--- a
+++ b/bin/naive_bayes.r
@@ -0,0 +1,69 @@
+setwd(".")
+options(stringsAsFactors = FALSE)
+# library("clusterSim")
+# library("PRROC")
+library("e1071")
+
+source("./confusion_matrix_rates.r")
+
+threshold <- 0.5
+
+cat("threshold = ", threshold, "\n", sep="")
+
+fileName <- "../data/LungCancerDataset_AllRecords_NORM_27reduced_features.csv"
+prc_data_norm <- read.csv(file=fileName,head=TRUE,sep=",",stringsAsFactors=FALSE)
+
+prc_data_norm <- prc_data_norm[sample(nrow(prc_data_norm)),] # shuffle the rows
+
+target_index <- dim(prc_data_norm)[2]
+
+training_set_perce = 80
+cat("training_set_perce = ", training_set_perce, "%\n", sep="")
+
+# the training set is the first 60% of the whole dataset
+training_set_first_index <- 1 # NEW
+training_set_last_index <- round(dim(prc_data_norm)[1]*training_set_perce/100) # NEW
+
+# the test set is the last 40% of the whole dataset
+test_set_first_index <- training_set_last_index+1 # NEW
+test_set_last_index <- dim(prc_data_norm)[1] # NEW
+
+cat("[Creating the subsets for the values]\n")
+prc_data_train <- prc_data_norm[training_set_first_index:training_set_last_index, 1:(target_index)] # NEW
+prc_data_test <- prc_data_norm[test_set_first_index:test_set_last_index, 1:(target_index)] # NEW
+
+cat("[Creating the subsets for the labels \"1\"-\"0\"]\n")
+prc_data_train_labels <- prc_data_norm[training_set_first_index:training_set_last_index, target_index] # NEW
+prc_data_test_labels <- prc_data_norm[test_set_first_index:test_set_last_index, target_index]   # NEW
+
+
+print("dim(prc_data_train)")
+print(dim(prc_data_train))
+
+print("dim(prc_data_test)")
+print(dim(prc_data_test))
+
+
+library(class)
+library(gmodels)
+
+naive_bayes_model <-  naiveBayes(as.factor(Metastasis) ~ . , data=prc_data_train)
+
+prc_data_test_PRED <- predict((naive_bayes_model), prc_data_test)
+prc_data_test_PRED_binary <- as.numeric(prc_data_test_PRED)-1
+
+prc_data_test_PRED_binary[prc_data_test_PRED_binary>=threshold]=1
+prc_data_test_PRED_binary[prc_data_test_PRED_binary<threshold]=0
+
+# print("predictions:")
+# print(prc_data_test_PRED_binary)
+# 
+# 
+# print("labels:")
+# print(prc_data_test$Metastasis)
+
+
+confusion_matrix_rates(prc_data_test_labels, prc_data_test_PRED_binary, "@@@ Test set @@@")
+
+
+