Compositional-package   Compositional Data Analysis
a.est                   Estimation of the value of alpha in the folded
                        model
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.test                Aitchison's test for two mean vectors and/or
                        covariance matrices
aitdist                 The alpha-IT-distance
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
alfa                    The alpha-transformation
alfa.contour            Contour plot of the alpha multivariate normal
                        in S^2
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.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
alfainv                 Inverse of the alpha-transformation
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
ascls                   The alpha-SCLS model for compositional
                        responses and predictors
atflr                   The alpha-TFLR model for compositional
                        responses and predictors
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
colbeta.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
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
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
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
esov                    The ESOV-distance
esov.mds                Principal coordinate analysis using the
                        Jensen-Shannon divergence
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
gendiri.contour         Contour plot of the generalised Dirichlet
                        distribution in S^2
glm.pcr                 Principal component generalised linear models
green                   Greenacre's power transformation
hd.meantest2            Two-sample test of high-dimensional means for
                        compositional data
helm                    The Helmert sub-matrix
hotel2T2                Hotelling's multivariate version of the 2
                        sample t-test for Euclidean data
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
james                   James multivariate version of the t-test
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
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
logpca                  Principal component analysis
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
multivreg               Multivariate linear regression
multivt                 MLE for the multivariate t distribution
ols.compreg             Non linear least squares regression for
                        compositional data
ols.prop.reg            Distance based regression models for
                        proportions
pcc                     Proportionality correlation coefficient matrix
pcr.tune                Tuning the principal components with GLMs
perturbation            Perturbation operation
pivot                   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
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
rmixcomp                Simulation of compositional data from Gaussian
                        mixture models
rmixdiri                Simulation of compositional data from mixtures
                        of Dirichlet distributions
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
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
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
zad.est                 MLE of the zero adjusted Dirichlet distribution
zadr                    Zero adjusted Dirichlet regression
zeroreplace             Non-parametric zero replacement strategies
