWithMeanCurve(CONNECTORList.FCM.k4.h2,CONNECTORList,k = 4,"FCM",feature = "Progeny",labels = c("Time","Volume"))
MalthusPlots<- ClusterWithMeanCurve(database = CONNECTORList,k = 4,model="Malthus",feature = "Progeny")
CONNECTORList.models <- FittingAndClustering(databaseTr = CONNECTORList, FCM_all = CONNECTORList.FCM, h = 2, k=4, feature = "Progeny", labels = c("time","volume"))
### Withinness and betweenness plot for FCM
Malthus.ClustCurve <- CONNECTORList.models$Malthus$Information$ClustCurve
Malthus.MeanCurves <- CONNECTORList.models$Malthus$Information$meancurves
PlotWithinnessBetweenness(Malthus.ClustCurve,Malthus.MeanCurves,Title = "Malthus Cluster betweenness and withinness")
Logistic.ClustCurve <- CONNECTORList.models$Logistic$Information$ClustCurve
Logistic.MeanCurves <- CONNECTORList.models$Logistic$Information$meancurves
PlotWithinnessBetweenness(Logistic.ClustCurve,Logistic.MeanCurves,Title = "Logistic Cluster betweenness and withinness")
Gompertz.ClustCurve <- CONNECTORList.models$Gompertz$Information$ClustCurve
Gompertz.MeanCurves <- CONNECTORList.models$Gompertz$Information$meancurves
PlotWithinnessBetweenness(Gompertz.ClustCurve,Gompertz.MeanCurves,Title = "Gompertz Cluster betweenness and withinness")
FCM.ClustCurve <- CONNECTORList.models$FCM$Information$ClustCurve
FCM.MeanCurves <- CONNECTORList.models$FCM$Information$meancurves
PlotWithinnessBetweenness(FCM.ClustCurve,FCM.MeanCurves,Title = "FCM Cluster betweenness and withinness")
fitclust_allmodels <- FittingAndClustering(databaseTr = data.tr, h = 2, k=k,FCM_all =
out$FCM_all, feature = "Progeny",save=TRUE,path="~/Desktop/ImagesPerFrancesca/",labels = c("time","volume"))
NumberSamples<-CountingSamples(CONNECTORList.models)
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