require(xgboost)

context("basic functions")

data(agaricus.train, package='xgboost')
data(agaricus.test, package='xgboost')
train <- agaricus.train
test <- agaricus.test
set.seed(1994)

test_that("train and predict binary classification", {
  nrounds = 2
  expect_output(
    bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
                  eta = 1, nthread = 2, nrounds = nrounds, objective = "binary:logistic")
  , "train-error")
  expect_equal(class(bst), "xgb.Booster")
  expect_equal(bst$niter, nrounds)
  expect_false(is.null(bst$evaluation_log))
  expect_equal(nrow(bst$evaluation_log), nrounds)
  expect_lt(bst$evaluation_log[, min(train_error)], 0.03)

  pred <- predict(bst, test$data)
  expect_length(pred, 1611)
  
  pred1 <- predict(bst, train$data, ntreelimit = 1)
  expect_length(pred1, 6513)
  err_pred1 <- sum((pred1 > 0.5) != train$label)/length(train$label)
  err_log <- bst$evaluation_log[1, train_error]
  expect_lt(abs(err_pred1 - err_log), 10e-6)
})

test_that("train and predict softprob", {
  lb <- as.numeric(iris$Species) - 1
  set.seed(11)
  expect_output(
    bst <- xgboost(data = as.matrix(iris[, -5]), label = lb,
                   max_depth = 3, eta = 0.5, nthread = 2, nrounds = 5,
                   objective = "multi:softprob", num_class=3)
  , "train-merror")
  expect_false(is.null(bst$evaluation_log))
  expect_lt(bst$evaluation_log[, min(train_merror)], 0.025)
  expect_equal(bst$niter * 3, xgb.ntree(bst))
  pred <- predict(bst, as.matrix(iris[, -5]))
  expect_length(pred, nrow(iris) * 3)
  # row sums add up to total probability of 1:
  expect_equal(rowSums(matrix(pred, ncol=3, byrow=TRUE)), rep(1, nrow(iris)), tolerance = 1e-7)
  # manually calculate error at the last iteration:
  mpred <- predict(bst, as.matrix(iris[, -5]), reshape = TRUE)
  expect_equal(as.numeric(t(mpred)), pred)
  pred_labels <- max.col(mpred) - 1
  err <- sum(pred_labels != lb)/length(lb)
  expect_equal(bst$evaluation_log[5, train_merror], err, tolerance = 5e-6)
  # manually calculate error at the 1st iteration:
  mpred <- predict(bst, as.matrix(iris[, -5]), reshape = TRUE, ntreelimit = 1)
  pred_labels <- max.col(mpred) - 1
  err <- sum(pred_labels != lb)/length(lb)
  expect_equal(bst$evaluation_log[1, train_merror], err, tolerance = 5e-6)
})

test_that("train and predict softmax", {
  lb <- as.numeric(iris$Species) - 1
  set.seed(11)
  expect_output(
    bst <- xgboost(data = as.matrix(iris[, -5]), label = lb,
                   max_depth = 3, eta = 0.5, nthread = 2, nrounds = 5,
                   objective = "multi:softmax", num_class=3)
  , "train-merror")
  expect_false(is.null(bst$evaluation_log))
  expect_lt(bst$evaluation_log[, min(train_merror)], 0.025)
  expect_equal(bst$niter * 3, xgb.ntree(bst))
  
  pred <- predict(bst, as.matrix(iris[, -5]))
  expect_length(pred, nrow(iris))
  err <- sum(pred != lb)/length(lb)
  expect_equal(bst$evaluation_log[5, train_merror], err, tolerance = 5e-6)
})

test_that("train and predict RF", {
  set.seed(11)
  lb <- train$label
  # single iteration
  bst <- xgboost(data = train$data, label = lb, max_depth = 5,
                 nthread = 2, nrounds = 1, objective = "binary:logistic",
                 num_parallel_tree = 20, subsample = 0.6, colsample_bytree = 0.1)
  expect_equal(bst$niter, 1)
  expect_equal(xgb.ntree(bst), 20)
  
  pred <- predict(bst, train$data)
  pred_err <- sum((pred > 0.5) != lb)/length(lb)
  expect_lt(abs(bst$evaluation_log[1, train_error] - pred_err), 10e-6)
  expect_lt(pred_err, 0.03)
  
  pred <- predict(bst, train$data, ntreelimit = 20)
  pred_err_20 <- sum((pred > 0.5) != lb)/length(lb)
  expect_equal(pred_err_20, pred_err)

  pred <- predict(bst, train$data, ntreelimit = 1)
  pred_err_1 <- sum((pred > 0.5) != lb)/length(lb)
  expect_lt(pred_err, pred_err_1)
  expect_lt(pred_err, 0.08)
})

test_that("train and predict RF with softprob", {
  lb <- as.numeric(iris$Species) - 1
  nrounds <- 15
  set.seed(11)
  bst <- xgboost(data = as.matrix(iris[, -5]), label = lb,
                 max_depth = 3, eta = 0.9, nthread = 2, nrounds = nrounds,
                 objective = "multi:softprob", num_class=3,
                 num_parallel_tree = 4, subsample = 0.5, colsample_bytree = 0.5)
  expect_equal(bst$niter, 15)
  expect_equal(xgb.ntree(bst), 15*3*4)
  # predict for all iterations:
  pred <- predict(bst, as.matrix(iris[, -5]), reshape=TRUE)
  expect_equal(dim(pred), c(nrow(iris), 3))
  pred_labels <- max.col(pred) - 1
  err <- sum(pred_labels != lb)/length(lb)
  expect_equal(bst$evaluation_log[nrounds, train_merror], err, tolerance = 5e-6)
  # predict for 7 iterations and adjust for 4 parallel trees per iteration
  pred <- predict(bst, as.matrix(iris[, -5]), reshape=TRUE, ntreelimit = 7 * 4)
  err <- sum((max.col(pred) - 1) != lb)/length(lb)
  expect_equal(bst$evaluation_log[7, train_merror], err, tolerance = 5e-6)
})

test_that("use of multiple eval metrics works", {
  expect_output(
    bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
                  eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic",
                  eval_metric = 'error', eval_metric = 'auc', eval_metric = "logloss")
  , "train-error.*train-auc.*train-logloss")
  expect_false(is.null(bst$evaluation_log))
  expect_equal(dim(bst$evaluation_log), c(2, 4))
  expect_equal(colnames(bst$evaluation_log), c("iter", "train_error", "train_auc", "train_logloss"))
})


test_that("training continuation works", {
  dtrain <- xgb.DMatrix(train$data, label = train$label)
  watchlist = list(train=dtrain)
  param <- list(objective = "binary:logistic", max_depth = 2, eta = 1, nthread = 2)

  # for the reference, use 4 iterations at once:
  set.seed(11)
  bst <- xgb.train(param, dtrain, nrounds = 4, watchlist)
  # first two iterations:
  set.seed(11)
  bst1 <- xgb.train(param, dtrain, nrounds = 2, watchlist)
  # continue for two more:
  bst2 <- xgb.train(param, dtrain, nrounds = 2, watchlist, xgb_model = bst1)
  expect_equal(bst$raw, bst2$raw)
  expect_false(is.null(bst2$evaluation_log))
  expect_equal(dim(bst2$evaluation_log), c(4, 2))
  expect_equal(bst2$evaluation_log, bst$evaluation_log)
  # test continuing from raw model data
  bst2 <- xgb.train(param, dtrain, nrounds = 2, watchlist, xgb_model = bst1$raw)
  expect_equal(bst$raw, bst2$raw)
  expect_equal(dim(bst2$evaluation_log), c(2, 2))
  # test continuing from a model in file
  xgb.save(bst1, "xgboost.model")
  bst2 <- xgb.train(param, dtrain, nrounds = 2, watchlist, xgb_model = "xgboost.model")
  expect_equal(bst$raw, bst2$raw)
  expect_equal(dim(bst2$evaluation_log), c(2, 2))
})


test_that("xgb.cv works", {
  set.seed(11)
  cv <- xgb.cv(data = train$data, label = train$label, max_depth = 2, nfold = 5,
               eta = 1., nthread = 2, nrounds = 2, objective = "binary:logistic",
               verbose=TRUE)
  expect_is(cv, 'xgb.cv.synchronous')
  expect_false(is.null(cv$evaluation_log))
  expect_lt(cv$evaluation_log[, min(test_error_mean)], 0.03)
  expect_lt(cv$evaluation_log[, min(test_error_std)], 0.004)
  expect_equal(cv$niter, 2)
  expect_false(is.null(cv$folds) && is.list(cv$folds))
  expect_length(cv$folds, 5)
  expect_false(is.null(cv$params) && is.list(cv$params))
  expect_false(is.null(cv$callbacks))
  expect_false(is.null(cv$call))
})