Compositional Data Analysis

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Documentation for package ‘Compositional’ version 7.6

• DESCRIPTION file.

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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
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

-- 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
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