robCompositions v2.1.0

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Compositional Data Analysis

Methods for analysis of compositional data including robust methods, imputation, methods to replace rounded zeros, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.

Readme

{robCompositions}

Robust Methods for Compositional Data

using robCompositions

data(expenditures)

p1 <- pcaCoDa(expenditures)

plot(p1)

Image

What is it?

  • Imputation of compositional data including robust methods, methods to impute rounded zeros
  • Outlier detection for compositional data using robust methods
  • Principal component analysis for compositional data using robust methods
  • Factor analysis for compositional data using robust methods
  • Discriminant analysis for compositional data (Fisher rule) using robust methods
  • Robust regression with compositional predictors
  • Anderson-Darling normality tests for compositional data
  • log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations).
  • In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the
         ternary diagram. 
    

Goals

  • never use classical statistical methods on raw compositional data again.

Getting Started

Dependencies

The package has dependencies on

R (>= 2.10), utils, robustbase, rrcov, car (>= 2.0-0), MASS, pls

Installation

Installion of robCompositions is really easy for registered users (when the R-tools are installed). Just use

library(devtools)
install_github("robCompositions", "matthias-da")

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)

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 <- isomLRinv(mvrnorm(100, mu=c(0,2), Sigma=Sigma))

Functions in robCompositions

Name Description
cenLR Centred logratio coefficients
cancerMN malignant neoplasms cancer
int2x2 Interaction 2x2 table
ced Compositional error deviation
gemas GEMAS geochemical data set
educFM education level of father (F) and mother (M)
gjovik gjovik
instw value added, output and input for different ISIC codes and countries.
election election data
machineOperators machine operators
cenLRinv Inverse centred logratio mapping
biplot.factanal Biplot method
alcoholreg regional alcohol per capita (15+) consumption by WHO region
coord Coordinate representation of compositional tables
pcaCoDa Robust principal component analysis for compositional data
corCoDa Correlations for compositional data
manu_abs Distribution of manufacturing output
arcticLake arctic lake sediment data
daFisher Discriminant analysis by Fisher Rule.
adtestWrapper Wrapper for Anderson-Darling tests
perturbation Perturbation and powering
biplot.pcaCoDa Biplot method
bootnComp Bootstrap to find optimal number of components
balances Balance calculation
biomarker biomarker
economy economic indicators
clustCoDa Cluster analysis for compositional data
cancer hospital discharges on cancer and distribution of age
chorizonDL C-horizon of the Kola data with rounded zeros
employment2 Employment in different countries by Sex, Age, Contract, Value
clustCoDa_qmode Q-mode cluster analysis for compositional parts
employment_df Employment in different countries by gender and status.
expendituresEU mean consumption expenditures data.
expenditures synthetic household expenditures toy data set
mcad metabolomics mcad data set
coffee coffee data set
electionATbp Austrian presidential election data
phd_totals PhD students in the EU (totals)
pivotCoord Pivot coordinates and their inverse
compareMahal Compares Mahalanobis distances from two approaches
missPatterns missing or zero pattern structure.
constSum Constant sum
cubeCoord Coordinate representation of a compositional cube and of a sample of compositional cubes
gm gmean
daCoDa Linear and quadratic discriminant analysis for compositional data.
indTab Independence table
gmean_sum Geometric mean
ind2x2 Independence 2x2 compositional table
rdcm relative difference between covariance matrices
orthbasis Orthonormal basis
employment employment in different countries by gender and status.
outCoDa Outlier detection for compositional data
isic32 ISIC codes by name
ilr.2x2 ilr coordinates in 2x2 compositional tables
robCompositions-package Robust Estimation for Compositional Data.
impAll Replacement of rounded zeros and missing values.
govexp government spending
laborForce labour force by status in employment
plot.imp Plot method for objects of class imp
plot.pcaCoDa Plot method
impCoda Imputation of missing values in compositional data
intArray Interaction array
imputeBDLs EM-based replacement of rounded zeros in compositional data
imputeUDLs Imputation of values above an upper detection limit in compositional data
haplogroups haplogroups data.
impRZalr alr EM-based imputation of rounded zeros
impKNNa Imputation of missing values in compositional data using knn methods
precipitation 24-hour precipitation
print.imp Print method for objects of class imp
intTab Interaction table
lifeExpGdp life expectancy and GDP (2008) for EU-countries
tabCoord Coordinate representation of compositional tables and a sample of compositional tables
impRZilr EM-based replacement of rounded zeros in compositional data
lmCoDaX Classical and robust regression of non-compositional (real) response on compositional predictors
stats Classical estimates for tables
ternaryDiagEllipse Adds tolerance ellipses to a ternary diagram.
teachingStuff teaching stuff
pTab Propability table
payments special payments
production production splitted by nationality on enterprise level
rSDev Relative simplicial deviance
summary.imp Summary method for objects of class imp
mortality mortality and life expectancy in the EU
mortality_tab mortality table
ternaryDiagPoints Add points or lines to a given ternary diagram.
nutrients nutrient contents
unemployed unemployed of young people
nutrients_branded nutrient contents (branded)
zeroOut Detection of outliers of zero-inflated data
rSDev.test Relative simplicial deviance tests
rcodes codes for UNIDO tables
variation Robust and classical variation matrix
pfa Factor analysis for compositional data
phd PhD students in the EU
skyeLavas aphyric skye lavas data
socExp social expenditures
trondelagC regional geochemical survey of soil C in Norway
trondelagO regional geochemical survey of soil O in Norway
ternaryDiag Ternary diagram
ternaryDiagAbline Adds a line to a ternary diagram.
SDev Simplicial deviance
GDPsatis GDP satisfaction
addLRinv Inverse additive logratio mapping
adjust Adjusting for original scale
ageCatWorld child, middle and eldery population
alcohol alcohol consumptions by country and type of alcohol
adtest Anderson-Darling Normality Tests
aDist Aitchison distance
addLR Additive logratio coordinates
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Vignettes of robCompositions

Name
CoDaWork.sty
boxplot.pdf
ilr.pdf
imputation-concordance.tex
imputation-plot1.pdf
imputation-plot4.pdf
imputation.Rnw
logo.pdf
pca1.pdf
pcaOrig.pdf
plainnat.bst
plot-acomp.pdf
ref.bib
refPCS.bib
refPCSn.bib
robCompositions-overview.Rnw
ternary.pdf
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Details

Type Package
Date 2019-04-15
LinkingTo Rcpp
VignetteBuilder knitr
License GPL (>= 2)
LazyLoad yes
LazyData true
RoxygenNote 6.1.1
NeedsCompilation yes
Packaged 2019-04-15 16:33:54 UTC; teml
Repository CRAN
Date/Publication 2019-04-15 17:22:43 UTC

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