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scmamp: Statistical Comparison of Multiple Algorithms in Multiple Problems

This is a simple R package aimed at simplifying the statistical analysis of the results in the comparison of algorithms in different problems.

It is mainly focused on non parametric methods and implements Shaffer static and Bergmann and Hommel dynamic corrections for pairwise tests.

The package also includes some plotting tools, such as the critical difference plots shown in Demšar, J., 2006. Indeed, the package is mainly based on the papers:

Demšar, J. (2006) Statistical Comparisons of Classifiers over Multiple Data Sets. Journal of Machine Learning Research, 7, 1-30.

García S. and Herrera, F. (2008) An Extension on "Statistical Comparisons of Classifiers over Multiple Data Sets" for all Pairwise Comparisons. Journal of Machine Learning Research, 9, 2677-2694.

García S. and Herrera, F. (2010) Advanced Nonparametric Tests for Multiple Comparison in the Design of Experiments in Computational Intelligence and Data Mining: Experimental Analysis of Power. Information Sciences, 180, 2044-2064.

Package installation

The last version of the package can be installed running the following commands:

if (!require("devtools")) {
  install.packages("devtools")
}

devtools::install_github("b0rxa/scmamp")

The package can also be installed using the tar.gz files in the root directory. First, download the scmamp_*.tar.gz file and install it running:

install.packages(path.tar.gz.file, reps=NULL)

where path.tar.gz.file refers to the path of the downloaded file. Note that these files may not be up to date.

Documentation

The package includes two vignettes, one for the basic use and another with information about the data manipulation. To access to the local versions of these vignettes (once the package is installed):

library("scmamp")
browseVignettes("scmamp")

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Version

Install

install.packages('scmamp')

Monthly Downloads

42

Version

0.2.55

License

GPL-2

Maintainer

Borja Calvo

Last Published

October 21st, 2016

Functions in scmamp (0.2.55)

adjustBergmannHommel

Bergmann and Hommel dynamic correction of p-values.
adjustRom

Rom correction of p-values
adjustHolland

Holland correction of p-values.
adjustShaffer

Shaffer's correction of p-values in pairwise comparisons. .
adjustFinner

Finner correction of p-values
anovaTest

ANOVA test for multiple comparisons
customPost

Function to use custom tests to perform post hoc comparisons.
contrastEstimationMatrix

Contrast estimation based on medians
booleanMatrix

Creation of boolean matrices for highlighting results
adjustLi

Li correction of p-values.
friedmanPost

Friedman's post hoc raw p-values
drawAlgorithmGraph

Hypotheses represented as a graph
filterData

Expression based row filtering
data.gh.2010

Example in Garcia and Herrera (2010)
friedmanAlignedRanksPost

Friedman's Aligned Ranks post hoc raw p-values
data.blum.2015

Comparison of optimization algorithms in Blum et al. (2015)
data.gh.2008

Example in Garcia and Herrera (2008)
friedmanTest

Friedman's test
friedmanAlignedRanksTest

Friedman's Aligned Ranks test
exhaustiveSets

Complete set of exhaustive sets.
postHocTest

Post hoc tests for multiple comparison analises
qqplotGaussian

Gaussian distribution quantile-quantile plot
plotPvalues

Plotting the p-value matrix
quadePost

Quade post hoc raw p-values
plotDensities

Kernel based density estimation of the samples
plotRanking

Ranking Plots
plotCD

Critical difference plot
multipleComparisonTest

Tests for multiple comparisons
imanDavenportTest

Iman Davenport's modification of Friedman's test
nemenyiTest

Nemenyi test
readComparisonFile

Read data from a comparison file
quadeTest

Quade's test
readExperimentFile

Read data from an experiment-like file
tukeyPost

Tukey post hoc test for ANOVA.
readComparisonDir

Read data from a directory of comparison-like files
scmamp

Statistical comparison of multiple algorithms
readExperimentDir

Read data from an experiment-like files in a directory
summarizeData

Summarization of data
rankMatrix

Get the ranking matrix.
tukeyTest

Tukey test
wilcoxonSignedTest

Wilcoxon signed-rank est
writeTabular

Write a table in LaTeX format