rm(list=ls(all=TRUE))
setwd("C:/Users/luigi/Dropbox/TOPIC MODEL")
getwd()
library(quanteda)
library(readtext)
library(caTools)
library(e1071)
library(randomForest)
library(caret)
library(naivebayes)
library(car)
library(cvTools)
library(reshape2)
library(dplyr)

#####################################################
# FIRST STEP: let's prepare the training-set
#####################################################

# let's focus on MOVIE reviews (either positive or negative)
x <- read.csv("train_review2.csv", stringsAsFactors=FALSE)
str(x)
myCorpusTwitterTrain <- corpus(x)
tok2 <- tokens(myCorpusTwitterTrain, remove_punct = TRUE, remove_numbers=TRUE, remove_symbols = TRUE, split_hyphens = TRUE, remove_separators = TRUE)
tok2 <- tokens_remove(tok2, stopwords("en"))
tok2 <- tokens_wordstem (tok2)
Dfm_train <- dfm( tok2)
# Let's trim the dfm in order to keep only tokens that appear in at least 5% of the reviews
Dfm_train <- dfm_trim(Dfm_train , min_docfreq = 0.05, verbose=TRUE, docfreq_type = "prop")
topfeatures(Dfm_train , 20)  # 20 top words
train <- as.matrix(Dfm_train)  # let's convert the dfm into a (dense) matrix

# our classes
table(Dfm_train@docvars$Sentiment)
# our benchmark: accuracy .524
prop.table(table(Dfm_train@docvars$Sentiment))

# Note: usually an hypergrid search can improve your Model Fitting with respect
# to the values you get when running a ML algorithm with its default hyperparamters values;
# but do not expect any drammatic change!

######################################################
######################################################
# Let's start to explore (let's tune!) the hyperparameters for the RF
######################################################
######################################################

# The main deafault hyperparameters in the case of a RF are the following ones: 

# 1) "ntree" (Number of trees to grow; default=500),

# 2) "mtry" (Number of variables randomly sampled as candidates at each split, where p is number of variables in x; the default is =sqrt(p);
# In our case p=length(Dfm_train@Dimnames$features)=1139!; sqrt(p)=33.75) 

# 3) "nodesize": Minimum size of terminal nodes. This controls the complexity of the trees. 
# Smaller node size allows for deeper, more complex trees while larger node results in shallower trees. 
# This is another bias-variance tradeoff where deeper trees introduce more variance (risk of overfitting) and shallower trees 
# introduce more bias (risk of not fully capturing unique patters and relatonships in the data). The default is nodesize=1

# 4) sampsize: the number of samples to train on. The default value is 63.25% of the training set since this is the expected value of 
# unique observations in the bootstrap sample. Lower sample sizes can reduce the training time but may introduce more bias 
# than necessary. Increasing the sample size can increase performance but at the risk of overfitting because it introduces more 
# variance. Typically, when tuning this parameter we stay near the 60-80% range. However, it also depends on how large is your
# training-set! With a very little training-set, increasing sampsize could be a reasonably choice

# Let's create an hyperparameter grid. We can add as many values and hyperparameters you want. 
# Here just two: ntree (100 and 200) and mtry (28 and 30) with nodesize fixed at 1

hyper_grid <- expand.grid(
  nodesize=c(1),
  ntree=c(100, 200),
  mtry =c(28, 30),
  min_error = 0,                     # a place to dump results
  accuracy = 0                       # a place to dump results
)

nrow(hyper_grid) # 4 possibilities by crossing ntree with mtry 
hyper_grid

# if you want to add several values you can write something like:
# ntree= seq(100, 300, by = 10)

# to tune the RF, let's exmploy the function "tune".
# By default, tune implements a 10-folds CV. But you can control such values
# by using the command tune.control. In our case we set the folds to 5 to make things faster

# grid search 
for(i in 1:nrow(hyper_grid)) {
  # create parameter list
  params <- list(
    nodesize= hyper_grid$nodesize[i],
   ntree= hyper_grid$ntree[i],
   mtry = hyper_grid$mtry [i]
  )
  set.seed(123)
# train model
rf.tune <- tune(randomForest, train.y= as.factor(Dfm_train@docvars$Sentiment), train.x=train,
 ranges = params, do.trace=TRUE, tunecontrol = tune.control(cross = 5))
  # add min training error and accuracy to grid
   hyper_grid$min_error[i] <- min(rf.tune$performances$error)
   hyper_grid$accuracy[i] <- 1-hyper_grid$min_error[i]
}

# number of folds for CV
rf.tune$ sampling 

str(hyper_grid)
# let's see the results
head(arrange(hyper_grid, min_error ), 10)

# Note that here we just estimate accuracy and not F1. However now we are selecting the best hyperparameters setting for each given ML; 
# then we have to go back to our previous script to run a full CV (with F1 included) across different MLs. 
# The ratio to focus only on accuracy is that, for a given ML, there is a correlation between accuracy and F1, and if a RF model is doing better 
# than another RF model in terms of accuracy, it will almost for sure do the same also in terms of F1

######################################################
######################################################
# Now let's explore (let's tune!) the hyperparameters for the SVM
######################################################
######################################################

# Let's stick to the linear kernel.

# beyond C ("cost"), another  main hypermaters for a linear kernel is "epsilon" (the parameter controlling the width of the -insensitive zone included 
# in the insensitive-loss function (default: 0.1))
# Accordingly, we can investigate different combination of values for C (default: C=1) as well of epsilon

# create hyperparameter grid: you can add as many values and hyperparameters you want. Here just two (cost and epsilon)

hyper_grid <- expand.grid(
  cost = c(0.1, 1),
  epsilon = c(0.1, 3),
  min_error = 0,                     # a place to dump results
  accuracy = 0                      # a place to dump results
)

nrow(hyper_grid) # 4 possibilities by crossing cost with epsilon
hyper_grid

# grid search 
for(i in 1:nrow(hyper_grid)) {

  # create parameter list
  params <- list(
    cost = hyper_grid$cost[i],
   epsilon  = hyper_grid$epsilon [i]
  )
  set.seed(123)
  # train model
sv.tune <- tune(svm, train.y= as.factor(Dfm_train@docvars$Sentiment), train.x=train,
            kernel="linear", ranges = params, tunecontrol = tune.control(cross = 5))
   hyper_grid$min_error[i] <- min(sv.tune$performances$error)
   hyper_grid$accuracy[i] <- 1-hyper_grid$min_error[i]
}

# number of folds for CV
sv.tune$ sampling 

head(arrange(hyper_grid, min_error ), 10)

# In this specific case, there is no change. 
# Of course changing the values of C and epsilon through which looking for (for example by looking for values of c also >10), 
# can change the final results

# For the other kernels (radial, polynomial), you also have the "gamma" hyperparameter - a scaling parameter used to fit nonlinear boundaries. 
# Intuitively, the gamma parameter defines how far the influence of a single training example reaches, 
# with low values meaning ‘far’ and high values meaning ‘close’. 
# If gamma is very large then we get quiet fluctuating and wiggly decision boundaries which accounts for high variance and overfitting.
# If gamma is small,the decision boundary is smoother and has low variance.
# (default: 1/(data dimension)) - in our case: 1/length(train)
# Finally, for polynomial kernel you also have "degree" (default: 3) and "coef0" (default: 0)

# Let's explore a radial kernel (the hyperparameter epsilon does not apply here)

hyper_grid2 <- expand.grid(
  cost = c(0.1, 1),
 gamma = c(0.001, 0.01, 1),
  min_error = 0,                     # a place to dump results
   accuracy = 0                      # a place to dump results
)

nrow(hyper_grid2) # 6 possibilities
hyper_grid2

# grid search 
for(i in 1:nrow(hyper_grid2)) {

  # create parameter list
  params <- list(
    cost = hyper_grid2$cost[i],
   gamma = hyper_grid2$gamma [i]
  )
  set.seed(123)
  # train model
sv.tune <- tune(svm, train.y= as.factor(Dfm_train@docvars$Sentiment), train.x=train,
            kernel="radial", ranges = params, tunecontrol = tune.control(cross = 5))
  # add min training error and trees to grid
   hyper_grid2$min_error[i] <- min(sv.tune$performances$error)
  hyper_grid2$accuracy[i] <- 1-hyper_grid2$min_error[i]
}

# number of folds for CV
sv.tune$ sampling 

head(arrange(hyper_grid2, min_error ), 10)
head(arrange(hyper_grid, min_error ), 10)

# best model here has gamma=0.001 when cost=1; note however how the error for the best model is worst
# than the one you get via linear kernel (not surpisingly as a result, as already discussed in class!)

######################################################
######################################################
# Now let's explore (let's tune!) the hyperparameters for the NB!
######################################################
######################################################

# The main hyperparameter is the value of Laplace.
# In the NB case you cannot use the "tune" function, so we will do with a different script. 
# A bit more complicated, but once written, you can always use that (with some minor modifications)!
# Let's see an example of changing the value of Laplace from 0.5 to 2.5 by 0.5

# STEP 1: create the folds
ttrain <- train # let's change the name of the original train data.frame, given that we are already going to use such name below in the loop
# let's split our training-set in 10 folds 
set.seed(123) # set the see for replicability
k <- 10 # the number of folds; it does not matter the number of folds you decide here; the below procedure always will work!
folds <- cvFolds(NROW(ttrain ), K=k)
str(folds)

for(i in 1:k){
  train <- ttrain [folds$subsets[folds$which != i], ] # Set the training set
  validation <- ttrain [folds$subsets[folds$which == i], ] # Set the validation set
for (j in seq(0.5, 2.5, by = 0.5)){ # here you can change the values of the Laplace hyperparameter
  set.seed(123)
  newrf <-  multinomial_naive_bayes(y= as.factor(Dfm_train[folds$subsets[folds$which != i], ]@docvars$Sentiment) ,x=train,  laplace = j) 
# (just fit on the train data) and ADD the name of the output (in this case "Sentiment")
  newpred <- predict(newrf,newdata=validation) # Get the predicitons for the validation set (from the model just fit on the train data)
class_table <- table("Predictions"= newpred, "Actual"=Dfm_train[folds$subsets[folds$which == i], ]@docvars$Sentiment)
print(class_table)  
  df<-confusionMatrix( class_table,  mode = "everything") 
  df.name<-paste0("conf.mat.nb",i, sep = "/", j) # create the name for the object that will save the confusion matrix for each loop (=5)  
  assign(df.name,df)
}
}

NBPredict <- data.frame(col1=vector(), col2=vector())  

for(i in  mget(ls(pattern = "conf.mat.nb")) ) {
Accuracy <-(i)$overall[1] # save in the matrix the accuracy value - we could have also saved the matrix for the F1 values as well
min_error <- 1-Accuracy
NBPredict <- rbind(NBPredict , cbind(Accuracy ,min_error))
 }

str(NBPredict)

nrow(NBPredict)/k # number of estimated values for Laplace
values <- nrow(NBPredict)/k
values

# the results in NBPredict are saved like that: first all the results of the first k-fold for all the values of Laplace, and so on.
# for example imagine that you have k-fold=5 and Laplace assume just 2 values: 0.5 and 1. Then the first two Accuracy results in NBPredict
# are the Accuracy results you get in k-fold=1 for Laplace first 0.5 and then 1; the third and fourth Accuracy results are the
# the Accuracy results you get in k-fold=2 for Laplace first 0.5 and then 1; and so on till k-fold=5

for (i in 1:values ) { # generate the list of numbers that correspond to all the k-folds results for each single value of Laplace 
id <- seq(i,nrow(NBPredict),values)
name <- paste0("index",i)
assign(name, id)
}

for(i in  mget(ls(pattern = "index")) ) { # extract the k-folds results for each value of Laplace 
id <- NBPredict [(i), ]
name <- paste0("laplace",i)
assign(name, id)
}

# Let's compare the average value for accuracy and f1

NBresults <- data.frame(col1=vector(), col2=vector()) # generate an empty database that you will fill with the average value of
# accuracy and min_error for each value of Laplace

for (i in 1:values){
database=get(paste0("laplace",i))
Avg_Accuracy <- mean(database [, 1] )
Avg_minError <- mean(database [, 2] )
NBresults <- rbind(NBresults , cbind(Avg_Accuracy, Avg_minError ))
}

row.names(NBresults) <- seq(0.5, 2.5, by = 0.5) # remember to write it here the range of the Laplace values you are exploring!
NBresults 
head(NBresults [order(-NBresults $Avg_Accuracy),]) # sorting by "Accuracy"

######################################################
######################################################
# Once you have estimated the best hyperparameters setting for the ML, you could replicate the
# K-fold analysis to see now which is the most advisable ML algorithm (given your training-set) 
######################################################
######################################################