mlearning (version 1.2.1)

mlRforest: Supervised classification and regression using random forest

Description

Unified (formula-based) interface version of the random forest algorithm provided by randomForest::randomForest().

Usage

mlRforest(train, ...)
ml_rforest(train, ...)
# S3 method for formula
mlRforest(
  formula,
  data,
  ntree = 500,
  mtry,
  replace = TRUE,
  classwt = NULL,
  ...,
  subset,
  na.action
)
# S3 method for default
mlRforest(
  train,
  response,
  ntree = 500,
  mtry,
  replace = TRUE,
  classwt = NULL,
  ...
)
# S3 method for mlRforest
predict(
  object,
  newdata,
  type = c("class", "membership", "both", "vote"),
  method = c("direct", "oob", "cv"),
  ...
)

Value

ml_rforest()/mlRforest() creates an mlRforest, mlearning

object containing the classifier and a lot of additional metadata used by the functions and methods you can apply to it like predict() or cvpredict(). In case you want to program new functions or extract specific components, inspect the "unclassed" object using unclass().

Arguments

train

a matrix or data frame with predictors.

...

further arguments passed to randomForest::randomForest() or its predict() method. There are many more arguments, see the corresponding help page.

formula

a formula with left term being the factor variable to predict (for supervised classification), a vector of numbers (for regression) or nothing (for unsupervised classification) and the right term with the list of independent, predictive variables, separated with a plus sign. If the data frame provided contains only the dependent and independent variables, one can use the class ~ . short version (that one is strongly encouraged). Variables with minus sign are eliminated. Calculations on variables are possible according to usual formula convention (possibly protected by using I()).

data

a data.frame to use as a training set.

ntree

the number of trees to generate (use a value large enough to get at least a few predictions for each input row). Default is 500 trees.

mtry

number of variables randomly sampled as candidates at each split. Note that the default values are different for classification (sqrt(p) where p is number of variables in x) and regression (p/3)?

replace

sample cases with or without replacement (TRUE by default)?

classwt

priors of the classes. Need not add up to one. Ignored for regression.

subset

index vector with the cases to define the training set in use (this argument must be named, if provided).

na.action

function to specify the action to be taken if NAs are found. For ml_rforest() na.fail is used by default. The calculation is stopped if there is any NA in the data. Another option is na.omit, where cases with missing values on any required variable are dropped (this argument must be named, if provided). For the predict() method, the default, and most suitable option, is na.exclude. In that case, rows with NAs in newdata= are excluded from prediction, but reinjected in the final results so that the number of items is still the same (and in the same order as newdata=).

response

a vector of factor (classification) or numeric (regression), or NULL (unsupervised classification).

object

an mlRforest object

newdata

a new dataset with same conformation as the training set (same variables, except may by the class for classification or dependent variable for regression). Usually a test set, or a new dataset to be predicted.

type

the type of prediction to return. "class" by default, the predicted classes. Other options are "membership" the membership (number between 0 and 1) to the different classes as assessed by the number of neighbors of these classes, or "both" to return classes and memberships. One can also use "vote", which returns the number of trees that voted for each class.

method

"direct" (default), "oob" or "cv". "direct" predicts new cases in newdata= if this argument is provided, or the cases in the training set if not. Take care that not providing newdata= means that you just calculate the self-consistency of the classifier but cannot use the metrics derived from these results for the assessment of its performances (in the case of Random Forest, these metrics would most certainly falsely indicate a perfect classifier). Either use a different data set in newdata= or use the alternate approaches: out-of-bag ("oob") or cross-validation ("cv"). The out-of-bag approach uses individuals that are not used to build the trees to assess performances. It is an unbiased estimates. If you specify method = "cv" then cvpredict() is used and you cannot provide newdata= in that case.

See Also

mlearning(), cvpredict(), confusion(), also randomForest::randomForest() that actually does the classification.

Examples

# Prepare data: split into training set (2/3) and test set (1/3)
data("iris", package = "datasets")
train <- c(1:34, 51:83, 101:133)
iris_train <- iris[train, ]
iris_test <- iris[-train, ]
# One case with missing data in train set, and another case in test set
iris_train[1, 1] <- NA
iris_test[25, 2] <- NA

iris_rf <- ml_rforest(data = iris_train, Species ~ .)
summary(iris_rf)
plot(iris_rf) # Useful to look at the effect of ntree=
# For such a relatively simple case, 50 trees are enough
iris_rf <- ml_rforest(data = iris_train, Species ~ ., ntree = 50)
summary(iris_rf)
predict(iris_rf) # Default type is class
predict(iris_rf, type = "membership")
predict(iris_rf, type = "both")
predict(iris_rf, type = "vote")
# Out-of-bag prediction (unbiased)
predict(iris_rf, method = "oob")
# Self-consistency (always very high for random forest, biased, do not use!)
confusion(iris_rf)
# This one is better
confusion(iris_rf, method = "oob") # Out-of-bag performances
# Cross-validation prediction is also a good choice when there is no test set
predict(iris_rf, method = "cv")  # Idem: cvpredict(res)
# Cross-validation for performances estimation
confusion(iris_rf, method = "cv")
# Evaluation of performances using a separate test set
confusion(predict(iris_rf, newdata = iris_test), iris_test$Species)

# Regression using random forest (from ?randomForest)
set.seed(131) # Useful for reproducibility (use a different number each time)
ozone_rf <- ml_rforest(data = airquality, Ozone ~ ., mtry = 3,
  importance = TRUE, na.action = na.omit)
summary(ozone_rf)
# Show "importance" of variables: higher value mean more important variables
round(randomForest::importance(ozone_rf), 2)
plot(na.omit(airquality)$Ozone, predict(ozone_rf))
abline(a = 0, b = 1)

# Unsupervised classification using random forest (from ?randomForest)
set.seed(17)
iris_urf <- ml_rforest(train = iris[, -5]) # Use only quantitative data
summary(iris_urf)
randomForest::MDSplot(iris_urf, iris$Species)
plot(stats::hclust(stats::as.dist(1 - iris_urf$proximity),
  method = "average"), labels = iris$Species)