Type: Package
Title: Random Ferns Classifier
Version: 5.0.0
Description: Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.
Encoding: UTF-8
URL: https://gitlab.com/mbq/rFerns
BugReports: https://gitlab.com/mbq/rFerns/-/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Suggests: testthat
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2021-09-21 12:11:46 UTC; mbq
Author: Miron Bartosz Kursa ORCID iD [aut, cre]
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Repository: CRAN
Date/Publication: 2021-09-22 10:00:13 UTC

Merge two random ferns models

Description

This function combines two compatible (same decision, same training data structure and same depth) models into a single ensemble. It can be used to distribute model training, perform it on batches of data, save checkouts or precisely investigate its course.

Usage

## S3 method for class 'rFerns'
merge(
  x,
  y,
  dropModel = FALSE,
  ignoreObjectConsistency = FALSE,
  trueY = NULL,
  ...
)

Arguments

x

Object of a class rFerns; a first model to be merged.

y

Object of a class rFerns; a second model to be merged. Can also be NULL, x is immediately returned in that case. Has to have be built on the same kind of training data as x, with the same depth.

dropModel

If TRUE, model structure will be dropped to save size. This disallows prediction using the merged model, but retains importance and OOB approximations.

ignoreObjectConsistency

If TRUE, merge will be done even if both models were built on a different sets of objects. This drops OOB approximations.

trueY

Copy of the training decision, used to re-construct OOB error and confusion matrix. Can be omitted, OOB error and confusion matrix will disappear in that case; ignored when ignoreObjectConsistency is TRUE.

...

Ignored, for S3 gerneric/method consistency.

Value

An object of class rFerns, which is a list with the following components:

model

The merged model in case both x and y had model structures included and dropModel was FALSE. Otherwise NULL.

oobErr

OOB approximation of accuracy, if can be computed. Namely, when oobScores could be and trueY is provided.

importance

The merged importance scores in case both x and y had importance calculated. Shadow importance appears only if both models had it enabled.

oobScores

OOB scores, if can be computed; namely if both models had it calculated and ignoreObjectConsistency was not used.

oobPreds

A vector of OOB predictions of class for each object in training set, if can be computed.

oobConfusionMatrix

OOB confusion matrix, if can be computed. Namely, when oobScores could be and trueY is provided.

timeTaken

Time used to train the model, calculated as a sum of training times of x and y.

parameters

Numerical vector of three elements: classes, depth and ferns.

classLabels

Copy of levels(Y) after purging unused levels.

isStruct

Copy of the train set structure.

merged

Set to TRUE to mark that merging was done.

Note

In case of different training object sets were used to build the merged models, merged importance is calculated but mileage may vary; for substantially different sets it may become biased. Your have been warned.

Shadow importance is only merged when both models have shadow importance and the same consistentSeed value; otherwise shadow importance would be biased down.

The order of objects in x and y is not important; the only exception is merging with NULL, in which case x must be an rFerns object for R to use proper merge method.

Examples

set.seed(77)
#Fetch Iris data
data(iris)
#Build models
rFerns(Species~.,data=iris)->modelA
rFerns(Species~.,data=iris)->modelB
modelAB<-merge(modelA,modelB)
print(modelA)
print(modelAB)

Naive feature selection method utilising the rFerns shadow imporance

Description

Proof-of-concept ensemble of rFerns models, built to stabilise and improve selection based on shadow importance. It employs a super-ensemble of iterations small rFerns forests, each built on a subspace of size attributes, which is selected randomly, but with a higher selection probability for attributes claimed important by previous sub-models. Final selection is a group of attributes which hold a substantial weight at the end of the procedure.

Usage

naiveWrapper(
  x,
  y,
  iterations = 1000,
  depth = 5,
  ferns = 100,
  size = 30,
  lambda = 5,
  threads = 0,
  saveHistory = FALSE
)

Arguments

x

Data frame containing attributes; must have unique names and contain only numeric, integer or (ordered) factor columns. Factors must have less than 31 levels. No NA values are permitted.

y

A decision vector. Must a factor of the same length as nrow(X) for ordinary many-label classification, or a logical matrix with each column corresponding to a class for multi-label classification.

iterations

Number of iterations i.e., the number of sub-models built.

depth

The depth of the ferns; must be in 1–16 range. Note that time and memory requirements scale with 2^depth.

ferns

Number of ferns to be build in each sub-model. This should be a small number, around 3-5 times size.

size

Number of attributes considered by each sub-model.

lambda

Lambda parameter driving the re-weighting step of the method.

threads

Number of parallel threads, copied to the underlying rFerns call.

saveHistory

Should weight history be stored.

Value

An object of class naiveWrapper, which is a list with the following components:

found

Names of all selected attributes.

weights

Vector of weights indicating the confidence that certain feature is relevant.

timeTaken

Time of computation.

weightHistory

History of weights over all iterations, present if saveHistory was TRUE.

params

Copies of algorithm parameters, iterations, depth, ferns and size, as a named vector.

References

Kursa MB (2017). Efficient all relevant feature selection with random ferns. In: Kryszkiewicz M., Appice A., Slezak D., Rybinski H., Skowron A., Ras Z. (eds) Foundations of Intelligent Systems. ISMIS 2017. Lecture Notes in Computer Science, vol 10352. Springer, Cham.

Examples

set.seed(77)
#Fetch Iris data
data(iris)
#Extend with random noise
noisyIris<-cbind(iris[,-5],apply(iris[,-5],2,sample))
names(noisyIris)[5:8]<-sprintf("Nonsense%d",1:4)
#Execute selection
naiveWrapper(noisyIris,iris$Species,iterations=50,ferns=20,size=8)

Prediction with random ferns model

Description

This function predicts classes of new objects with given rFerns object.

Usage

## S3 method for class 'rFerns'
predict(object, x, scores = FALSE, ...)

Arguments

object

Object of a class rFerns; a model that will be used for prediction.

x

Data frame containing attributes; must have corresponding names to training set (although order is not important) and do not introduce new factor levels. If this argument is not given, OOB predictions on the training set will be returned.

scores

If TRUE, the result will contain score matrix instead of simple predictions.

...

Additional parameters.

Value

Predictions. If scores is TRUE, a factor vector (for many-class classification) or a logical data.frame (for multi-class classification) with predictions, else a data.frame with class' scores.

Examples

set.seed(77)
#Fetch Iris data
data(iris)
#Split into tRain and tEst set
iris[c(TRUE,FALSE),]->irisR
iris[c(FALSE,TRUE),]->irisE
#Build model
rFerns(Species~.,data=irisR)->model
print(model)

#Test
predict(model,irisE)->p
print(table(
 Predictions=p,
 True=irisE[["Species"]]))
err<-mean(p!=irisE[["Species"]])
print(paste("Test error",err,sep=" "))

#Show first OOB scores
head(predict(model,scores=TRUE))

Classification with random ferns

Description

This function builds a random ferns model on the given training data.

Usage

rFerns(x, ...)

## S3 method for class 'formula'
rFerns(formula, data = .GlobalEnv, ...)

## S3 method for class 'matrix'
rFerns(x, y, ...)

## Default S3 method:
rFerns(
  x,
  y,
  depth = 5,
  ferns = 1000,
  importance = "none",
  saveForest = TRUE,
  consistentSeed = NULL,
  threads = 0,
  ...
)

Arguments

x

Data frame containing attributes; must have unique names and contain only numeric, integer or (ordered) factor columns. Factors must have less than 31 levels. No NA values are permitted.

...

For formula and matrix methods, a place to state parameters to be passed to default method. For the print method, arguments to be passed to print.

formula

alternatively, formula describing model to be analysed.

data

in which to interpret formula.

y

A decision vector. Must a factor of the same length as nrow(X) for ordinary many-label classification, or a logical matrix with each column corresponding to a class for multi-label classification.

depth

The depth of the ferns; must be in 1–16 range. Note that time and memory requirements scale with 2^depth.

ferns

Number of ferns to be build.

importance

Set to calculate attribute importance measure (VIM); "simple" will calculate the default mean decrease of true class score (MDTS, something similar to Random Forest's MDA/MeanDecreaseAccuracy), "shadow" will calculate MDTS and additionally MDTS of this attribute shadow, an implicit feature build by shuffling values within it, thus stripping it from information (which is slightly slower). Shadow importance is useful as a reference to judge significance of a regular importance. "none" turns importance calculation off, for a slightly faster execution. For compatibility with pre-1.2 rFerns, TRUE will resolve to "simple" and FALSE to "none". Abbreviation can be used instead of a full value.

saveForest

Should the model be saved? It must be TRUE if you want to use the model for prediction; however, if you are interested in importance or OOB error only, setting it to FALSE significantly improves memory requirements, especially for large depth and ferns.

consistentSeed

PRNG seed used for shadow importance only. Must be either a 2-element integer vector or NULL, which corresponds to seeding from the default PRNG.

threads

Number or OpenMP threads to use. The default value of 0 means all available to OpenMP. It should be set to the same value in two merged models to make shadow importance meaningful.

Value

An object of class rFerns, which is a list with the following components:

model

The built model; NULL if saveForest was FALSE.

oobErr

OOB approximation of accuracy. Ignores never-OOB-tested objects (see oobScores element).

importance

The importance scores or NULL if importance was set to "none". In a first case it is a data.frame with two or three columns: MeanScoreLoss which is a mean decrease of a score of a correct class when a certain attribute is permuted, Tries which is number of ferns which utilised certain attribute, and, only when importance was set to "shadow", Shadow, which is a mean decrease of accuracy for the correct class for a permuted copy of an attribute (useful as a baseline for normal importance). The rownames are set and equal to the names(x).

oobScores

A matrix of OOB scores of each class for each object in training set. Rows correspond to classes in the same order as in levels(Y). If the ferns is too small, some columns may contain NAs, what means that certain objects were never in test set.

oobPreds

A vector of OOB predictions of class for each object in training set. Never-OOB-tested objects (see above) have predictions equal to NA.

oobConfusionMatrix

Confusion matrix build from oobPreds and y.

timeTaken

Time used to train the model (smaller than wall time because data preparation and model final touches are excluded; however it includes the time needed to compute importance, if it applies). An object of difftime class.

parameters

Numerical vector of three elements: classes, depth and ferns, containing respectively the number of classes in decision and copies of depth and ferns parameters.

classLabels

Copy of levels(Y) after purging unused levels.

consistentSeed

Consistent seed used; only present for importance="shadow". Can be used to seed a new model via consistentSeed argument.

isStruct

Copy of the train set structure, required internally by predict method.

Note

The unused levels of the decision will be removed; on the other hand unused levels of categorical attributes will be preserved, so that they could be present in the data later predicted with the model. The levels of ordered factors in training and predicted data must be identical.

Do not use formula interface for a data with large number of attributes; the overhead from handling the formula may be significant.

References

Ozuysal M, Calonder M, Lepetit V & Fua P. (2009). Fast Keypoint Recognition using Random Ferns, IEEE Transactions on Pattern Analysis and Machine Intelligence, 32(3), 448-461.

Kursa MB (2014). rFerns: An Implementation of the Random Ferns Method for General-Purpose Machine Learning, Journal of Statistical Software, 61(10), 1-13.

Examples

set.seed(77)
#Fetch Iris data
data(iris)
#Build model
rFerns(Species~.,data=iris)
##Importance
rFerns(Species~.,data=iris,importance="shadow")->model
print(model$imp)