micompr package | R Documentation

micompr v1.1.0

Multivariate Independent Comparison of Observations

A procedure for comparing multivariate samples associated with different groups. It uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. The procedure is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. It is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.

Readme

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Summary

The micompr R package implements a procedure for comparing multivariate samples associated with different groups. The procedure uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. This technique is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. The procedure is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.

How to install

Install the development version from GitHub with the following command (requires the devtools package):

devtools::install_github("fakenmc/micompr")

A stable version of the package is available on CRAN and can be installed with the following instruction:

install.packages("micompr")

Documentation

All methods and functions are fully documented and can be queried using the built-in help system. After installation, to access the man pages, invoke the micompr help page as follows:

help("micompr")

Additionally, the package contains two vignettes with a number of examples.

References

Practice

Fachada N, Rodrigues J, Lopes VV, Martins RC, Rosa AC. (2016) micompr: An R Package for Multivariate Independent Comparison of Observations. The R Journal 8(2):405–420. https://journal.r-project.org/archive/2016-2/fachada-rodrigues-lopes-etal.pdf

Theory

Fachada N, Lopes VV, Martins RC, Rosa AC. (2017) Model-independent comparison of simulation output. Simulation Modelling Practice and Theory. 72:131–149. http://dx.doi.org/10.1016/j.simpat.2016.12.013 (arXiv preprint)

License

MIT License

Functions in micompr

Name	Description
cmpoutput	Compares output observations from two or more groups
concat_outputs	Concatenate multiple outputs with multiple observations
plot.assumptions_paruv	Plot p-values for testing the assumptions of the parametric tests used in output comparison
plot.cmpoutput	Plot comparison of an output
pphpc_noshuff	Data from two implementations of the PPHPC model, one of which has agent list shuffling deactivated
pphpc_ok	Data from two similar implementations of the PPHPC model
summary.assumptions_cmpoutput	Summary method for the assumptions of parametric tests used in a comparison of an output
summary.assumptions_micomp	Summary method for the assumptions of parametric tests used in multiple comparisons of outputs
assumptions.micomp	Get assumptions for parametric tests performed on each comparisons
assumptions_manova	Determine the assumptions for the MANOVA test
plotcols	Default colors for plots in micomp package
pphpc_diff	Data from two implementations of the PPHPC model, one of which setup with a different parameter
print.assumptions_manova	Print information about the assumptions of the MANOVA test
print.assumptions_micomp	Print information about the assumptions concerning the parametric tests performed on multiple comparisons of outputs
grpoutputs	Load and group outputs from files
micomp	Multiple independent comparisons of observations
plot.assumptions_manova	Plot p-values for testing the multivariate normality assumptions of the MANOVA test
pst	Concatenate strings without any separator characters
plot.assumptions_micomp	Plot p-values for testing the assumptions of the parametric tests used in multiple output comparison
pvalcol	Associate colors to p-values
pphpc_testvlo	Data for testing variable length outputs
toLatex.cmpoutput	Convert cmpoutput object to LaTeX table
toLatex.micomp	Convert micomp object to LaTeX table
print.assumptions_cmpoutput	Print method for the assumptions of parametric tests used in a comparison of an output
summary.cmpoutput	Summary method for comparison of an output
summary.grpoutputs	Summary method for grouped outputs
assumptions	Parametric tests assumptions
assumptions.cmpoutput	Get assumptions for parametric tests performed on output comparisons
plot.grpoutputs	Plot grouped outputs
plot.micomp	Plot projection of output observations on the first two dimensions of the principal components space
print.assumptions_paruv	Print information about the assumptions of the parametric test
print.cmpoutput	Print information about comparison of an output
summary.micomp	Summary method for multiple comparisons of outputs
tikzscat	Simple TikZ scatter plot
assumptions_paruv	Determine the assumptions for the parametric comparison test
print.grpoutputs	Print information about grouped outputs
centerscale	Center and scale vector
plot.assumptions_cmpoutput	Plot p-values for testing the assumptions of the parametric tests used in output comparison
micompr	micompr: multivariate independent comparison of observations
print.micomp	Print information about multiple comparisons of outputs
pvalf	Format p-values
pvalf.default	Default p-value formatting method
tscat_apply	Multiple TikZ 2D scatter plots for a list of output comparisons.
No Results!

Name

Description

cmpoutput

Compares output observations from two or more groups

concat_outputs

Concatenate multiple outputs with multiple observations

plot.assumptions_paruv

Plot p-values for testing the assumptions of the parametric tests used in output comparison

plot.cmpoutput

Plot comparison of an output

pphpc_noshuff

Data from two implementations of the PPHPC model, one of which has agent list shuffling deactivated

pphpc_ok

Data from two similar implementations of the PPHPC model

summary.assumptions_cmpoutput

Summary method for the assumptions of parametric tests used in a comparison of an output

summary.assumptions_micomp

Summary method for the assumptions of parametric tests used in multiple comparisons of outputs

assumptions.micomp

Get assumptions for parametric tests performed on each comparisons

assumptions_manova

Determine the assumptions for the MANOVA test

plotcols

Default colors for plots in micomp package

pphpc_diff

Data from two implementations of the PPHPC model, one of which setup with a different parameter

print.assumptions_manova

Print information about the assumptions of the MANOVA test

print.assumptions_micomp

Print information about the assumptions concerning the parametric tests performed on multiple comparisons of outputs

grpoutputs

Load and group outputs from files

micomp

Multiple independent comparisons of observations

plot.assumptions_manova

Plot p-values for testing the multivariate normality assumptions of the MANOVA test

pst

Concatenate strings without any separator characters

plot.assumptions_micomp

Plot p-values for testing the assumptions of the parametric tests used in multiple output comparison

pvalcol

Associate colors to p-values

pphpc_testvlo

Data for testing variable length outputs

toLatex.cmpoutput

Convert cmpoutput object to LaTeX table

toLatex.micomp

Convert micomp object to LaTeX table

print.assumptions_cmpoutput

Print method for the assumptions of parametric tests used in a comparison of an output

summary.cmpoutput

Summary method for comparison of an output

summary.grpoutputs

Summary method for grouped outputs

assumptions

Parametric tests assumptions

assumptions.cmpoutput

Get assumptions for parametric tests performed on output comparisons

plot.grpoutputs

Plot grouped outputs

plot.micomp

Plot projection of output observations on the first two dimensions of the principal components space

print.assumptions_paruv

Print information about the assumptions of the parametric test

print.cmpoutput

Print information about comparison of an output

summary.micomp

Summary method for multiple comparisons of outputs

tikzscat

Simple TikZ scatter plot

assumptions_paruv

Determine the assumptions for the parametric comparison test

print.grpoutputs

Print information about grouped outputs

centerscale

Center and scale vector

plot.assumptions_cmpoutput

Plot p-values for testing the assumptions of the parametric tests used in output comparison

micompr

micompr: multivariate independent comparison of observations

print.micomp

Print information about multiple comparisons of outputs

pvalf

Format p-values

pvalf.default

Default p-value formatting method

tscat_apply

Multiple TikZ 2D scatter plots for a list of output comparisons.

No Results!

Name
paper.Rnw
tolatex-examples.Rnw
No Results!

Name

paper.Rnw

tolatex-examples.Rnw