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Introduction to the R Language - Functions

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Package ‘pracma’ - The Comprehensive R Archive Network

Package ‘pracma’ January 23, 2021 Type Package Version 2 3 3 Date 2021-01-22 Title Practical Numerical Math Functions Depends R (>= 3 1 0) Imports graphics, grDevices, stats, utils



Package ‘RWeka’ - The Comprehensive R Archive Network

Title R/Weka Interface Description An R interface to Weka (Version 3 9 3) Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization Package 'RWeka' contains the interface code, the



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Package 'RWeka"

March 7, 2023

Version0.4-46

TitleR/Weka Interface

DescriptionAn R interface to Weka (Version 3.9.3). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package "RWeka" contains the interface code, the Weka jar is in a separate package "RWekajars". For more information on Weka see .

DependsR (>= 2.6.0)

ImportsRWekajars (>= 3.9.3-1), rJava (>= 0.6-3), graphics, stats, utils, grid

Suggestspartykit (>= 0.8.0), mlbench, e1071

SystemRequirementsJava (>= 8)

LicenseGPL-2

NeedsCompilationno

AuthorKurt Hornik [aut, cre] (),

Christian Buchta [ctb],

Torsten Hothorn [ctb],

Alexandros Karatzoglou [ctb],

David Meyer [ctb],

Achim Zeileis [ctb] ()

MaintainerKurt Hornik

RepositoryCRAN

Date/Publication2023-03-07 14:18:59 UTC

Rtopics documented:

dot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 evaluate_Weka_classifier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 predict_Weka_classifier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 predict_Weka_clusterer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1 2dot read.arff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Weka_associators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Weka_attribute_evaluators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Weka_classifiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Weka_classifier_functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Weka_classifier_lazy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Weka_classifier_meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Weka_classifier_rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Weka_classifier_trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Weka_clusterers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Weka_control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Weka_converters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Weka_filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Weka_interfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Weka_stemmers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Weka_tokenizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
WOW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
WPM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
write.arff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Index33dotCreate DOT RepresentationsDescription

Write a DOT language representation of an object for processing via Graphviz. Usage write_to_dot(x, con = stdout(), ...) ## S3 method for class?Weka_classifier? write_to_dot(x, con = stdout(), ...)

Arguments

xanRobject. conaconnection for writing the representation to. ...additional arguments to be passed from or to methods. evaluate_Weka_classifier3

Details

Graphviz (https://www.graphviz.org) is open source graph visualization software providing several main graph layout programs, of whichdotmakes "hierarchical" or layered drawings of directed graphs, and hence is typically most suitable for visualizing classification trees. Usingdot, therepresentationinfile'foo.dot"canbetransformedtoPostScriptorotherdisplayable graphical formats using (a variant of)dot -Tps foo.dot >foo.ps. Some Weka classifiers (e.g., tree learners such as J48 and M5P) implement a "Drawable" interface providing DOT representations of the fitted models. For such classifiers, thewrite_to_dotmethod writes the representation to the specified connection.evaluate_Weka_classifier Model Statistics for R/Weka ClassifiersDescription Compute model performance statistics for a fitted Weka classifier. Usage evaluate_Weka_classifier(object, newdata = NULL, cost = NULL, numFolds = 0, complexity = FALSE, class = FALSE, seed = NULL, ...)

Arguments

objectaWeka_classifierobject. newdataan optional data frame in which to look for variables with which to evaluate. If omitted orNULL, the training instances are used. costa square matrix of (mis)classification costs. numFoldsthe number of folds to use in cross-validation. complexityoption to include entropy-based statistics. classoption to include class statistics. seedoptional seed for cross-validation. ...further arguments passed to other methods (see details).

Details

The function computes and extracts a non-redundant set of performance statistics that is suitable for

model interpretation. By default the statistics are computed on the training data. the cost matrix so that the cost of a correct classification is zero. Note that if the class variable is numeric only a subset of the statistics are available. Arguments complexityandclassare then not applicable and therefore ignored.

4predict_Weka_classifier

Value An object of classWeka_classifier_evaluation, a list of the following components: stringcharacter, concatenation of the string representations of the performance statis- tics. detailsvector, base statistics, e.g., the percentage of instances correctly classified, etc. detailsComplexity vector, entropy-based statistics (if selected). detailsClassmatrix, class statistics, e.g., the true positive rate, etc., for each level of the response variable (if selected). confusionMatrix table, cross-classification of true and predicted classes.

References

I. H. Witten and E. Frank (2005).Data Mining: Practical Machine Learning Tools and Techniques.

2nd Edition, Morgan Kaufmann, San Francisco.

Examples

## Use some example data. w <- read.arff(system.file("arff","weather.nominal.arff", package = "RWeka")) ## Identify a decision tree. m <- J48(play~., data = w) m ## Use 10 fold cross-validation. e <- evaluate_Weka_classifier(m, cost = matrix(c(0,2,1,0), ncol = 2), numFolds = 10, complexity = TRUE, seed = 123, class = TRUE) e summary(e) e$detailspredict_Weka_classifier Model Predictions for R/Weka ClassifiersDescription Predicted values based on fitted Weka classifier models. predict_Weka_clusterer5 Usage ## S3 method for class?Weka_classifier? predict(object, newdata = NULL, type = c("class", "probability"), ...)

Arguments

objectan object of class inheriting fromWeka_classifier. newdataan optional data frame in which to look for variables with which to predict. If omitted orNULL, the training instances are used. typecharacter string determining whether classes should be predicted (numeric for regression, factor for classification) or class probabilities (only available for classification). May be abbreviated. ...further arguments passed to or from other methods. Value

Either a vector with classes or a matrix with the posterior class probabilities, with rows correspond-

ing to instances and columns to classes.predict_Weka_clusterer Class Predictions for R/Weka ClusterersDescription Predict class ids or memberships based on fitted Weka clusterers. Usage ## S3 method for class?Weka_clusterer? predict(object, newdata = NULL, type = c("class_ids", "memberships"), ...)

Arguments

objectan object of class inheriting fromWeka_clusterer. newdataan optional data set for predictions are sought. This must be given for predict- ing class memberships. If omitted orNULL, the training instances are used for predicting class ids. typea character string indicating whether class ids or memberships should be re- turned. May be abbreviated. ...further arguments passed to or from other methods.

6read.arff

Details

method.read.arffRead Data from ARFF FilesDescription Reads data from Weka Attribute-Relation File Format (ARFF) files. Usage read.arff(file)

Arguments

filea character string with the name of theARFFfile to read from, or aconnection which will be opened if necessary, and if so closed at the end of the function call. Value A data frame containing the data from theARFFfile.

References

arff/

See Also

write.arff

Examples

read.arff(system.file("arff", "contact-lenses.arff", package = "RWeka")) Weka_associators7Weka_associatorsR/Weka AssociatorsDescription R interfaces to Weka association rule learning algorithms. Usage

Apriori(x, control = NULL)

Tertius(x, control = NULL)

Arguments

xan R object with the data to be associated. controlan object of classWeka_control, or a character vector of control options, or NULL(default). Available options can be obtained on-line using the Weka Option

WizardWOW, or the Weka documentation.

Details

Aprioriimplements an Apriori-type algorithm, which iteratively reduces the minimum support until it finds the required number of rules with the given minimum confidence.

Tertiusimplements a Tertius-type algorithm.

See the references for more information on these algorithms. Value A list inheriting from classWeka_associatorswith components including associatora reference (of classjobjRef) to a Java object obtained by applying the Weka buildAssociationsmethod to the training instances using the given control options. Note Tertiusrequires Weka packagetertiusto be installed.

References

R. Agrawal and R. Srikant (1994). Fast algorithms for mining association rules in large databases. Proceedings of the International Conference on Very Large Databases, 478-499. Santiago, Chile:

Morgan Kaufmann, Los Altos, CA.

P. A. Flach and N. Lachiche (1999). Confirmation-guided discovery of first-order rules with Tertius. Machine Learning,42, 61-95.doi:10.1023/A:1007656703224 . I. H. Witten and E. Frank (2005).Data Mining: Practical Machine Learning Tools and Techniques.

2nd Edition, Morgan Kaufmann, San Francisco.

8Weka_attribute_evaluators

Examples

x <- read.arff(system.file("arff", "contact-lenses.arff", package = "RWeka")) ## Apriori with defaults.

Apriori(x)

## Some options: set required number of rules to 20.

Apriori(x, Weka_control(N = 20))

## Not run: ## Requires Weka package?tertius?to be installed. ## Tertius with defaults.

Tertius(x)

## Some options: only classification rules (single item in the RHS).

Tertius(x, Weka_control(S = TRUE))

## End(Not run)Weka_attribute_evaluators

R/Weka Attribute EvaluatorsDescription

R interfaces to Weka attribute evaluators.

Usage GainRatioAttributeEval(formula, data, subset, na.action, control = NULL) InfoGainAttributeEval(formula, data, subset, na.action, control = NULL)

Arguments

formulaa symbolic description of a model. Note that for unsupervised filters the re- sponse can be omitted. dataan optional data frame containing the variables in the model. subsetan optional vector specifying a subset of observations to be used in the fitting process. na.actiona function which indicates what should happen when the data containNAs. See model.framefor details. controlan object of classWeka_control, or a character vector of control options, or NULL(default). Available options can be obtained on-line using the Weka Option

WizardWOW, or the Weka documentation.

Weka_classifiers9

Details

GainRatioAttributeEvalevaluates the worth of an attribute by measuring the gain ratio with respect to the class. InfoGainAttributeEvalevaluates the worth of an attribute by measuring the information gain with respect to the class.

Currently, only interfaces to classes which evaluate single attributes (as opposed to subsets, techni-

cally, which implement the Weka AttributeEvaluator interface) are possible. Value A numeric vector with the figures of merit for the attributes specified by the right hand side of formula.

Examples

InfoGainAttributeEval(Species ~ . , data = iris)Weka_classifiersR/Weka ClassifiersDescription

R interfaces to Weka classifiers.

Details

Supervised learners, i.e., algorithms for classification and regression, are termed "classifiers" by Weka. (Numeric prediction, i.e., regression, is interpreted as prediction of a continuous class.) R interface functions to Weka classifiers are created bymake_Weka_classifier, and have formals formula,data,subset,na.action, andcontrol(default: none), where the first four have the "usual" meanings for statistical modeling functions in R, and the last again specifies the control options to be employed by the Weka learner.

By default, the model formulae should only use the '+" and '-" operators to indicate the variables to

be included or not used, respectively.

Seemodel.framefor details on howna.actionis used.

Objects created by these interfaces always inherit from classWeka_classifier, and have at least suitableprint,summary(viaevaluate_Weka_classifier), andpredictmethods.

See Also

Available "standard" interface functions are documented in

W eka_classifier_functions

(re gression and classification function learners),

W eka_classifier_lazy

(lazy l earners),

W eka_classifier_meta

(meta learners),

W eka_classifier_rules

(rule learners), and

W eka_classifier_trees

(re gressionand classification tree learners).

R/Weka Classifier FunctionsDescription

R interfaces to Weka regression and classification function learners. Usage LinearRegression(formula, data, subset, na.action, control = Weka_control(), options = NULL)

Logistic(formula, data, subset, na.action,

control = Weka_control(), options = NULL)

SMO(formula, data, subset, na.action,

control = Weka_control(), options = NULL)

Arguments

formulaa symbolic description of the model to be fit. dataan optional data frame containing the variables in the model. subsetan optional vector specifying a subset of observations to be used in the fittingquotesdbs_dbs16.pdfusesText_22