# Compositional Data Analysis

## Documentation for package ‘Compositional’ version 8.1

- DESCRIPTION file.

## Help Pages

A B C D E F G H I J K L M O P R S T U Z

Compositional-package | Compositional Data Analysis

## -- A --

a.est | Estimation of the value of alpha in the folded model
a.mle | MLE of the folded model for a given value of alpha
acor | alpha-generalised correlations between two compositional datasets
acor.tune | Tuning of the alpha-generalised correlations between two compositional datasets
aeqdist.etest | Energy test of equality of distributions using the alpha-transformation
ait | The alpha-IT transformation
ait.knn | The k-NN algorithm for compositional data
ait.test | Aitchison's test for two mean vectors and/or covariance matrices
aitdist | The alpha-IT-distance
aitdista | The alpha-IT-distance
aitknn.tune | Tuning of the k-NN algorithm for compositional data
akern.reg | The alpha-kernel regression with compositional response data
akernreg.tune | cross-validation for the alpha-kernel regression with compositional response data
aknn.reg | The alpha-k-NN regression for compositional response data
aknnreg.tune | cross-validation for the alpha-k-NN regression with compositional response data
alef | The alpha-transformation
alfa | The alpha-transformation
alfa.contour | Contour plot of the alpha multivariate normal in S^2
alfa.fda | Regularised and flexible discriminant analysis for compositional data using the alpha-transformation
alfa.knn | The k-NN algorithm for compositional data
alfa.knn.reg | The alpha-k-NN regression with compositional predictor variables
alfa.lasso | LASSO with compositional predictors using the alpha-transformation
alfa.mds | Principal coordinate analysis using the alpha-distance
alfa.mix.norm | Gaussian mixture models for compositional data using the alpha-transformation
alfa.nb | Naive Bayes classifiers for compositional data using the alpha-transformation
alfa.pca | Principal component analysis using the alpha-transformation
alfa.pcr | Multivariate or univariate regression with compositional data in the covariates side using the alpha-transformation
alfa.pprcomp | Projection pursuit regression with compositional predictor variables using the alpha-transformation
alfa.profile | Estimation of the value of alpha via the alfa profile log-likelihood
alfa.rda | Regularised and flexible discriminant analysis for compositional data using the alpha-transformation
alfa.reg | Regression with compositional data using the alpha-transformation
alfa.reg2 | Regression with compositional data using the alpha-transformation
alfa.reg3 | Regression with compositional data using the alpha-transformation
alfa.ridge | Ridge regression with compositional data in the covariates side using the alpha-transformation
alfa.tune | Fast estimation of the value of alpha
alfadist | The alpha-distance
alfadista | The alpha-distance
alfafda.tune | cross-validation for the regularised and flexible discriminant analysis with compositional data using the alpha-transformation
alfainv | Inverse of the alpha-transformation
alfaknn.tune | Tuning of the k-NN algorithm for compositional data
alfaknnreg.tune | cross-validation for the alpha-k-NN regression with compositional predictor variables
alfalasso.tune | Cross-validation for LASSO with compositional predictors using the alpha-transformation
alfanb.tune | Cross-validation for the naive Bayes classifiers for compositional data using the alpha-transformation
alfann | The k-nearest neighbours using the alpha-distance
alfapcr.tune | Tuning the number of PCs in the PCR with compositional data using the alpha-transformation
alfapprcomp.tune | Tuning of the projection pursuit regression with compositional predictor variables using the alpha-transformation
alfarda.tune | cross-validation for the regularised and flexible discriminant analysis with compositional data using the alpha-transformation
alfareg.tune | Tuning the value of alpha in the alpha-regression
alfaridge.plot | Ridge regression plot
alfaridge.tune | cross-validation for the ridge regression with compositional data as predictor using the alpha-transformation
alpha.mle | MLE of the folded model for a given value of alpha
alr | The additive log-ratio transformation and its inverse
alr.all | All pairwise additive log-ratio transformations
alrinv | The additive log-ratio transformation and its inverse
ascls | The alpha-SCLS model for compositional responses and predictors
atflr | The alpha-TFLR model for compositional responses and predictors

## -- B --

bc | The Box-Cox transformation applied to ratios of components
beta.est | MLE of distributions defined in the (0, 1) interval
beta.reg | Beta regression
bic.alfamixnorm | Mixture model selection with the alpha-transformation using BIC
bic.mixcompnorm | Mixture model selection via BIC
bivt.contour | Contour plot of the t distribution in S^2

## -- C --

colbeta.est | Column-wise MLE of some univariate distributions
collogitnorm.est | Column-wise MLE of some univariate distributions
colunitweibull.est | Column-wise MLE of some univariate distributions
colzilogitnorm.est | Column-wise MLE of some univariate distributions
comp.den | Estimating location and scatter parameters for compositional data
comp.kern | Multivariate kernel density estimation for compositional data
comp.kerncontour | Contour plot of the kernel density estimate in S^2
comp.knn | The k-NN algorithm for compositional data
comp.nb | Naive Bayes classifiers for compositional data
comp.ppr | Projection pursuit regression for compositional data
comp.reg | Multivariate regression with compositional data
comp.test | Hypothesis testing for two or more compositional mean vectors
compknn.tune | Tuning of the k-NN algorithm for compositional data
compnorm.contour | Contour plot of the normal distribution in S^2
compppr.tune | Tuning of the projection pursuit regression for compositional data
cv.ascls | Cross-validation for the alpha-SCLS model
cv.atflr | Cross-validation for the alpha-TFLR model
cv.comp.reg | cross-validation for some compositional regression models
cv.compnb | Cross-validation for the naive Bayes classifiers for compositional data
cv.dda | Cross-validation for the Dirichlet discriminant analysis
cv.lasso.compreg | Cross-validation for the LASSO log-ratio regression with compositional response
cv.lasso.klcompreg | Cross-validation for the LASSO Kullback-Leibler divergence based regression
cv.scls | Cross-validation for the SCLS model
cv.scrq | Cross-validation for the SCRQ model
cv.tflr | cross-validation for the TFLR model

## -- D --

dda | Dirichlet discriminant analysis
ddiri | Density values of a Dirichlet distribution
dfd | Density of the Flexible Dirichlet distribution
dfolded | Density of the folded model normal distribution
dgendiri | Density values of a generalised Dirichlet distribution
diri.contour | Contour plot of the Dirichlet distribution in S^2
diri.est | MLE of the a Dirichlet distribution
diri.nr | MLE of the Dirichlet distribution via Newton-Rapshon
diri.reg | Dirichlet regression
diri.reg2 | Dirichlet regression
diri.reg3 | Dirichlet regression
diria0.est | MLE of the Dirichlet distribution assuming a common parameter
dirimean.test | Log-likelihood ratio test for a Dirichlet mean vector
divergence | Divergence matrix of compositional data
dmix.compnorm | Simulation of compositional data from Gaussian mixture models
dmixdiri | Density values of a mixture of Dirichlet distributions
dptest | Projections based test for distributional equality of two groups

## -- E --

eel.test2 | Exponential empirical likelihood hypothesis testing for two mean vectors
el.test2 | Empirical likelihood hypothesis testing for two mean vectors
eqdist.etest | Energy test of equality of two distributions
es | The ESOV-distance
esov | The ESOV-distance
esov.mds | Principal coordinate analysis using the Jensen-Shannon divergence
esova | The ESOV-distance

## -- F --

fd.contour | Contour plot of the Flexible Dirichlet distribution in S^2
folded.contour | Contour plot of the alpha-folded model in S^2
fp | The folded power transformation
frechet | The Frechet mean for compositional data
frechet2 | Helper Frechet mean for compositional data

## -- G --

gendiri.contour | Contour plot of the generalised Dirichlet distribution in S^2
glm.pcr | Principal component generalised linear models
glmpcr.tune | Tuning the principal components with GLMs
green | Greenacre's power transformation

## -- H --

hd.meantest2 | Two-sample test of high-dimensional means for compositional data
helling.prop.reg | Distance based regression models for proportions
hellinger.compreg | Divergence based regression for compositional data
helm | The Helmert sub-matrix
hotel2T2 | Hotelling's multivariate version of the 2 sample t-test for Euclidean data
hsecant01.est | MLE of distributions defined in the (0, 1) interval

## -- I --

ibeta.est | MLE of distributions defined in the (0, 1) interval
ice.akernreg | ICE plot for the alpha-kernel regression
ice.aknnreg | ICE plot for the alpha-k-NN regression
ice.kernreg | ICE plot for univariate kernel regression
ice.pprcomp | ICE plot for projection pursuit regression with compositional predictor variables

## -- J --

james | James multivariate version of the t-test
js.compreg | Divergence based regression for compositional data

## -- K --

kern.reg | Kernel regression with a numerical response vector or matrix
kernreg.tune | cross-validation for the kernel regression with Euclidean response data
kl.alfapcr | Divergence based regression for compositional data with compositional data in the covariates side using the alpha-transformation
kl.compreg | Divergence based regression for compositional data
kl.compreg2 | Helper functions for the Kullback-Leibler regression
kl.diri | Kullback-Leibler divergence and Bhattacharyya distance between two Dirichlet distributions
kl.diri.normal | Minimized Kullback-Leibler divergence between Dirichlet and logistic normal
klalfapcr.tune | Tuning of the divergence based regression for compositional data with compositional data in the covariates side using the alpha-transformation
klcompreg.boot | Helper functions for the Kullback-Leibler regression
kumar.est | MLE of distributions defined in the (0, 1) interval

## -- L --

lasso.compreg | LASSO log-ratio regression with compositional response
lasso.klcompreg | LASSO Kullback-Leibler divergence based regression
lassocoef.plot | Plot of the LASSO coefficients
lc.glm | Log-contrast GLMS with compositional predictor variables
lc.glm2 | Log-contrast logistic or Poisson regression with with multiple compositional predictors
lc.reg | Log-contrast regression with compositional predictor variables
lc.reg2 | Log-contrast regression with multiple compositional predictors
lc.rq | Log-contrast quantile regression with compositional predictor variables
lc.rq2 | Log-contrast quantile regression with with multiple compositional predictors
lcglm.aov | ANOVA for the log-contrast GLM versus the uncostrained GLM
lcreg.aov | ANOVA for the log-contrast regression versus the uncostrained linear regression
logitnorm.est | MLE of distributions defined in the (0, 1) interval
logpca | Principal component analysis

## -- M --

makefolds | Generate random folds for cross-validation
maov | Multivariate analysis of variance assuming equality of the covariance matrices
maovjames | Multivariate analysis of variance (James test)
mix.compnorm | Gaussian mixture models for compositional data
mix.compnorm.contour | Contour plot of the Gaussian mixture model in S^2
mixdiri.contour | Contour plot of mixtures of Dirichlet distributions in S^2
mkde | Multivariate kernel density estimation
mkde.tune | Tuning of the bandwidth h of the kernel using the maximum likelihood cross-validation
mlr | The multiplicative log-ratio transformation and its inverse
mlrinv | The multiplicative log-ratio transformation and its inverse
multinompcr.tune | Tuning the principal components with GLMs
multivreg | Multivariate linear regression
multivt | MLE for the multivariate t distribution

## -- O --

ols.compreg | Non linear least squares regression for compositional data
ols.prop.reg | Distance based regression models for proportions

## -- P --

pcc | Proportionality correlation coefficient matrix
pcr.tune | Tuning the principal components with GLMs
perturbation | Perturbation operation
pivot | The pivot coordinate transformation and its inverse
pivotinv | The pivot coordinate transformation and its inverse
pow | Power operation
pprcomp | Projection pursuit regression with compositional predictor variables
pprcomp.tune | Tuning of the projection pursuit regression with compositional predictor variables
probout | Estimation of the probability left outside the simplex when using the alpha-transformation
propreg | Quasi binomial regression for proportions
propregs | Quasi binomial regression for proportions
pyramid | Pyramid diagram

## -- R --

rbeta1 | Random values generation from some univariate distributions defined on the (0,1) interval
rcompnorm | Multivariate normal random values simulation on the simplex
rcompsn | Multivariate skew normal random values simulation on the simplex
rcompt | Multivariate t random values simulation on the simplex
rda | Regularised discriminant analysis for Euclidean data
rda.tune | Tuning the parameters of the regularised discriminant analysis
rdiri | Dirichlet random values simulation
read.fbm | Read a file as a Filebacked Big Matrix
rfd | Simulation of compositional data from the Flexible Dirichlet distribution
rfolded | Simulation of compositional data from the folded model normal distribution
rgendiri | Generalised Dirichlet random values simulation
ridge.plot | Ridge regression plot
ridge.reg | Ridge regression
ridge.tune | cross-validation for the ridge regression
rlogitnorm | Random values generation from some univariate distributions defined on the (0,1) interval
rmixcomp | Simulation of compositional data from Gaussian mixture models
rmixdiri | Simulation of compositional data from mixtures of Dirichlet distributions
runitweibull | Random values generation from some univariate distributions defined on the (0,1) interval

## -- S --

scls | Simplicial constrained linear least squares (SCLS) for compositional responses and predictors
scls.betest | Permutation test for the matrix of coefficients in the SCLS model
scls.indeptest | Permutation linear independence test in the SCLS model
scls2 | The SCLS model with multiple compositional predictors
scrq | Simplicial constrained median regression for compositional responses and predictors
skewnorm.contour | Contour plot of the skew skew-normal distribution in S^2
spatmed.reg | Spatial median regression
sym.test | Log-likelihood ratio test for a symmetric Dirichlet distribution
symkl.compreg | Divergence based regression for compositional data

## -- T --

ternary | Ternary diagram
ternary.coef | Ternary diagram with the coefficients of the simplicial-simplicial regression models
ternary.coefcr | Ternary diagram with confidence region for the matrix of coefficients of the SCLS or the TFLR model
ternary.mcr | Ternary diagram with confidence region for the mean
ternary.reg | Ternary diagram of regression models
tflr | Transformation-free linear regression (TFLR) for compositional responses and predictors
tflr.betest | Permutation test for the matrix of coefficients in the TFLR model
tflr.indeptest | Permutation linear independence test in the TFLR model
tflr.irls | Transformation-free linear regression (TFLR) for compositional responses and predictors
tflr2 | The TFLR model with multiple compositional predictors
totvar | Total variability
tv.compreg | Divergence based regression for compositional data

## -- U --

ulc.glm | Unconstrained GLMs with compositional predictor variables
ulc.glm2 | Unconstrained logistic or Poisson regression with multiple compositional predictors
ulc.reg | Unconstrained linear regression with compositional predictor variables
ulc.reg2 | Unconstrained linear regression with multiple compositional predictors
ulc.rq | Unconstrained quantile regression with compositional predictor variables
ulc.rq2 | Unconstrained quantile regression with multiple compositional predictors
unitweib.reg | Unit-Weibull regression models for proportions
unitweibull.est | MLE of distributions defined in the (0, 1) interval

## -- Z --

zad.est | MLE of the zero adjusted Dirichlet distribution
zadr | Zero adjusted Dirichlet regression
zadr2 | Zero adjusted Dirichlet regression
zeroreplace | Non-parametric zero replacement strategies
zilogitnorm.est | MLE of distributions defined in the (0, 1) interval