classifierOutput-class: Class "classifierOutput"

In MLInterfaces: Uniform interfaces to R machine learning procedures for data in Bioconductor containers

Description

This class summarizes the output values from different classifiers.

Objects from the Class

Objects are typically created during the application of a supervised machine learning algorithm to data and are the value returned. It is very unlikely that any user would create such an object by hand.

Slots

testOutcomes:

Object of class "factor" that lists the actual outcomes in the records on the test set

testPredictions:

Object of class "factor" that lists the predictions of outcomes in the test set

testScores:

Object of class "ANY" – this element will include matrices or vectors or arrays that include information that is typically related to the posterior probability of occupancy of the predicted class or of all classes. The actual contents of this slot can be determined by inspecting the converter element of the learnerSchema used to select the model.

trainOutcomes:

Object of class "factor" that lists the actual outcomes in records on the training set

trainPredictions:

Object of class "factor" that lists the predicted outcomes in the training set

trainScores:

Object of class "ANY" see the description of testScores above; the same information is returned, but applicable to the training set records.

trainInd:

Object of class "numeric" with of indices of data to be used for training.

RObject:

Object of class "ANY" – when the trainInd parameter of the MLearn call is numeric, this slot holds the return value of the underlying R function that carried out the predictive modeling. For example, if rpartI was used as MLearn method, Robject holds an instance of the rpart S3 class, and plot and text methods can be applied to this. When the trainInd parameter of the MLearn call is an instance of xvalSpec, this slot holds a list of results of cross-validatory iterations. Each element of this list has two elements: test.idx, giving the numeric indices of the test cases for the associated cross-validation iteration, and mlans, which is the classifierOutput for the associated iteration. See the example for an illustration of 'digging out' the predicted probabilities associated with each cross-validation iteration executed through an xvalSpec specification.

embeddedCV:

logical value that is TRUE if the procedure in use performs its own cross-validation

fsHistory:

list of features selected through cross-validation process

learnerSchema:

propagation of the learner schema object used in the call

call:

Object of class "call" – records the call used to generate the classifierOutput RObject

Methods

confuMat

signature(obj = "classifierOutput"): Compute the confusion matrix for test records.

confuMatTrain

signature(obj = "classifierOutput"): Compute the confusion matrix for training set. Typically yields optimistically biased information on misclassification rate.

RObject

signature(obj = "classifierOutput"): The R object returned by the underlying classifier. This can then be passed on to specific methods for those objects, when they exist.

trainInd

signature(obj = "classifierOutput"): Returns the indices of data used for training.

show

signature(object = "classifierOutput"): A print method that provides a summary of the output of the classifier.

predictions

signature(object = "classifierOutput"): Print the predicted classes for each sample/individual. The predictions for the training set are the training outcomes.

predictions

signature(object = "classifierOutput", t = "numeric"): Print the predicted classes for each sample/individual that have a testScore greater or equal than t. The predictions for the training set are the training outcomes. Non-predicted cases and cases that matche multiple classes are returned as NAs.

predScore

signature(object = "classifierOutput"): Returns the scores for predicted class for each sample/individual. The scores for the training set are set to 1.

predScores

signature(object = "classifierOutput"): Returns the prediction scores for all classes for each sample/individual. The scores for the training set are set to 1 for the appropriate class, 0 otherwise.

testScores

signature(object = "classifierOutput"): ...

testPredictions

signature(object = "classifierOutput"): Print the predicted classes for each sample/individual in the test set.

testPredictions

signature(object = "classifierOutput", t = "numeric"): Print the predicted classes for each sample/individual in the test set that have a testScore greater or equal than t. Non-predicted cases and cases that matche multiple classes are returned as NAs.

trainScores

signature(object = "classifierOutput"): ...

trainPredictions

signature(object = "classifierOutput"): Print the predicted classes for each sample/individual in the train set.

trainPredictions

signature(object = "classifierOutput", t = "numeric"): Print the predicted classes for each sample/individual in the train set that have a testScore greater or equal than t. Non-predicted cases and cases that matche multiple classes are returned as NAs.

fsHistory

signature(object = "classifierOutput"): ...

Author(s)

V. Carey

Examples

showClass("classifierOutput")
library(golubEsets)
data(Golub_Train) # now cross-validate a neural net
set.seed(1234)
xv5 = xvalSpec("LOG", 5, balKfold.xvspec(5))
m2 = MLearn(ALL.AML~., Golub_Train[1000:1050,], nnetI, xv5, 
   size=5, decay=.01, maxit=1900 )
testScores(RObject(m2)[[1]]$mlans)
alls = lapply(RObject(m2), function(x) testScores(x$mlans))

MLInterfaces documentation built on Nov. 8, 2020, 8:14 p.m.