CMA (version 1.30.0)

compare: Compare different classifiers

Description

Classifiers can be evaluated separately using the method evaluation. Normally, several classifiers are used for the same dataset and their performance is compared. This comparison procedure is essentially facilitated by this method. For S4 method information, s. compare-methods

Usage

compare(clresultlist, measure = c("misclassification", "sensitivity",
"specificity", "average probability", "brier score", "auc"), aggfun =
meanrm, plot = FALSE, ...)

Arguments

clresultlist

A list of lists (!) of objects of class cloutput or clvarseloutput. Each inner list is usually returned by classification. Additionally, the different list elements of the outer list should have been created by different classifiers, s. also example below.

measure

A character vector containing one or more of the elements listed below. By default, all measures are computed, using evaluation with scheme = "iterationwise". Note that "sensitivity", "specificity", "auc" cannot be computed for the multiclass case.

"misclassification"

The missclassifcation rate.

"sensitivity"

The sensitivity or 1-false negative rate. Can only be computed for binary classifcation.

"specificity"

The specificity or 1-false positive rate. Can only be computed for binary classification.

"average probability"

The average probability assigned to the correct class. Requirement is that the used classifier provides probability estimations. The optimum performance is 1.

"brier score"

The Brier Score is generally defined as (I(y_i=k)-P(k))^2, with I() denoting the indicator function and P(k) the estimated probability for class k. The optimum performance is 0.

"auc"

The Area under the Curve (AUC) belonging to the empirical ROC curve computed from the estimated probabilities and the true class labels. Can only be computed for binary classification and if "scheme = iterationwise", s. below. S. also roc,cloutput-method.

aggfun

Function that determines how performance among different iterations are aggregared. Default is meanrm, which computes the mean using na.rm=T. Other possible choices are quantiles.

plot

Should the performance of different classifiers be visualized by a joint boxplot ? Default is FALSE.

...

Further arguments passed to boxplot in the case that plot = TRUE.

Value

data.frame with rows corresponding to the compared classifiers and columns to the performance measures, aggregated by aggfun, s. above.

References

Dudoit, S., Fridlyand, J., Speed, T. P. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. Journal of the American Statistical Association 97, 77-87 Slawski, M. Daumer, M. Boulesteix, A.-L. (2008) CMA - A comprehensive Bioconductor package for supervised classification with high dimensional data. BMC Bioinformatics 9: 439

See Also

classification, evaluation

Examples

## Not run: 
# ### compare the performance of several discriminant analysis methods
# ### for the Khan dataset:
# data(khan)
# khanX <- as.matrix(khan[,-1])
# khanY <- khan[,1]
# set.seed(27611)
# fiveCV10iter <- GenerateLearningsets(y=khanY, method = "CV", fold = 5, niter = 2, strat = TRUE)
# ### candidate methods:  DLDA, LDA, QDA, pls_LDA, sclda
# class_dlda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = dldaCMA)
# ### peform GeneSlection for LDA, FDA, QDA (using F-Tests):
# genesel_da <- GeneSelection(X=khanX, y=khanY, learningsets = fiveCV10iter, method = "f.test")
# ###
# class_lda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = ldaCMA, genesel= genesel_da, nbgene = 10)
# 
# class_qda <- classification(X = khanX, y=khanY, learningsets = fiveCV10iter, classifier = qdaCMA, genesel = genesel_da, nbgene = 2)
# 
# ### We now make a comparison concerning the performance (sev. measures):
# ### first, collect in a list:
# dalike <- list(class_dlda, class_lda, class_qda)
# ### use pre-defined compare function:
# comparison <- compare(dalike, plot = TRUE, measure = c("misclassification", "brier score", "average probability"))
# print(comparison)
# ## End(Not run)