Package: robCompositions 2.4.1

robCompositions: Compositional Data Analysis

Methods for analysis of compositional data including robust methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>), count zeros (<doi:10.1177/1471082X14535524>), methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (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, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>), contingency (<doi:10.1080/03610926.2013.824980>) and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>) 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.

Authors:Matthias Templ [aut, cre], Karel Hron [aut], Peter Filzmoser [aut], Kamila Facevicova [ctb], Petra Kynclova [ctb], Jan Walach [ctb], Veronika Pintar [ctb], Jiajia Chen [ctb], Dominika Miksova [ctb], Bernhard Meindl [ctb], Alessandra Menafoglio [ctb], Alessia Di Blasi [ctb], Federico Pavone [ctb], Nikola Stefelova [ctb], Gianluca Zeni [ctb], Roman Wiederkehr [ctb]

# Install 'robCompositions' in R:

install.packages('robCompositions', repos = c('https://matthias-da.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/matthias-da/robcompositions/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

GDPsatis - GDP satisfaction
ageCatWorld - Child, middle and eldery population
alcohol - Alcohol consumptions by country and type of alcohol
alcoholreg - Regional alcohol per capita (15+) consumption by WHO region
arcticLake - Arctic lake sediment data
cancer - Hospital discharges on cancer and distribution of age
cancerMN - Malignant neoplasms cancer
chorizonDL - C-horizon of the Kola data with rounded zeros
coffee - Coffee data set
economy - Economic indicators
educFM - Education level of father
efsa - Efsa nutrition consumption
election - Election data
electionATbp - Austrian presidential election data
employment - Employment in different countries by gender and status.
employment2 - Employment in different countries by Sex, Age, Contract, Value
employment_df - Employment in different countries by gender and status.
expenditures - Synthetic household expenditures toy data set
expendituresEU - Mean consumption expenditures data.
foodbalance - Country food balances
gemas - GEMAS geochemical data set
gjovik - Gjovik
govexp - Government spending
haplogroups - Haplogroups data.
honey - Honey compositions
instw - Value added, output and input for different ISIC codes and countries.
isic32 - ISIC codes by name
laborForce - Labour force by status in employment
landcover - European land cover
lifeExpGdp - Life expectancy and GDP (2008) for EU-countries
machineOperators - Machine operators
manu_abs - Distribution of manufacturing output
mcad - Metabolomics mcad data set
mortality - Mortality and life expectancy in the EU
mortality_tab - Mortality table
nutrients - Nutrient contents
nutrients_branded - Nutrient contents
payments - Special payments
phd - PhD students in the EU
phd_totals - PhD students in the EU
precipitation - 24-hour precipitation
production - Production splitted by nationality on enterprise level
rcodes - Codes for UNIDO tables
saffron - Saffron compositions
skyeLavas - Aphyric skye lavas data
socExp - Social expenditures
teachingStuff - Teaching stuff
trondelagC - Regional geochemical survey of soil C in Norway
trondelagO - Regional geochemical survey of soil O in Norway
unemployed - Unemployed of young people

On CRAN:

89 exports 11 stars 4.23 score 127 dependencies 2 dependents 28 mentions 191 scripts 1.1k downloads

Last updated 9 months agofrom:b64cac27a6. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 11 2024
R-4.5-win-x86_64	NOTE	Sep 11 2024
R-4.5-linux-x86_64	NOTE	Sep 11 2024
R-4.4-win-x86_64	NOTE	Sep 11 2024
R-4.4-mac-x86_64	NOTE	Sep 11 2024
R-4.4-mac-aarch64	NOTE	Sep 11 2024
R-4.3-win-x86_64	NOTE	Sep 11 2024
R-4.3-mac-x86_64	NOTE	Sep 11 2024
R-4.3-mac-aarch64	NOTE	Sep 11 2024

Exports:addLR addLRinv aDist adjust adjustImputed adtest adtestWrapper balances biomarker bootnComp bpc bpcPca bpcPcaTab bpcReg bpcRegTab bpcTab bpcTabWrapper ced cenLR cenLRinv checkData clustCoDa clustCoDa_qmode compareMahal compositionalSpline constSum coord corCoDa cubeCoord cubeCoordWrapper daCoDa daFisher fcenLR fcenLRinv fcenLRp fcenLRu gm gmean gmean_sum ilr.2x2 impAll impCoda impKNNa impRZalr impRZilr imputeBDLs imputeUDLs ind2x2 indTab int2x2 intArray intTab iprod is.equivalent isomLR isomLRinv isomLRinvp isomLRp lmCoDaX missPatterns norm1 orthbasis outCoDa pcaCoDa perturbation pfa pivotCoord pivotCoordInv powering pTab rdcm rSDev rSDev.test SDev smoothSplines smoothSplinesVal stats tabCoord tabCoordWrapper ternaryDiag ternaryDiagAbline ternaryDiagEllipse ternaryDiagPoints trapzc variation weightedPivotCoord ZBsplineBasis zeroOut zeroPatterns

Dependencies:abind ash backports bit bit64 bitops boot broom broom.helpers car carData cards class cli clipr cluster colorspace cowplot cpp11 crayon cvTools data.table DEoptimR Deriv deSolve diptest doBy dplyr e1071 fansi farver fda fds flexmix FNN forcats fpc generics GGally ggfortify ggplot2 ggstats glue gridExtra gtable haven hdrcde hms isoband kernlab KernSmooth ks labeling labelled laeken lattice lifecycle lme4 lmtest locfit magrittr MASS Matrix MatrixModels mclust mgcv microbenchmark minqa modelr modeltools multicool munsell mvtnorm NADA nlme nloptr nnet numDeriv patchwork pbkrtest pcaPP perry pillar pkgconfig pls plyr prabclus pracma prettyunits progress proxy purrr quantreg R6 rainbow ranger RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 rlang robustbase robustHD rrcov scales sp SparseM stringi stringr survival tibble tidyr tidyselect truncnorm tzdb utf8 vcd vctrs VIM viridisLite vroom withr zCompositions zoo

Imputation Methods in robCompositions

Rendered fromimputation.Rnwusingknitr::knitron Sep 11 2024.

Last update: 2019-05-14
Started: 2013-11-20

Overview of the robCompostions package

Rendered fromrobCompositions-overview.Rnwusingutils::Sweaveon Sep 11 2024.

Last update: 2013-11-20
Started: 2013-11-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Robust Estimation for Compositional Data.	robCompositions-package robCompositions
Additive logratio coordinates	addLR
Inverse additive logratio mapping	addLRinv
Aitchison distance	aDist iprod
Adjusting for original scale	adjust
Anderson-Darling Normality Tests	adtest
Wrapper for Anderson-Darling tests	adtestWrapper print.adtestWrapper summary.adtestWrapper
child, middle and eldery population	ageCatWorld
alcohol consumptions by country and type of alcohol	alcohol
regional alcohol per capita (15+) consumption by WHO region	alcoholreg
arctic lake sediment data	arcticLake
Balance calculation	balances
biomarker	biomarker plot.biomarker print.biomarker summary.biomarker
Biplot method	biplot.factanal
Biplot method	biplot.pcaCoDa
Bootstrap to find optimal number of components	bootnComp
Backwards pivot coordinates and their inverse	bpc
Principal component analysis based on backwards pivot coordinates	bpcPca
Principal component analysis of compositional tables based on backwards pivot coordinates	bpcPcaTab
Classical and robust regression based on backwards pivot coordinates	bpcReg
Classical and robust regression based on backwards pivot coordinates	bpcRegTab
Backwards pivot coordinates and their inverse	bpcTab
Backwards pivot coordinates and their inverse	bpcTabWrapper
hospital discharges on cancer and distribution of age	cancer
malignant neoplasms cancer	cancerMN
Compositional error deviation	ced
Centred logratio coefficients	cenLR
Inverse centred logratio mapping	cenLRinv
C-horizon of the Kola data with rounded zeros	chorizonDL
Cluster analysis for compositional data	clustCoDa plot.clustCoDa
Q-mode cluster analysis for compositional parts	clustCoDa_qmode plot.clustCoDa_qmode
coffee data set	coffee
Compares Mahalanobis distances from two approaches	compareMahal getEstimates plot.estimates plot.mahal print.estimates
Compositional spline	compositionalSpline
Constant sum	constSum
Coordinate representation of compositional tables	coord print.coord
Correlations for compositional data	corCoDa
Coordinate representation of a compositional cube and of a sample of compositional cubes	cubeCoord cubeCoordWrapper
Linear and quadratic discriminant analysis for compositional data.	daCoDa
Discriminant analysis by Fisher Rule.	daFisher predict.daFisher print.daFisher summary.daFisher
economic indicators	economy
education level of father (F) and mother (M)	educFM
efsa nutrition consumption	efsa
election data	election
Austrian presidential election data	electionATbp
employment in different countries by gender and status.	employment
Employment in different countries by gender and status.	employment_df
Employment in different countries by Sex, Age, Contract, Value	employment2
synthetic household expenditures toy data set	expenditures
mean consumption expenditures data.	expendituresEU
fcenLR transformation (functional)	fcenLR
Inverse of fcenLR transformations (functional)	fcenLRinv
fcenLRp transformation (functional)	fcenLRp
fcenLRu transformation (functional)	fcenLRu
country food balances	foodbalance
GDP satisfaction	GDPsatis
GEMAS geochemical data set	gemas
gjovik	gjovik
gmean	gm
Geometric mean	gmean gmean_sum
government spending	govexp
haplogroups data.	haplogroups
honey compositions	honey
ilr coordinates in 2x2 compositional tables	ilr.2x2
Replacement of rounded zeros and missing values.	impAll
Imputation of missing values in compositional data	impCoda
Imputation of missing values in compositional data using knn methods	impKNNa
alr EM-based imputation of rounded zeros	impRZalr
EM-based replacement of rounded zeros in compositional data	impRZilr
EM-based replacement of rounded zeros in compositional data	adjustImputed checkData imputeBDLs print.replaced
Imputation of values above an upper detection limit in compositional data	imputeUDLs
Independence 2x2 compositional table	ind2x2
Independence table	indTab
value added, output and input for different ISIC codes and countries.	instw
Interaction 2x2 table	int2x2
Interaction array	intArray
Interaction table	intTab
equivalence class	is.equivalent
ISIC codes by name	isic32
labour force by status in employment	laborForce
European land cover	landcover
life expectancy and GDP (2008) for EU-countries	lifeExpGdp
Classical and robust regression of non-compositional (real) response on compositional and non-compositional predictors	ilrregression lmCoDaX robilrregression
machine operators	machineOperators
Distribution of manufacturing output	manu_abs
metabolomics mcad data set	mcad
missing or zero pattern structure.	missPatterns zeroPatterns
mortality and life expectancy in the EU	mortality
mortality table	mortality_tab
Normalize a vector to length 1	norm1
nutrient contents	nutrients
nutrient contents (branded)	nutrients_branded
Orthonormal basis	orthbasis
Outlier detection for compositional data	outCoDa plot.outCoDa print.outCoDa
special payments	payments
Robust principal component analysis for compositional data	pcaCoDa print.pcaCoDa summary.pcaCoDa
Perturbation and powering	perturbation powering
Factor analysis for compositional data	pfa
PhD students in the EU	phd
PhD students in the EU (totals)	phd_totals
Pivot coordinates and their inverse	isomLR isomLRinv isomLRinvp isomLRp pivotCoord pivotCoordInv
Plot method for objects of class imp	plot.imp
Plot method	plot.pcaCoDa
plot smoothSpl	plot.smoothSpl
24-hour precipitation	precipitation
Print method for objects of class imp	print.imp
production splitted by nationality on enterprise level	production
Propability table	pTab
codes for UNIDO tables	rcodes
relative difference between covariance matrices	rdcm
Relative simplicial deviance	rSDev
Relative simplicial deviance tests	rSDev.test
saffron compositions	saffron
Simplicial deviance	SDev
aphyric skye lavas data	skyeLavas
Estimate density from histogram	smoothSplines
Estimate density from histogram - for different 'alpha'	smoothSplinesVal
social expenditures	socExp
Classical estimates for tables	stats
Summary method for objects of class imp	summary.imp
Coordinate representation of compositional tables and a sample of compositional tables	tabCoord tabCoordWrapper
teaching stuff	teachingStuff
Ternary diagram	ternaryDiag
Adds a line to a ternary diagram.	ternaryDiagAbline
Adds tolerance ellipses to a ternary diagram.	ternaryDiagEllipse
Add points or lines to a given ternary diagram.	ternaryDiagLines ternaryDiagPoints
Trapezoidal formula for numerical integration	trapzc
regional geochemical survey of soil C in Norway	trondelagC
regional geochemical survey of soil O in Norway	trondelagO
unemployed of young people	unemployed
Robust and classical variation matrix	variation
Weighted pivot coordinates	weightedPivotCoord
ZB-spline basis	ZBsplineBasis
Detection of outliers of zero-inflated data	zeroOut