"The format of predictions is incorrect" - r

Implementation of ROCR curve, kNN ,K 10 fold cross validation.
I am using Ionosphere dataset.
Here is the attribute information for your reference:
-- All 34 are continuous, as described above
-- The 35th attribute is either "good" or "bad" according to the definition
summarized above. This is a binary classification task.
data1<-read.csv('https://archive.ics.uci.edu/ml/machine-learning-databases/ionosphere/ionosphere.data',header = FALSE)
knn on its own works, kNN with kfold also works. But when I put in the ROCR code it doesnt like it.
I get the error: "The format of predictions is incorrect".
I checked the dataframes pred and Class 1. The dimensions are same. I tried with data.test$V35 instead of Class1 I get the same error with this option.
install.packages("class")
library(class)
nrFolds <- 10
data1[,35]<-as.numeric(data1[,35])
# generate array containing fold-number for each sample (row)
folds <- rep_len(1:nrFolds, nrow(data1))
# actual cross validation
for(k in 1:nrFolds) {
# actual split of the data
fold <- which(folds == k)
data.train <- data1[-fold,]
data.test <- data1[fold,]
Class<-data.train[,35]
Class1<-data.test[,35]
# train and test your model with data.train and data.test
pred<-knn(data.train, data.test, Class, k = 5, l = 0, prob = FALSE, use.all = TRUE)
data<-data.frame('predict'=pred, 'actual'=Class1)
count<-nrow(data[data$predict==data$actual,])
total<-nrow(data.test)
avg = (count*100)/total
avg =format(round(avg, 2), nsmall = 2)
method<-"KNN"
accuracy<-avg
cat("Method = ", method,", accuracy= ", accuracy,"\n")
}
install.packages("ROCR")
library(ROCR)
rocrPred=prediction(pred, Class1, NULL)
rocrPerf=performance(rocrPred, 'tpr', 'fpr')
plot(rocrPerf, colorize=TRUE, text.adj=c(-.2,1.7))
Any help is appreciated.

This worked for me..
install.packages("class")
library(class)
library(ROCR)
nrFolds <- 10
data1[,35]<-as.numeric(data1[,35])
# generate array containing fold-number for each sample (row)
folds <- rep_len(1:nrFolds, nrow(data1))
# actual cross validation
for(k in 1:nrFolds) {
# actual split of the data
fold <- which(folds == k)
data.train <- data1[-fold,]
data.test <- data1[fold,]
Class<-data.train[,35]
Class1<-data.test[,35]
# train and test your model with data.train and data.test
pred<-knn(data.train, data.test, Class, k = 5, l = 0, prob = FALSE, use.all = TRUE)
data<-data.frame('predict'=pred, 'actual'=Class1)
count<-nrow(data[data$predict==data$actual,])
total<-nrow(data.test)
avg = (count*100)/total
avg =format(round(avg, 2), nsmall = 2)
method<-"KNN"
accuracy<-avg
cat("Method = ", method,", accuracy= ", accuracy,"\n")
pred <- prediction(Class1,pred)
perf <- performance(pred, "tpr", "fpr")
plot(perf, colorize=T, add=TRUE)
abline(0,1)
}

Related

SVM Plot e1071 plots single color

I am trying to plot my SVM classification with usinf e1071 library.However, the classification plot shows only single value for my parameters.Even though I change the selected parameters to create 2d classification plot it is wrong.
require(caTools)
library(caret)
dataset <-read.csv("income_evaluation.csv")
# fnlwgt row remowed since it is not necessary
df_income <- subset(dataset,select=-c(fnlwgt))
# turn binary attribute into 0 and 1
df_income$income <-ifelse(df_income$income==" >50K",1,0)
df_income$native.country
apply(X=df_income,2,FUN=function(x) length(which(x==' ?')))
# handling missing values
#define function to calculate mode
find_mode <- function(x) {
u <- unique(x)
tab <- tabulate(match(x, u))
u[tab == max(tab)]
}
mod_workclass_df = find_mode(df_income$workclass)
mod_occupation_df = find_mode(df_income$occupation)
mod_country_df = find_mode(df_income$native.country)
# replacing the missing values with the mod values
df_income$workclass[df_income$workclass == ' ?'] <- mod_workclass_df
df_income$occupation[df_income$occupation == ' ?'] <- mod_occupation_df
df_income$native.country[df_income$native.country == ' ?'] <- mod_country_df
# one hot encoding for train set
dmy <- dummyVars(" ~ .", data = df_income, fullRank = T)
df_income <- data.frame(predict(dmy, newdata = df_income))
# sampling
set.seed(101)
sample = sample.split(df_income$income, SplitRatio = .75)
trainingSet = subset(df_income, sample == TRUE)
testSet = subset(df_income, sample == TRUE)
# isolaate y cariable
Y_train <- trainingSet$income
Y_test <- testSet$income
#isolate x cariable
X_test <- subset(testSet,select=-c(income))
# evalution of svm
library(e1071)
svm_classifier = svm(formula=income ~ .,data=trainingSet,type="C-classification",kernel="radial",scale=TRUE,cost=10)
Y_pred = predict(svm_classifier,newdata= X_test)
confusionMatrix(table(Y_test,Y_pred))
# cross validation
# in creating the folds we specify the target feature (dependent variable) and # of folds
folds = createFolds(trainingSet$income, k = 10)
# in cv we are going to applying a created function to our 'folds'
cv = lapply(folds, function(x) { # start of function
# in the next two lines we will separate the Training set into it's 10 pieces
training_fold = trainingSet[-x, ] # training fold = training set minus (-) it's sub test fold
test_fold = trainingSet[x, ] # here we describe the test fold individually
# now apply (train) the classifer on the training_fold
classifier = svm_classifier
Y_pred = predict(svm_classifier,newdata= test_fold[-97])
cm = table(test_fold[, 97], Y_pred)
accuracy = (cm[1,1] + cm[2,2]) / (cm[1,1] + cm[2,2] + cm[1,2] + cm[2,1])
return(accuracy)
})
accuracy = mean(as.numeric(cv))
accuracy
trainingSet$income <-as.factor(trainingSet$income)
# Visualising the Training set results
plot(svm_classifier,trainingSet,education.num~age)
library(ggplot2)
svm_classifier
table(predicted=svm_classifier$fitted,actual=trainingSet$income)
Here is my code above and the plot below.I could not find the problem why there is only one color background and why there is any red color in the background.

R: Multiclass Matrices

I am working with the R programming language. I am trying to learn how to make a "confusion matrix" for multiclass variables (e.g. How to construct the confusion matrix for a multi class variable).
Suppose I generate some data and fit a decision tree model :
#load libraries
library(rpart)
library(caret)
#generate data
a <- rnorm(1000, 10, 10)
b <- rnorm(1000, 10, 5)
d <- rnorm(1000, 5, 10)
group_1 <- sample( LETTERS[1:3], 1000, replace=TRUE, prob=c(0.33,0.33,0.34) )
e = data.frame(a,b,d, group_1)
e$group_1 = as.factor(d$group_1)
#split data into train and test set
trainIndex <- createDataPartition(e$group_1, p = .8,
list = FALSE,
times = 1)
training <- e[trainIndex,]
test <- e[-trainIndex,]
fitControl <- trainControl(## 10-fold CV
method = "repeatedcv",
number = 5,
## repeated ten times
repeats = 1)
#fit decision tree model
TreeFit <- train(group_1 ~ ., data = training,
method = "rpart2",
trControl = fitControl)
From here, I am able to store the results into a "confusion matrix":
pred <- predict(TreeFit,test)
table_example <- table(pred,test$group_1)
This satisfies my requirements - but this "table" requires me to manually calculate the different accuracy metrics of "A", "B" and "C" (as well as the total accuracy).
My question: Is it possible to use the caret::confusionMatrix() command for this problem?
e.g.
pred <- predict(TreeFit, test, type = "prob")
labels_example <- as.factor(ifelse(pred[,2]>0.5, "1", "0"))
con <- confusionMatrix(labels_example, test$group_1)
This way, I would be able to directly access the accuracy measurements from the confusion matrix. E.g. metric = con$overall[1]
Thanks
Is this what you're looking for?
pred <- predict(
TreeFit,
test)
con <- confusionMatrix(
test$group_1,
pred)
con
con$overall[1]
Same output as in:
table(test$group_1, pred)
Plus accuracy metrics.

How can I calculate F1-measure and ROC in multiclass classification problem in R?

I have this code for a multiclass classification problem:
data$Class = as.factor(data$Class)
levels(data$Class) <- make.names(levels(factor(data$Class)))
trainIndex <- createDataPartition(data$Class, p = 0.6, list = FALSE, times=1)
trainingSet <- data[ trainIndex,]
testingSet <- data[-trainIndex,]
train_x <- trainingSet[, -ncol(trainingSet)]
train_y <- trainingSet$Class
testing_x <- testingSet[, -ncol(testingSet)]
testing_y <- testingSet$Class
oneRM <- OneR(trainingSet, verbose = TRUE)
oneRM
summary(oneRM)
plot(oneRM)
oneRM_pred <- predict(oneRM, testing_x)
oneRM_pred
eval_model(oneRM_pred, testing_y)
AUC_oneRM_pred <- auc(roc(oneRM_pred,testing_y))
cat ("AUC=", oneRM_pred)
# Recall-Precision curve
oneRM_prediction <- prediction(oneRM_pred, testing_y)
RP.perf <- performance(oneRM_prediction, "tpr", "fpr")
plot (RP.perf)
plot(roc(oneRM_pred,testing_y))
But code does not work, after this line:
oneRM_prediction <- prediction(oneRM_pred, testing_y)
I get this error:
Error in prediction(oneRM_pred, testing_y) : Format of predictions is
invalid.
In addition, I donĀ“t know how I can get easily the F1-measure.
Finally, a question, does it make sense to calculate AUC in a multi-class classification problem?
Let's start from F1.
Assuming that you are using the iris dataset, first, we need to load everything, train the model and perform the predictions as you did.
library(datasets)
library(caret)
library(OneR)
library(pROC)
trainIndex <- createDataPartition(iris$Species, p = 0.6, list = FALSE, times=1)
trainingSet <- iris[ trainIndex,]
testingSet <- iris[-trainIndex,]
train_x <- trainingSet[, -ncol(trainingSet)]
train_y <- trainingSet$Species
testing_x <- testingSet[, -ncol(testingSet)]
testing_y <- testingSet$Species
oneRM <- OneR(trainingSet, verbose = TRUE)
oneRM_pred <- predict(oneRM, testing_x)
Then, you should calculate the precision, recall, and F1 for each class.
cm <- as.matrix(confusionMatrix(oneRM_pred, testing_y))
n = sum(cm) # number of instances
nc = nrow(cm) # number of classes
rowsums = apply(cm, 1, sum) # number of instances per class
colsums = apply(cm, 2, sum) # number of predictions per class
diag = diag(cm) # number of correctly classified instances per class
precision = diag / colsums
recall = diag / rowsums
f1 = 2 * precision * recall / (precision + recall)
print(" ************ Confusion Matrix ************")
print(cm)
print(" ************ Diag ************")
print(diag)
print(" ************ Precision/Recall/F1 ************")
print(data.frame(precision, recall, f1))
After that, you are able to find the macro F1.
macroPrecision = mean(precision)
macroRecall = mean(recall)
macroF1 = mean(f1)
print(" ************ Macro Precision/Recall/F1 ************")
print(data.frame(macroPrecision, macroRecall, macroF1))
To find the ROC (precisely the AUC), it best to use pROC library.
print(" ************ AUC ************")
roc.multi <- multiclass.roc(testing_y, as.numeric(oneRM_pred))
print(auc(roc.multi))
Hope that it helps you.
Find details on this link for F1 and this for AUC.
If I use levels(oneRM_pred) <- levels(testing_y) in this way:
...
oneRM <- OneR(trainingSet, verbose = TRUE)
oneRM
summary(oneRM)
plot(oneRM)
oneRM_pred <- predict(oneRM, testing_x)
levels(oneRM_pred) <- levels(testing_y)
...
The accuracy is very much lower than before. So, I am not sure if to enforce the same levels is a good solution.

prSummary in r caret package for imbalance data

I have an imbalanced data, and I want to do stratified cross validation and use precision recall auc as my evaluation metric.
I use prSummary in r package caret with stratified index, and I encounter an error when computing performance.
The following is a sample which can be reproduced. I found that there are only ten sample to compute p-r auc, and because of the imbalanced, there is only one class so that it cannot compute p-r auc. (The reason that I found that only ten sample to compute p-r auc is because I modified the prSummary to force this function to print out the data)
library(randomForest)
library(mlbench)
library(caret)
# Load Dataset
data(Sonar)
dataset <- Sonar
x <- dataset[,1:60]
y <- dataset[,61]
# make this data very imbalance
y[4:length(y)] <- "M"
y <- as.factor(y)
dataset$Class <- y
# create index and indexOut
seed <- 1
set.seed(seed)
folds <- 2
idxAll <- 1:nrow(x)
cvIndex <- createFolds(factor(y), folds, returnTrain = T)
cvIndexOut <- lapply(1:length(cvIndex), function(i){
idxAll[-cvIndex[[i]]]
})
names(cvIndexOut) <- names(cvIndex)
# set the index, indexOut and prSummaryCorrect
control <- trainControl(index = cvIndex, indexOut = cvIndexOut,
method="cv", summaryFunction = prSummary, classProbs = T)
metric <- "AUC"
set.seed(seed)
mtry <- sqrt(ncol(x))
tunegrid <- expand.grid(.mtry=mtry)
rf_default <- train(Class~., data=dataset, method="rf", metric=metric, tuneGrid=tunegrid, trControl=control)
Here is the error message:
Error in ROCR::prediction(y_pred, y_true) :
Number of classes is not equal to 2.
ROCR currently supports only evaluation of binary classification tasks.
I think I found the weird thing...
Even I specified the cross validation index, the summary function(no matter prSummary or other summary function) will still randomly(I am not sure) select ten sample to computing performance.
The way I did is defined a summary function with tryCatch to avoid this error occur.
prSummaryCorrect <- function (data, lev = NULL, model = NULL) {
print(data)
print(dim(data))
library(MLmetrics)
library(PRROC)
if (length(levels(data$obs)) != 2)
stop(levels(data$obs))
if (length(levels(data$obs)) > 2)
stop(paste("Your outcome has", length(levels(data$obs)),
"levels. The prSummary() function isn't appropriate."))
if (!all(levels(data[, "pred"]) == levels(data[, "obs"])))
stop("levels of observed and predicted data do not match")
res <- tryCatch({
auc <- MLmetrics::PRAUC(y_pred = data[, lev[2]], y_true = ifelse(data$obs == lev[2], 1, 0))
}, warning = function(war) {
print(war)
auc <- NA
}, error = function(e){
print(dim(data))
auc <- NA
}, finally = {
print("finally")
auc <- NA
})
c(AUC = res,
Precision = precision.default(data = data$pred, reference = data$obs, relevant = lev[2]),
Recall = recall.default(data = data$pred, reference = data$obs, relevant = lev[2]),
F = F_meas.default(data = data$pred, reference = data$obs, relevant = lev[2]))
}

binning continuous variables by IV value in R

I am building a logistic regression model in R. I want to bin continuous predictors in an optimal way in relationship to the target variable. There are two things that I know of:
the continuous variables are binned such that its IV (information value) is maximized
maximize the chi-square in the two way contingency table -- the target has two values 0 and 1, and the binned continuous variable has the binned buckets
Does anyone know of any functions in R that can perform such binning?
Your help will be greatly appreciated.
For the first point, you could bin using the weight of evidence (woe) with the package woebinning which optimizes the number of bins for the IV
library(woeBinning)
# get the bin cut points from your dataframe
cutpoints <- woe.binning(dataset, "target_name", "Variable_name")
woe.binning.plot(cutpoints)
# apply the cutpoints to your dataframe
dataset_woe <- woe.binning.deploy(dataset, cutpoint, add.woe.or.dum.var = "woe")
It returns your dataset with two extra columns
Variable_name.binned which is the labels
Variable_name.woe.binned which is the replaced values that you can then parse into your regression instead of Variable_name
For the second point, on chi2, the package discretization seems to handle it but I haven't tested it.
The methods used by regression splines to set knot locations might be considered. The rpart package probably has relevant code. You do need to penalize the inferential statistics because this results in an implicit hiding of the degrees of freedom expended in the process of moving the breaks around to get the best fit. Another common method is to specify breaks at equally spaced quantiles (quartiles or quintiles) within the subset with IV=1. Something like this untested code:
cont.var.vec <- # names of all your continuous variables
breaks <- function(var,n) quantiles( dfrm[[var]],
probs=seq(0,1,length.out=n),
na.rm=TRUE)
lapply(dfrm[ dfrm$IV == 1 , cont.var.vec] , breaks, n=5)
s
etwd("D:")
rm(list=ls())
options (scipen = 999)
read.csv("dummy_data.txt") -> dt
head(dt)
summary(dt)
mydata <- dt
head(mydata)
summary(mydata)
##Capping
for(i in 1:ncol(mydata)){
if(is.numeric(mydata[,i])){
val.quant <- unname(quantile(mydata[,i],probs = 0.75))
mydata[,i] = sapply(mydata[,i],function(x){if(x > (1.5*val.quant+1)){1.5*val.quant+1}else{x}})
}
}
library(randomForest)
x <- mydata[,!names(mydata) %in% c("Cust_Key","Y")]
y <- as.factor(mydata$Y)
set.seed(21)
fit <- randomForest(x,y,importance=T,ntree = 70)
mydata2 <- mydata[,!names(mydata) %in% c("Cust_Key")]
mydata2$Y <- as.factor(mydata2$Y)
fit$importance
####var reduction#####
vartoremove <- ncol(mydata2) - 20
library(rminer)
#####
for(i in 1:vartoremove){
rf <- fit(Y~.,data=mydata2,model = "randomForest", mtry = 10 ,ntree = 100)
varImportance <- Importance(rf,mydata2,method="sensg")
Z <- order(varImportance$imp,decreasing = FALSE)
IND <- Z[2]
var_to_remove <- names(mydata2[IND])
mydata2[IND] = NULL
print(i)
}
###########
library(smbinning)
as.data.frame(mydata2) -> inp
summary(inp)
attach(inp)
rm(result)
str(inp)
inp$target <- as.numeric(inp$Y) *1
table(inp$target)
ftable(inp$Y,inp$target)
inp$target <- inp$target -1
result= smbinning(df=inp, y="target", x="X37", p=0.0005)
result$ivtable
smbinning.plot(result,option="badrate",sub="test")
summary(inp)
result$ivtable
boxplot(inp$X2~inp$Y,horizontal=T, frame=F, col="red",main="Distribution")
###Sample
require(caTools)
inp$Y <- NULL
sample = sample.split(inp$target, SplitRatio = .7)
train = subset(inp, sample == TRUE)
test = subset(inp, sample == FALSE)
head(train)
nrow(train)
fit1 <- glm(train$target~.,data=train,family = binomial)
summary(rf)
prediction1 <- data.frame(actual = test$target, predicted = predict(fit1,test ,type="response") )
result= smbinning(df=prediction1, y="actual", x="predicted", p=0.005)
result$ivtable
smbinning.plot(result,option="badrate",sub="test")
tail(prediction1)
write.csv(prediction1 , "test_pred_logistic.csv")
predict_train <- data.frame(actual = train$target, predicted = predict(fit1,train ,type="response") )
write.csv(predict_train , "train_pred_logistic.csv")
result= smbinning(df=predict_train, y="actual", x="predicted", p=0.005)
result$ivtable
smbinning.plot(result,option="badrate",sub="train")
####random forest
rf <- fit(target~.,data=train,model = "randomForest", mtry = 10 ,ntree = 200)
prediction2 <- data.frame(actual = test$target, predicted = predict(rf,train))
result= smbinning(df=prediction2, y="actual", x="predicted", p=0.005)
result$ivtable
smbinning.plot(result,option="badrate",sub="train")
###########IV
library(devtools)
install_github("riv","tomasgreif")
library(woe)
##### K-fold Validation ########
library(caret)
cv_fold_count = 2
folds = createFolds(mydata2$Y,cv_fold_count,list=T);
smpl = folds[[i]];
g_train = mydata2[-smpl,!names(mydata2) %in% c("Y")];
g_test = mydata2[smpl,!names(mydata2) %in% c("Y")];
cost_train = mydata2[-smpl,"Y"];
cost_test = mydata2[smpl,"Y"];
rf <- randomForest(g_train,cost_train)
logit.data <- cbind(cost_train,g_train)
logit.fit <- glm(cost_train~.,data=logit.data,family = binomial)
prediction <- data.f
rame(actual = test$Y, predicted = predict(rf,test))

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