Caret package Custom metric - r

Question

I'm using the caret function "train()" in one of my project and I'd like to add
a "custom metric" F1-score. I looked at this url caret package
But I cannot understand how I can build this score with the parameter available.
There is an example of custom metric which is the following:
## Example with a custom metric
madSummary <- function (data,
lev = NULL,
model = NULL) {
out <- mad(data$obs - data$pred,
na.rm = TRUE)
names(out) <- "MAD"
out
}
robustControl <- trainControl(summaryFunction = madSummary)
marsGrid <- expand.grid(degree = 1, nprune = (1:10) * 2)
earthFit <- train(medv ~ .,
data = BostonHousing,
method = "earth",
tuneGrid = marsGrid,
metric = "MAD",
maximize = FALSE,
trControl = robustControl)
Update:
I tried your code but the problem is that it doesn't work with multiple classes like with the code below (The F1 score is displayed, but it is weird) I'm not sure but I think the function F1_score works only on binary classes
library(caret)
library(MLmetrics)
set.seed(346)
dat <- iris
## See http://topepo.github.io/caret/training.html#metrics
f1 <- function(data, lev = NULL, model = NULL) {
print(data)
f1_val <- F1_Score(y_pred = data$pred, y_true = data$obs)
c(F1 = f1_val)
}
# Split the Data into .75 input
in_train <- createDataPartition(dat$Species, p = .70, list = FALSE)
trainClass <- dat[in_train,]
testClass <- dat[-in_train,]
set.seed(35)
mod <- train(Species ~ ., data = trainClass ,
method = "rpart",
metric = "F1",
trControl = trainControl(summaryFunction = f1,
classProbs = TRUE))
print(mod)
I coded a manual F1 score as well, with one input the confusion matrix: (I'm not sure if we can have a confusion matrix in "summaryFunction"
F1_score <- function(mat, algoName){
##
## Compute F1-score
##
# Remark: left column = prediction // top = real values
recall <- matrix(1:nrow(mat), ncol = nrow(mat))
precision <- matrix(1:nrow(mat), ncol = nrow(mat))
F1_score <- matrix(1:nrow(mat), ncol = nrow(mat))
for(i in 1:nrow(mat)){
recall[i] <- mat[i,i]/rowSums(mat)[i]
precision[i] <- mat[i,i]/colSums(mat)[i]
}
for(i in 1:ncol(recall)){
F1_score[i] <- 2 * ( precision[i] * recall[i] ) / ( precision[i] + recall[i])
}
# We display the matrix labels
colnames(F1_score) <- colnames(mat)
rownames(F1_score) <- algoName
# Display the F1_score for each class
F1_score
# Display the average F1_score
mean(F1_score[1,])
}

Answer 1

You should look at The caret Package - Alternate Performance Metrics for details. A working example:
library(caret)
library(MLmetrics)
set.seed(346)
dat <- twoClassSim(200)
## See https://topepo.github.io/caret/model-training-and-tuning.html#metrics
f1 <- function(data, lev = NULL, model = NULL) {
f1_val <- F1_Score(y_pred = data$pred, y_true = data$obs, positive = lev[1])
c(F1 = f1_val)
}
set.seed(35)
mod <- train(Class ~ ., data = dat,
method = "rpart",
tuneLength = 5,
metric = "F1",
trControl = trainControl(summaryFunction = f1,
classProbs = TRUE))

Answer 2

For the two-class case, you can try the following:
mod <- train(Class ~ .,
data = dat,
method = "rpart",
tuneLength = 5,
metric = "F",
trControl = trainControl(summaryFunction = prSummary,
classProbs = TRUE))
or define a custom summary function that combines both twoClassSummary and prSummary current favorite which provides the following possible evaluation metrics - AUROC, Spec, Sens, AUPRC, Precision, Recall, F - any of which can be used as the metric argument. This also includes the special case I mentioned in my comment on the accepted answer (F is NA).
comboSummary <- function(data, lev = NULL, model = NULL) {
out <- c(twoClassSummary(data, lev, model), prSummary(data, lev, model))
# special case missing value for F
out$F <- ifelse(is.na(out$F), 0, out$F)
names(out) <- gsub("AUC", "AUPRC", names(out))
names(out) <- gsub("ROC", "AUROC", names(out))
return(out)
}
mod <- train(Class ~ .,
data = dat,
method = "rpart",
tuneLength = 5,
metric = "F",
trControl = trainControl(summaryFunction = comboSummary,
classProbs = TRUE))