library(SSLR)
library(caret)

## Load Wine data set
data(wine)

cls <- which(colnames(wine) == "Wine")
x <- wine[, - cls] # instances without classes
y <- wine[, cls] # the classes
x <- scale(x) # scale the attributes

## Prepare data
set.seed(20)
# Use 50% of instances for training
tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
xtrain <- x[tra.idx,] # training instances
ytrain <- y[tra.idx] # classes of training instances
# Use 70% of train instances as unlabeled set
tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances

# Use the other 50% of instances for inductive testing
tst.idx <- setdiff(1:length(y), tra.idx)
xitest <- x[tst.idx,] # testing instances
yitest <- y[tst.idx] # classes of testing instances

# Compute distances between training instances
D <- as.matrix(proxy::dist(x = xtrain, method = "euclidean", by_rows = TRUE))

## Example: Training from a set of instances with 1-NN (knn3) as base classifier.
# Compute distances between training instances
D <- as.matrix(proxy::dist(x = xtrain, method = "euclidean", by_rows = TRUE))

## Example: Training from a set of instances with 1-NN (knn3) as base classifier.
gen.learner <- function(indexes, cls)
  caret::knn3(x = xtrain[indexes,], y = cls, k = 1)
gen.pred <- function(model, indexes)
  predict(model, xtrain[indexes,])

trControl_SETRED1 <- list(D = D, gen.learner = gen.learner,
                             gen.pred = gen.pred)
md1 <- train_generic(ytrain, method = "setredG", trControl = trControl_SETRED1)

'md1 <- setredG(y = ytrain, D, gen.learner, gen.pred)'

cls1 <- predict(md1$model, xitest, type = "class")
table(cls1, yitest)

confusionMatrix(cls1, yitest)$overall[1]


## Example: Training from a distance matrix with 1-NN (oneNN) as base classifier
gen.learner <- function(indexes, cls) {
  m <- SSLR::oneNN(y = cls)
  attr(m, "tra.idxs") <- indexes
  m
}

gen.pred <- function(model, indexes) {
  tra.idxs <- attr(model, "tra.idxs")
  d <- D[indexes, tra.idxs]
  prob <- predict(model, d, distance.weighting = "none")
  prob
}

trControl_SETRED2 <- list(D = D, gen.learner = gen.learner,
                          gen.pred = gen.pred)
md2 <- train_generic(ytrain, method = "setredG", trControl = trControl_SETRED2)


ditest <- proxy::dist(x = xitest, y = xtrain[md2$instances.index,],
                      method = "euclidean", by_rows = TRUE)

cls2 <- predict(md2$model, ditest, type = "class")
table(cls2, yitest)

confusionMatrix(cls2, yitest)$overall[1]





