robCompositions: robCompositions-package – R documentation

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robCompositions-package

Robust Estimation for Compositional Data.

Description

The package contains methods for imputation of compositional data including robust methods, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis (Fisher rule) and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (alr, clr, ilr, and their inverse transformations).

Details

Package:	robCompositions
Type:	Package
Version:	1.3.3
Date:	2009-11-28
License:	GPL 2
LazyLoad:	yes

Author(s)

Matthias Templ, Peter Filzmoser, Karel Hron,

Maintainer: Matthias Templ <templ@tuwien.ac.at>

References

Aitchison, J. (1986) The Statistical Analysis of Compositional Data Monographs on Statistics and Applied Probability. Chapman \& Hall Ltd., London (UK). 416p. \

Filzmoser, P., and Hron, K. (2008) Outlier detection for compositional data using robust methods. Math. Geosciences, 40 233-248.

Filzmoser, P., Hron, K., Reimann, C. (2009) Principal Component Analysis for Compositional Data with Outliers. Environmetrics, 20 (6), 621–632.

P. Filzmoser, K. Hron, C. Reimann, R. Garrett (2009): Robust Factor Analysis for Compositional Data. Computers and Geosciences, 35 (9), 1854–1861.

Hron, K. and Templ, M. and Filzmoser, P. (2010) Imputation of missing values for compositional data using classical and robust methods Computational Statistics and Data Analysis, 54 (12), 3095–3107.

C. Reimann, P. Filzmoser, R.G. Garrett, and R. Dutter (2008): Statistical Data Analysis Explained. Applied Environmental Statistics with R. John Wiley and Sons, Chichester, 2008.

Examples

## k nearest neighbor imputation
data(expenditures)
expenditures[1,3]
expenditures[1,3] <- NA
impKNNa(expenditures)$xImp[1,3]

## iterative model based imputation
data(expenditures)
x <- expenditures
x[1,3]
x[1,3] <- NA
xi <- impCoda(x)$xImp
xi[1,3]
s1 <- sum(x[1,-3])
impS <- sum(xi[1,-3])
xi[,3] * s1/impS

xi <- impKNNa(expenditures)
xi
summary(xi)
## Not run: plot(xi, which=1)
plot(xi, which=2)
plot(xi, which=3)

## pca
data(expenditures)
p1 <- pcaCoDa(expenditures)
p1
plot(p1)

## outlier detection
data(expenditures)
oD <- outCoDa(expenditures)
oD
plot(oD)

## transformations
data(arcticLake)
x <- arcticLake
x.alr <- addLR(x, 2)
y <- addLRinv(x.alr)
addLRinv(addLR(x, 3))
data(expenditures)
x <- expenditures
y <- addLRinv(addLR(x, 5))
head(x)
head(y)
addLRinv(x.alr, ivar=2, useClassInfo=FALSE)

data(expenditures)
eclr <- cenLR(expenditures)
inveclr <- cenLRinv(eclr)
head(expenditures)
head(inveclr)
head(cenLRinv(eclr$x.clr))

require(MASS)
Sigma <- matrix(c(5.05,4.95,4.95,5.05), ncol=2, byrow=TRUE)
z <- pivotCoordInv(mvrnorm(100, mu=c(0,2), Sigma=Sigma))

robCompositions

Compositional Data Analysis

v2.3.0

GPL (>= 2)

Authors

Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>), Karel Hron [aut] (<https://orcid.org/0000-0002-1847-6598>), Peter Filzmoser [aut] (<https://orcid.org/0000-0002-8014-4682>), Kamila Facevicova [ctb], Petra Kynclova [ctb], Jan Walach [ctb], Veronika Pintar [ctb], Jiajia Chen [ctb], Dominika Miksova [ctb], Bernhard Meindl [ctb], Alessandra Menafoglio [ctb] (<https://orcid.org/0000-0003-0682-6412>), Alessia Di Blasi [ctb], Federico Pavone [ctb], Gianluca Zeni [ctb]

Initial release

2020-11-18