.Rhistory

p1=predict(mymodel, train, type = 'response')
# Confidence level
pred1=ifelse(p1>0.5,1,0)
pred1[1:10]
tab1=table(Predicted = pred1, Actual = song_hotttnesss)
tab1
mean1=mean(pred1==train$song_hotttnesss)
mean1
lm.fit=lm(song_hotttnesss~duration+artist_familiarity+artist_hotttnesss+year+tempo+danceability+energy+loudness+key+time_signature+analysis_sample_rate+end_of_fade_in+mode+start_of_fade_out)
lm.fit
summary(lm.fit)
names(lm.fit)
coef(lm.fit)
ind=sample(1,nrow(mydata)-1,replace=T)
ind
train=mydata[ind==1,]
mymodel=glm(song_hotttnesss~duration+artist_familiarity+artist_hotttnesss+year+tempo+danceability+energy+loudness+key+time_signature+analysis_sample_rate+end_of_fade_in+mode+start_of_fade_out,data=train,family = 'binomial')
summary(mymodel)
# Prediction
p1=predict(mymodel, train, type = 'response')
train$song_hotttnesss=ifelse(train$song_hotttnesss>0.5,1,0)
# Confidence level
pred1=ifelse(p1>0.5,1,0)
pred1[1:10]
tab1=table(Predicted = pred1, Actual = song_hotttnesss)
tab1
mean1=mean(pred1==train$song_hotttnesss)
mean1
train$song_hotttnesss[1:10]
#Linear Regression
library(MASS)
# Read data file
mydata=read.csv(file.choose(),header = T)
attach(mydata)
lm.fit=lm(song_hotttnesss~duration+artist_familiarity+artist_hotttnesss+year+tempo+danceability+energy+loudness+key+time_signature+analysis_sample_rate+end_of_fade_in+mode+start_of_fade_out)
lm.fit
summary(lm.fit)
names(lm.fit)
coef(lm.fit)
ind=sample(1,nrow(mydata)-1,replace=T)
ind
train=mydata[ind==1,]
mymodel=glm(song_hotttnesss~duration+artist_familiarity+artist_hotttnesss+year+tempo+danceability+energy+loudness+key+time_signature+analysis_sample_rate+end_of_fade_in+mode+start_of_fade_out,data=train,family = 'binomial')
summary(mymodel)
# Prediction
p1=predict(mymodel, train, type = 'response')
train$song_hotttnesss=ifelse(train$song_hotttnesss>0.5,1,0)
train$song_hotttnesss[1:10]
# Confidence level
pred1=ifelse(p1>0.5,1,0)
pred1[1:10]
tab1=table(Predicted = pred1, Actual = song_hotttnesss)
tab1
mean1=mean(pred1==train$song_hotttnesss)
mean1
require(MASS)
require(class)
require(boot)
require(leaps)
require(glmnet)
require(splines)
require(gam)
require(tree)
require(randomForest)
require(gbm)
require(e1071)
require(ROCR)
# Read data file
setwd("F:/sem4/ml/project")
mydat1=read.csv('training_data.csv',header = T)
mydat=log10(mydat1+1)
mytest1=read.csv('testing_data.csv',header = T)
mytest=log10(mytest1+1)
attach(mydat)
names(mydat)
summary(mydat)
#Simple linear regression
plot(song_hotttnesss~artist_familiarity,mydat,main = "Artist familiarity vs Song hotness")
fit0=lm(song_hotttnesss~artist_familiarity,data=mydat)
fit0
summary(fit0)
abline(fit0,col='red')
confint(fit0)
predict(fit0,data.frame(artist_familiarity=c(0.6,0.8)),interval="confidence")
#Multiple linear regression
fit1=lm(song_hotttnesss~.,data=mydat)
fit1
summary(fit1)
confint(fit1)
par(mfrow=c(2,2))
plot(fit1,main = "Linear regression")
fit2=update(fit1,~.-tempo-key-time_signature-mode-end_of_fade_in)
fit2
summary(fit2)
confint(fit2)
plot(fit2,main = "Linear regression with smaller model")
#Non linear terms and interactions
fit3=lm(song_hotttnesss~poly(artist_familiarity,2))
summary(fit3)
par(mfrow=c(1,1))
plot(song_hotttnesss~artist_familiarity,main = "Artist familiarity vs Song hotness")
points(artist_familiarity,fitted(fit3),col="red")
fit4=lm(song_hotttnesss~poly(artist_familiarity,3))
summary(fit4)
points(artist_familiarity,fitted(fit4),col="blue")
#Simple linear regression using functions
regplot=function(x,y){
fit=lm(y~x)
plot(x,y,main = "Artist familiarity vs Song hotness using functions")
abline(fit,col="red")
}
regplot(artist_familiarity,song_hotttnesss)
#Logistic regression
glm.fit=glm(song_hotttnesss~.,data = mydat,family = binomial)
summary(glm.fit)
confint(glm.fit)
par(mfrow=c(2,2))
plot(glm.fit,main = "Logistic regression")
#Finding prediction accuracy using probability
glm.probs=predict(glm.fit,type = "response")
glm.probs[1:5]
threshold=0.25
glm.pred=ifelse(glm.probs>threshold,"Hit","Fail")
song_hotttnesss_check=ifelse(song_hotttnesss>threshold,"Hit","Fail")
tab=table(glm.pred,song_hotttnesss_check)
tab
accuracy=sum(diag(tab))/sum(tab)
error=1-accuracy
accuracy
error
#Testing accuracy
glm.probs_test=predict(glm.fit,newdata = mytest,type="response")
glm.probs_test[1:5]
threshold_test=0.22
glm.pred_test=ifelse(glm.probs_test>threshold_test,"Hit","Fail")
song_hotttnesss_check_test=ifelse(mytest$song_hotttnesss>threshold_test,"Hit","Fail")
tab_test=table(glm.pred_test,song_hotttnesss_check_test)
tab_test
accuracy_test=sum(diag(tab_test))/sum(tab_test)
error_test=1-accuracy_test
accuracy_test
error_test
#Fitting smaller model with impactful parameters for better accuracy
glm.fit1=glm(song_hotttnesss~.-tempo-key-time_signature-mode-end_of_fade_in
-duration-start_of_fade_out,data = mydat,family = binomial)
summary(glm.fit1)
confint(glm.fit1)
par(mfrow=c(2,2))
plot(glm.fit1)
glm.probs1=predict(glm.fit1,type = "response")
glm.probs1[1:5]
glm.pred1=ifelse(glm.probs1>threshold,"Hit","Fail")
tab1=table(glm.pred1,song_hotttnesss_check)
tab1
accuracy1=sum(diag(tab1))/sum(tab1)
error1=1-accuracy1
accuracy1
error1
#Testing accuracy for the same
glm.probs1_test=predict(glm.fit1,newdata=mytest,type = "response")
glm.probs1_test[1:5]
glm.pred1_test=ifelse(glm.probs1_test>threshold_test,"Hit","Fail")
tab1_test=table(glm.pred1_test,song_hotttnesss_check_test)
tab1_test
accuracy1_test=sum(diag(tab1_test))/sum(tab1_test)
error1_test=1-accuracy1_test
accuracy1_test
error1_test
#Thus we find that there is no change in the accuracy as we reached the saturation in both training
#and testing data
#Linear discriminant analysis(LDA)
lda.fit=lda(song_hotttnesss_check~artist_familiarity+artist_hotttnesss+loudness,data=mydat)
lda.fit
plot(lda.fit)
lda.pred=predict(lda.fit,mydat)
data.frame(lda.pred)[1:5,]
tab2=table(lda.pred$class,song_hotttnesss_check)
tab2
accuracy2=sum(diag(tab2))/sum(tab2)
error2=1-accuracy2
accuracy2
error2
#Testing accuracy
lda.pred_test=predict(lda.fit,mytest)
data.frame(lda.pred_test)[1:5,]
tab2_test=table(lda.pred_test$class,song_hotttnesss_check_test)
tab2_test
accuracy2_test=sum(diag(tab2_test))/sum(tab2_test)
error2_test=1-accuracy2_test
accuracy2_test
error2_test
#Here we get a low accuracy compared to logistic regression model
#But at the same time we notice that the accuracy of the test data is slightly higher than the
#training data. This was opposite in logistic regression where the training had higher accuracy
#than the test
#Quadratic discriminant analysis(QDA)
qda.fit=qda(song_hotttnesss_check~artist_familiarity+artist_hotttnesss+loudness,data = mydat)
qda.fit
qda.pred=predict(qda.fit,mydat)
data.frame(qda.pred)[1:5,]
tab3=table(qda.pred$class,song_hotttnesss_check)
tab3
accuracy3=sum(diag(tab3))/sum(tab3)
error3=1-accuracy3
accuracy3
error3
#Analysing with the test data
qda.pred_test=predict(qda.fit,mytest)
data.frame(qda.pred_test)[1:5,]
tab3_test=table(qda.pred_test$class,song_hotttnesss_check_test)
tab3_test
accuracy3_test=sum(diag(tab3_test))/sum(tab3_test)
error3_test=1-accuracy3_test
accuracy3_test
error3_test
#Thus QDA gives the highest accuracy with the testing data compared with Logistic regression and LDA
#K-Nearest Neighbors
Xlag=cbind(artist_familiarity,artist_hotttnesss,loudness)
Xlag_test=cbind(mytest$artist_familiarity,mytest$artist_hotttnesss,mytest$loudness)
Xlag_test[1:5,]
set.seed(1)
pts=c()
par(mfrow=c(1,1))
for(i in 1:20){
knn.prob=knn(Xlag,Xlag_test,song_hotttnesss,k=i)
knn.prob=as.numeric(as.character(knn.prob))
knn.pred=ifelse(knn.prob>threshold_test,"Hit","Fail")
tab4_test=table(knn.pred,song_hotttnesss_check_test)
tab4_test
accuracy4_test=sum(diag(tab4_test))/sum(tab4_test)
error4_test=1-accuracy4_test
pts=append(pts,accuracy4_test)
error4_test
}
plot(c(1:20),pts,main = "KNN",xlab = "k-values",ylab = "accuracies",col="red")
points(which.max(pts),max(pts),pch=20,col="red")
#This gives better results than logistic regression but LDA and QDA
#still performs better than KNN
#For storing all training accuracies
all_accuracy_train=c(accuracy,accuracy1,accuracy2,accuracy3,0.86)
#For storing all testing accuracies
all_accuracy_test=c(accuracy_test,accuracy1_test,accuracy2_test,accuracy3_test,max(pts))
types=c(1,2,3,4,5)
plot(types,all_accuracy_train,type = 'b',col='red',main = "Training vs Testing accuracies",xlab = "Various models",ylab = "Accuracies")
lines(factor(types),all_accuracy_test,type = 'b',col='blue')
legend("topright", legend=c("Training", "Testing"),col=c("red","blue"), lty=1:1)
legend(1,0.96, legend = c("1-Logistic","2-Logistic with smaller model",
"3-LDA","4-QDA","5-KNN"))
points(which.max(all_accuracy_train),max(all_accuracy_train),pch=20,col="red")
points(which.max(all_accuracy_test),max(all_accuracy_test),pch=20,col="blue")
#From the graph by looking at the accuracies we see that all the models
#are consistent apart from knn
#A glimpse of all our accuracies till now
#Logistic regression:
#Train:0.9671554
#Test:0.9061288
#For smaller model
#Train:0.9671554
#Test:0.9061288
#LDA
#Train:0.9671554
#Test:0.9022498
#QDA
#Train:0.9627566
#Test:0.9045722
#KNN for k=18(Max accuracy)
#Test:0.8758728
#This CV is used to find which degree of polynomial helps in best fitting the model
#Leave one out validation(LOOCV) using function
glm.fit_cv=glm(song_hotttnesss~artist_familiarity,data = mydat)
cv.glm(mydat,glm.fit_cv)$delta
#Using formula
loocv=function(fit){
h=lm.influence(fit)$h
mean((residuals(fit)/(1-h))^2)
}
loocv(glm.fit_cv)
cv.error=rep(0,5)
degree=1:5
for(d in degree){
glm.fit_cv=glm(song_hotttnesss~poly(artist_familiarity,d),data = mydat)
cv.error[d]=loocv(glm.fit_cv)
}
par(mfrow=c(1,1))
plot(degree,cv.error,type='b',main = "Leave one out cross validation")
#10-fold CV
cv.error10=rep(0,5)
for(d in degree){
glm.fit_cv10=glm(song_hotttnesss~poly(artist_familiarity,d),data = mydat)
cv.error10[d]=cv.glm(mydat,glm.fit_cv10,K=10)$delta[1]
}
plot(degree,cv.error,type='b',main = "Leave one out cross validation vs 10-fold CV")
lines(degree,cv.error10,type = 'b',col='red')
legend("topright", legend=c("LOOCV", "10-fold CV"),col=c("black", "red"), lty=1:1)
#Thus we can clearly see that both LOOCV and 10-fold CV performs almost exactly same way
#But it is preffered that we use 10-fold here because of its high computational speed compared to LOOCV
#Best subset regression
regfit.full=regsubsets(song_hotttnesss~.,data = mydat)
summary(regfit.full)
#Here by default only 8 variable subset is printed
#But we have 10 variables so lets do for that
regfit.full_var=regsubsets(song_hotttnesss~.,data = mydat, nvmax = 10)
reg.summary=summary(regfit.full_var)
reg.summary
names(reg.summary)
coef(regfit.full_var,3)
#Forward stepwise selection
regfit.fwd=regsubsets(song_hotttnesss~.,data = mydat,nvmax = 10,method = "forward")
reg.summary_fwd=summary(regfit.fwd)
reg.summary_fwd
coef(regfit.fwd,3)
#Backward stepwise selection
regfit.bwd=regsubsets(song_hotttnesss~.,data = mydat,nvmax = 10,method = "backward")
reg.summary_bwd=summary(regfit.bwd)
reg.summary_bwd
coef(regfit.bwd,3)
par(mfrow=c(1,2))
#Plot to see bic statistic for both the models
plot(reg.summary$bic,main = "Best Subset",xlab = "Number of variables", ylab = "bic")
which.min(reg.summary$bic)
points(3,reg.summary$bic[3],pch=20,col="red")
plot(reg.summary_fwd$bic,main = "Forward Stepwise",xlab = "Number of variables", ylab = "bic")
which.min(reg.summary_fwd$bic)
points(3,reg.summary_fwd$bic[3],pch=20,col="red")
plot(reg.summary_bwd$bic,main = "Backward Stepwise",xlab = "Number of variables", ylab = "bic")
which.min(reg.summary_bwd$bic)
points(3,reg.summary_bwd$bic[3],pch=20,col="red")
#Plot to see the difference in both the models
plot(regfit.full_var,scale = "bic",main = "Best Subset")
plot(regfit.fwd,scale="bic",main = "Forward Stepwise")
plot(regfit.bwd,scale="bic",main = "Backward Stepwise")
par(mfrow=c(1,1))
plot(sqrt(regfit.fwd$rss[-1]/180),col="blue",main = "Validation",xlab = "Predictor count",ylab = "RSS error",pch=10,type = 'b')
#The Root mean RSS error shows that error is monotonically decreasing in forward stepwise. This is true
#because everytime when a new variable is included it improves the fit and hence error decreases
#This CV is used in model selection
#Here we use 10 fold cross validation to find model selection
predict.regsubsets=function(object,newdata,id,...){
form=as.formula(object$call[[2]])
mat=model.matrix(form,newdata)
coefi=coef(object,id=id)
mat[,names(coefi)]%*%coefi
}
set.seed(11)
folds=sample(rep(1:10,length=nrow(mydat)))
table(folds)
cv.error_model=matrix(NA,10,10)
for(k in 1:10){
best.fit=regsubsets(song_hotttnesss~.,data = mydat[folds!=k,],nvmax = 10,method = "forward")
for(i in 1:10){
pred=predict(best.fit,mydat[folds==k,],id=i)
cv.error_model[k,i]=mean((song_hotttnesss[folds==k]-pred)^2)
}
}
rmse.cv=sqrt(apply(cv.error_model,2,mean))
plot(rmse.cv,pch=10,col="red",main = "10-fold Cross Validation",xlab = "Predictor count",ylab = "Root mean squared error",type = 'b')
#This favours model of size 6 as it gets lowest RMSE
#Ridge regression
x=model.matrix(song_hotttnesss~.-1,data = mydat)
y=song_hotttnesss
fit.ridge=glmnet(x,y,alpha = 0)
plot(fit.ridge,xvar="lambda",label=TRUE)
#Here coefficients are the beta terms
#Higher the lambda lower the beta and becomes 0 at one point
#When lambda is 0, then model behaves as normal RSS
#Unlike forward or best subset, here no predictor is dropped, it only shrinks the parameter
#10-fold cross validation for the same
cv.ridge=cv.glmnet(x,y,alpha=0)
plot(cv.ridge)
#Here the two vertical lines in the graph indicates one is the minimum and
#the other is within 1 standard error of the minimum
#This is not restricted model as the 1 standard error doesnt have a considerable width between
#Lasso model
fit.lasso=glmnet(x,y)#by default alpha is taken as 1
plot(fit.lasso,xvar="lambda",label=TRUE)
plot(fit.lasso,xvar = "dev",label = TRUE)
#This deviance graph and x-axis is r-squared
#And there is sudden jump of coefficients which shows that model is not overfit
coef(cv.ridge)
#We can see that apart from artist familiarity, artist hotttnesss and loudness
#The weight of other coefficients are very very small and doesnt make any considerable impact to the fit
cv.lasso=cv.glmnet(x,y)
plot(cv.lasso)
#The top of the plot shows how many coefficients are present at all instances
#It is doing shrinkage and variable selection
#From the plot we infer that minimum cross validation is when model selection is 6
#And it is pretty flat untill we have 1 standard error of the minimum which happenes at 3
coef(cv.lasso)
#Here the coefficients of the best model will be printed
#Clearly we can see that model with 3predictors gives best fit as we got in other methods also
#And also in both the ridge and lasso
#We notice that only 3 coefficients seems to be significant beacause
#others tend to zero which means model selection gives 3 as the best fit
#Non linear models
#Polynomial logistic regression
glm.poly=predict(glm.fit,newdata = mydat,type="response",se=T)
se.bands=cbind(glm.poly$fit+2*glm.poly$se,glm.poly$fit-2*glm.poly$se)
plot(artist_familiarity,song_hotttnesss)
points(artist_familiarity,fitted(fit4),col='blue')
matpoints(artist_familiarity,se.bands,col='red',cex=0.7)
legend("topleft", legend=c("1-Hit","2-Fail"),col='red')
#Here we can see that the polynomial logstic regression does a good work in classifying the data
#Splines
#Fix knot regression splines
fita=lm(song_hotttnesss~bs(artist_familiarity,knots = c(0.10,0.15,0.25)),data=mydat)
plot(artist_familiarity,song_hotttnesss)
points(artist_familiarity,fitted(fit4),col='darkgreen')
abline(v=c(0.1,0.15,0.25),lty=2,col='darkgreen')
summary(fita)
#Here is df is taken as 6
#Smooth splines using degrees of freedom
plot(artist_familiarity,song_hotttnesss)
fitb=smooth.spline(artist_familiarity,song_hotttnesss,df=16)
lines(fitb,col='blue',lwd=2)
#We can also determine the smoothing parameter using CV
#Here we use LOOCV
plot(artist_familiarity,song_hotttnesss)
fitc=smooth.spline(artist_familiarity,song_hotttnesss,cv=TRUE)
lines(fitc,col='purple',lwd=2)
fitc
#Here we find out that df is taken as 4.64
#Generalised additive models(GAM)
#For linear regression
gam1=gam(song_hotttnesss~s(artist_familiarity,df=4)+s(artist_hotttnesss,df=4)+s(loudness,df=2),data = mydat)
par(mfrow=c(1,3))
plot(gam1,se=T)
#We can see clearly that as artist familiarity and artist hotttnesss increases
#Song hotttnesss also increases accordingly
#But as the loudness increases we see that song hotttnesss decreases
#Thus it has a negative slope and that is why coefficient of loudness is
#also negative
#For logistic regression
gam2=gam(I(song_hotttnesss>threshold)~s(artist_familiarity,df=4)+s(artist_hotttnesss,df=4)+s(loudness,df=2),data = mydat,family = binomial)
plot(gam2,se=T)
#The point of these graphs is that the show the contribution to the y-predictor
#by looking at the probability of each x as a seperate function
#Non linear terms that are required
gam2a=gam(I(song_hotttnesss>threshold)~s(artist_familiarity,df=4)+artist_hotttnesss+s(loudness,df=2),data = mydat,family = binomial)
anova(gam2a,gam2,test='Chisq')
#We infer that we highly need non linear term in the variables after analysing the chisq test
#Decision trees
hit=ifelse(song_hotttnesss<=threshold,"Fail","Hit")
mydat_tree=data.frame(mydat,hit)
trees.song=tree(hit~.-song_hotttnesss-tempo-duration,data = mydat_tree)
trees.song
summary(trees.song)
par(mfrow=c(1,1))
plot(trees.song)
text(trees.song,pretty = 5)
#Testing the same
hit_test=ifelse(mytest$song_hotttnesss<=threshold_test,"Fail","Hit")
mytest_tree=data.frame(mytest,hit_test)
tree.pred=predict(trees.song,mytest_tree,type = 'class')
tab5_test=table(tree.pred,hit_test)
tab5_test
accuracy5_test=sum(diag(tab5_test))/sum(tab5_test)
error5_test=1-accuracy5_test
accuracy5_test
error5_test
#Pruning
cv.mydat=cv.tree(trees.song,FUN=prune.misclass)
cv.mydat
plot(cv.mydat)
prune.song=prune.misclass(trees.song,best = 5)
plot(prune.song)
text(prune.song,pretty = 5)
#Now that we pruned using cross validation we are able to see the tree more
#clearly and can interpret conditions when the song is a hit or a fail
tree.pred_prune=predict(prune.song,mytest_tree,type = 'class')
tab6_test=table(tree.pred_prune,hit_test)
tab6_test
#We didnt get much from pruning seeing the same accuracy
#But we can interpret the data more clearly now
#Random forests
set.seed(175)
rf.song=randomForest(song_hotttnesss~.,data = mydat)
rf.song
oob.err=double(10)
test.err=double(10)
for(mtry in 1:10){
fit_random=randomForest(song_hotttnesss~.,mytest,mtry=mtry,ntree=400)
oob.err[mtry]=fit_random$mse[400]
pred_random=predict(fit_random,mytest)
test.err[mtry]=mean((mytest$song_hotttnesss)^2)
cat(mtry," ")
}
matplot(1:mtry,oob.err,pch = 19,col='red', type = 'b',
ylab = 'Mean squared error',main='OOB error rate')
matplot(1:mtry,test.err,pch = 19, col='blue',type = 'b',
ylab = 'Mean squared error',main='Test error rate')
#We observe that for both oob error and test error, for mtry =2, we have least MSE
#Boosting
boost.song=gbm(song_hotttnesss~.,data=mydat,distribution = 'gaussian',
n.trees = 10000,shrinkage = 0.01,interaction.depth = 4)
summary(boost.song)
#Clearly we can see that which variables are important by looking at the bar plot
plot(boost.song,i='artist_hotttnesss')
plot(boost.song,i='artist_familiarity')
plot(boost.song,i='loudness')
#We can see clearly that as artist familiarity and artist hotttnesss increases
#Song hotttnesss also increases accordingly
#But as the loudness increases we see that song hotttnesss decreases
#Thus it has a negative slope and that is why coefficient of loudness is
#also negative
n.trees=seq(from = 100, to = 10000, by=100)
predmat=predict(boost.song,mytest,n.trees = n.trees)
dim(predmat)
boost_err=apply((predmat-mytest$song_hotttnesss)^2,2,mean)
plot(n.trees,boost_err,pch=19,ylab = 'Mean squared error',xlab = 'Number of trees',main = 'Boosting test error')
plot(as.factor(c("Boosting","Random forest")),c(min(boost_err),min(test.err)),main = "Random forest vs Boosting for testing",ylab = "Error rate")
#We notice there is drastic drop in the error rate which shows that boosting is ideal here
1-min(boost_err)