CRTreeForest_pred: Complete-Random Tree Forest Predictor implementation in R
In Laurae2/Laurae: Advanced High Performance Data Science Toolbox for R

Description Usage Arguments Details Value Examples

This function attempts to predict from Complete-Random Tree Forests using xgboost. Predictions are deferred to CRTreeForest_pred_internals.

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CRTreeForest_pred(model, data, folds = NULL, prediction = FALSE,
  multi_class = NULL, data_start = NULL, return_list = TRUE,
  work_dir = NULL)

`model`	Type: list. A model trained by `CRTreeForest`.
`data`	Type: data.table. A data to predict on. If passing training data, it will predict as if it was out of fold and you will overfit (so, use the list `train_preds` instead please).
`folds`	Type: list. The folds as list for cross-validation if using the training data. Otherwise, leave `NULL`. Defaults to `NULL`.
`prediction`	Type: logical. Whether the predictions of the forest ensemble are averaged. Set it to `FALSE` for debugging / feature engineering. Setting it to `TRUE` overrides `return_list`. Defaults to `FALSE`.
`multi_class`	Type: numeric. How many classes you got. Set to 2 for binary classification, or regression cases. Set to `NULL` to let it try guessing by reading the `model`. Defaults to `NULL`.
`data_start`	Type: vector of numeric. The initial prediction labels. Set to `NULL` if you do not know what you are doing. Defaults to `NULL`.
`return_list`	Type: logical. Whether lists should be returned instead of concatenated frames for predictions. Defaults to `TRUE`.
`work_dir`	Type: character, without slash at end (ex: "dev/tools/save_in_this_folder"). The working directory where models are stored, if using external model files as memory. Defaults to `NULL`, which means models are in memory. It will attempt to detect automatically the working directory from the model if it is available.

For implementation details of Cascade Forest / Complete-Random Tree Forest / Multi-Grained Scanning / Deep Forest, check this: https://github.com/Microsoft/LightGBM/issues/331#issuecomment-283942390 by Laurae.

A data.table or a list based on data predicted using model.

## Not run: 
# Load libraries
library(data.table)
library(Matrix)
library(xgboost)

# Create data
data(agaricus.train, package = "lightgbm")
data(agaricus.test, package = "lightgbm")
agaricus_data_train <- data.table(as.matrix(agaricus.train$data))
agaricus_data_test <- data.table(as.matrix(agaricus.test$data))
agaricus_label_train <- agaricus.train$label
agaricus_label_test <- agaricus.test$label
folds <- Laurae::kfold(agaricus_label_train, 5)

# Train a model (binary classification)
model <- CRTreeForest(training_data = agaricus_data_train, # Training data
                      validation_data = agaricus_data_test, # Validation data
                      training_labels = agaricus_label_train, # Training labels
                      validation_labels = agaricus_label_test, # Validation labels
                      folds = folds, # Folds for cross-validation
                      nthread = 1, # Change this to use more threads
                      lr = 1, # Do not touch this unless you are expert
                      training_start = NULL, # Do not touch this unless you are expert
                      validation_start = NULL, # Do not touch this unless you are expert
                      n_forest = 5, # Number of forest models
                      n_trees = 10, # Number of trees per forest
                      random_forest = 2, # We want only 2 random forest
                      seed = 0,
                      objective = "binary:logistic",
                      eval_metric = Laurae::df_logloss,
                      return_list = TRUE, # Set this to FALSE for a data.table output
                      multi_class = 2, # Modify this for multiclass problems
                      verbose = " ")

# Predict from model
new_preds <- CRTreeForest_pred(model, agaricus_data_test, return_list = FALSE)

# We can check whether we have equal predictions, it's all TRUE!
all.equal(model$train_preds, CRTreeForest_pred(model, agaricus_data_train, folds = folds))
all.equal(model$valid_preds, CRTreeForest_pred(model, agaricus_data_test))
all.equal(model$train_means, CRTreeForest_pred(model,
                                               agaricus_data_train,
                                               folds = folds,
                                               return_list = FALSE,
                                               prediction = TRUE))
all.equal(model$valid_means, CRTreeForest_pred(model,
                                               agaricus_data_test,
                                               return_list = FALSE,
                                               prediction = TRUE))

# Attempt to perform fake multiclass problem
agaricus_label_train[1:100] <- 2

# Train a model (multiclass classification)
model <- CRTreeForest(training_data = agaricus_data_train, # Training data
                      validation_data = agaricus_data_test, # Validation data
                      training_labels = agaricus_label_train, # Training labels
                      validation_labels = agaricus_label_test, # Validation labels
                      folds = folds, # Folds for cross-validation
                      nthread = 1, # Change this to use more threads
                      lr = 1, # Do not touch this unless you are expert
                      training_start = NULL, # Do not touch this unless you are expert
                      validation_start = NULL, # Do not touch this unless you are expert
                      n_forest = 5, # Number of forest models
                      n_trees = 10, # Number of trees per forest
                      random_forest = 2, # We want only 2 random forest
                      seed = 0,
                      objective = "multi:softprob",
                      eval_metric = Laurae::df_logloss,
                      return_list = TRUE, # Set this to FALSE for a data.table output
                      multi_class = 3, # Modify this for multiclass problems
                      verbose = " ")

# Predict from model for mutliclass problems
new_preds <- CRTreeForest_pred(model, agaricus_data_test, return_list = FALSE)

# We can check whether we have equal predictions, it's all TRUE!
all.equal(model$train_preds, CRTreeForest_pred(model, agaricus_data_train, folds = folds))
all.equal(model$valid_preds, CRTreeForest_pred(model, agaricus_data_test))
all.equal(model$train_means, CRTreeForest_pred(model,
                                               agaricus_data_train,
                                               folds = folds,
                                               return_list = FALSE,
                                               prediction = TRUE))
all.equal(model$valid_means, CRTreeForest_pred(model,
                                               agaricus_data_test,
                                               return_list = FALSE,
                                               prediction = TRUE))

## End(Not run)