| Compositional Data Analysis | Compositional-package |
| Aitchison's test for two mean vectors and/or covariance matrices | ait.test |
| All pairwise additive log-ratio transformations | alr.all |
| alpha-generalised correlations between two compositional datasets | acor |
| ANOVA for the log-contrast GLM versus the uncostrained GLM | lcglm.aov |
| ANOVA for the log-contrast regression versus the uncostrained linear regression | lcreg.aov |
| Beta regression | beta.reg |
| Column-wise MLE of some univariate distributions | colbeta.est collogitnorm.est colunitweibull.est colzilogitnorm.est |
| Contour plot of mixtures of Dirichlet distributions in S^2 | mixdiri.contour |
| Contour plot of the alpha multivariate normal in S^2 | alfa.contour |
| Contour plot of the alpha-folded model in S^2 | folded.contour |
| Contour plot of the Dirichlet distribution in S^2 | diri.contour |
| Contour plot of the Flexible Dirichlet distribution in S^2 | fd.contour |
| Contour plot of the Gaussian mixture model in S^2 | mix.compnorm.contour |
| Contour plot of the generalised Dirichlet distribution in S^2 | gendiri.contour |
| Contour plot of the kernel density estimate in S^2 | comp.kerncontour |
| Contour plot of the normal distribution in S^2 | compnorm.contour |
| Contour plot of the skew skew-normal distribution in S^2 | skewnorm.contour |
| Contour plot of the t distribution in S^2 | bivt.contour |
| Cross validation for some compositional regression models | cv.comp.reg |
| Cross validation for the alpha-k-NN regression with compositional predictor variables | alfaknnreg.tune |
| Cross validation for the alpha-k-NN regression with compositional response data | aknnreg.tune |
| Cross validation for the alpha-kernel regression with compositional response data | akernreg.tune |
| Cross validation for the kernel regression with Euclidean response data | kernreg.tune |
| Cross validation for the regularised and flexible discriminant analysis with compositional data using the alpha-transformation | alfafda.tune alfarda.tune |
| Cross validation for the ridge regression | ridge.tune |
| Cross validation for the ridge regression with compositional data as predictor using the alpha-transformation | alfaridge.tune |
| Cross validation for the TFLR model | cv.tflr |
| Cross-validation for LASSO with compositional predictors using the alpha-transformation | alfalasso.tune |
| Cross-validation for the alpha-SCLS model | cv.ascls |
| Cross-validation for the alpha-TFLR model | cv.atflr |
| Cross-validation for the Dirichlet discriminant analysis | cv.dda |
| Cross-validation for the LASSO Kullback-Leibler divergence based regression | cv.lasso.klcompreg |
| Cross-validation for the LASSO log-ratio regression with compositional response | cv.lasso.compreg |
| Cross-validation for the naive Bayes classifiers for compositional data | cv.compnb |
| Cross-validation for the naive Bayes classifiers for compositional data using the alpha-transformation | alfanb.tune |
| Cross-validation for the SCLS model | cv.scls |
| Cross-validation for the SCRQ model | cv.scrq |
| Simulation of compositional data from Gaussian mixture models | dmix.compnorm |
| Density of the Flexible Dirichlet distribution | dfd |
| Density of the folded model normal distribution | dfolded |
| Density values of a Dirichlet distribution | ddiri |
| Density values of a generalised Dirichlet distribution | dgendiri |
| Density values of a mixture of Dirichlet distributions | dmixdiri |
| Dirichlet discriminant analysis | dda |
| Dirichlet random values simulation | rdiri |
| Dirichlet regression | diri.reg diri.reg2 diri.reg3 |
| Distance based regression models for proportions | helling.prop.reg ols.prop.reg |
| Divergence based regression for compositional data | hellinger.compreg js.compreg kl.compreg symkl.compreg tv.compreg |
| Divergence based regression for compositional data with compositional data in the covariates side using the alpha-transformation | kl.alfapcr |
| Divergence matrix of compositional data | divergence |
| Empirical likelihood hypothesis testing for two mean vectors | el.test2 |
| Energy test of equality of distributions using the alpha-transformation | aeqdist.etest |
| Estimating location and scatter parameters for compositional data | comp.den |
| Estimation of the probability left outside the simplex when using the alpha-transformation | probout |
| Estimation of the value of alpha in the folded model | a.est |
| Estimation of the value of alpha via the alfa profile log-likelihood | alfa.profile |
| Exponential empirical likelihood hypothesis testing for two mean vectors | eel.test2 |
| Fast estimation of the value of alpha | alfa.tune |
| Gaussian mixture models for compositional data | mix.compnorm |
| Gaussian mixture models for compositional data using the alpha-transformation | alfa.mix.norm |
| Generalised Dirichlet random values simulation | rgendiri |
| Generate random folds for cross-validation | makefolds |
| Greenacre's power transformation | green |
| Helper Frechet mean for compositional data | frechet2 |
| Helper functions for the Kullback-Leibler regression | kl.compreg2 klcompreg.boot |
| Hotelling's multivariate version of the 2 sample t-test for Euclidean data | hotel2T2 |
| Hypothesis testing for two or more compositional mean vectors | comp.test |
| ICE plot for projection pursuit regression with compositional predictor variables | ice.pprcomp |
| ICE plot for the alpha-k-NN regression | ice.aknnreg |
| ICE plot for the alpha-kernel regression | ice.akernreg |
| ICE plot for univariate kernel regression | ice.kernreg |
| Inverse of the alpha-transformation | alfainv |
| James multivariate version of the t-test | james |
| Kernel regression with a numerical response vector or matrix | kern.reg |
| Kullback-Leibler divergence and Bhattacharyya distance between two Dirichlet distributions | kl.diri |
| LASSO Kullback-Leibler divergence based regression | lasso.klcompreg |
| LASSO log-ratio regression with compositional response | lasso.compreg |
| LASSO with compositional predictors using the alpha-transformation | alfa.lasso |
| Log-contrast GLMS with compositional predictor variables | lc.glm |
| Log-contrast logistic or Poisson regression with with multiple compositional predictors | lc.glm2 |
| Log-contrast quantile regression with compositional predictor variables | lc.rq |
| Log-contrast quantile regression with with multiple compositional predictors | lc.rq2 |
| Log-contrast regression with compositional predictor variables | lc.reg |
| Log-contrast regression with multiple compositional predictors | lc.reg2 |
| Log-likelihood ratio test for a Dirichlet mean vector | dirimean.test |
| Log-likelihood ratio test for a symmetric Dirichlet distribution | sym.test |
| Minimized Kullback-Leibler divergence between Dirichlet and logistic normal | kl.diri.normal |
| Mixture model selection via BIC | bic.mixcompnorm |
| Mixture model selection with the alpha-transformation using BIC | bic.alfamixnorm |
| MLE for the multivariate t distribution | multivt |
| MLE of distributions defined in the (0, 1) interval | beta.est hsecant01.est ibeta.est kumar.est logitnorm.est unitweibull.est zilogitnorm.est |
| MLE of the a Dirichlet distribution | diri.est |
| MLE of the Dirichlet distribution via Newton-Rapshon | diri.nr |
| MLE of the folded model for a given value of alpha | a.mle alpha.mle |
| MLE of the zero adjusted Dirichlet distribution | zad.est |
| Multivariate analysis of variance (James test) | maovjames |
| Multivariate analysis of variance assuming equality of the covariance matrices | maov |
| Multivariate kernel density estimation | mkde |
| Multivariate kernel density estimation for compositional data | comp.kern |
| Multivariate linear regression | multivreg |
| Multivariate normal random values simulation on the simplex | rcompnorm |
| Multivariate or univariate regression with compositional data in the covariates side using the alpha-transformation | alfa.pcr |
| Multivariate regression with compositional data | comp.reg |
| Multivariate skew normal random values simulation on the simplex | rcompsn |
| Multivariate t random values simulation on the simplex | rcompt |
| Naive Bayes classifiers for compositional data | comp.nb |
| Naive Bayes classifiers for compositional data using the alpha-transformation | alfa.nb |
| Non linear least squares regression for compositional data | ols.compreg |
| Non-parametric zero replacement strategies | zeroreplace |
| Permutation linear independence test in the SCLS model | scls.indeptest |
| Permutation linear independence test in the TFLR model | tflr.indeptest |
| Permutation test for the matrix of coefficients in the SCLS model | scls.betest |
| Permutation test for the matrix of coefficients in the TFLR model | tflr.betest |
| Perturbation operation | perturbation |
| Plot of the LASSO coefficients | lassocoef.plot |
| Power operation | pow |
| Principal component analysis | logpca |
| Principal component analysis using the alpha-transformation | alfa.pca |
| Principal component generalised linear models | glm.pcr |
| Principal coordinate analysis using the alpha-distance | alfa.mds |
| Principal coordinate analysis using the Jensen-Shannon divergence | esov.mds |
| Projection pursuit regression for compositional data | comp.ppr |
| Projection pursuit regression with compositional predictor variables | pprcomp |
| Projection pursuit regression with compositional predictor variables using the alpha-transformation | alfa.pprcomp |
| Projections based test for distributional equality of two groups | dptest |
| Proportionality correlation coefficient matrix | pcc |
| Quasi binomial regression for proportions | propreg propregs |
| Random values generation from some univariate distributions defined on the (0,1) interval | rbeta1 rlogitnorm runitweibull |
| Read a file as a Filebacked Big Matrix | read.fbm |
| Regression with compositional data using the alpha-transformation | alfa.reg alfa.reg2 alfa.reg3 |
| Regularised and flexible discriminant analysis for compositional data using the alpha-transformation | alfa.fda alfa.rda |
| Regularised discriminant analysis for Euclidean data | rda |
| Ridge regression | ridge.reg |
| Ridge regression plot | ridge.plot |
| Ridge regression with compositional data in the covariates side using the alpha-transformation | alfa.ridge |
| Ridge regression plot | alfaridge.plot |
| Simplicial constrained median regression for compositional responses and predictors | scrq |
| Simulation of compositional data from Gaussian mixture models | rmixcomp |
| Simulation of compositional data from mixtures of Dirichlet distributions | rmixdiri |
| Simulation of compositional data from the Flexible Dirichlet distribution | rfd |
| Simulation of compositional data from the folded model normal distribution | rfolded |
| Spatial median regression | spatmed.reg |
| Ternary diagram | ternary |
| Ternary diagram of regression models | ternary.reg |
| Ternary diagram with confidence region for the matrix of coefficients of the SCLS or the TFLR model | ternary.coefcr |
| Ternary diagram with confidence region for the mean | ternary.mcr |
| Ternary diagram with the coefficients of the simplicial-simplicial regression models | ternary.coef |
| The additive log-ratio transformation and its inverse | alr alrinv |
| The alpha-distance | alfadist alfadista |
| The alpha-IT transformation | ait |
| The alpha-IT-distance | aitdist aitdista |
| The alpha-k-NN regression for compositional response data | aknn.reg |
| The alpha-k-NN regression with compositional predictor variables | alfa.knn.reg |
| The alpha-kernel regression with compositional response data | akern.reg |
| The alpha-SCLS model for compositional responses and predictors | ascls |
| The alpha-TFLR model for compositional responses and predictors | atflr |
| The alpha-transformation | alef alfa |
| The Box-Cox transformation applied to ratios of components | bc |
| The ESOV-distance | es esov esova |
| The folded power transformation | fp |
| The Frechet mean for compositional data | frechet |
| The Helmert sub-matrix | helm |
| The k-nearest neighbours using the alpha-distance | alfann |
| The k-NN algorithm for compositional data | ait.knn alfa.knn comp.knn |
| The multiplicative log-ratio transformation and its inverse | mlr mlrinv |
| The pivot coordinate transformation and its inverse | pivot pivotinv |
| Simplicial constrained linear least squares (SCLS) for compositional responses and predictors | scls |
| The SCLS model with multiple compositional predictors | scls2 |
| The TFLR model with multiple compositional predictors | tflr2 |
| Transformation-free linear regression (TFLR) for compositional responses and predictors | tflr |
| Total variability | totvar |
| Tuning of the alpha-generalised correlations between two compositional datasets | acor.tune |
| Tuning of the bandwidth h of the kernel using the maximum likelihood cross validation | mkde.tune |
| Tuning of the divergence based regression for compositional data with compositional data in the covariates side using the alpha-transformation | klalfapcr.tune |
| Tuning of the k-NN algorithm for compositional data | aitknn.tune alfaknn.tune compknn.tune |
| Tuning of the projection pursuit regression for compositional data | compppr.tune |
| Tuning of the projection pursuit regression with compositional predictor variables | pprcomp.tune |
| Tuning of the projection pursuit regression with compositional predictor variables using the alpha-transformation | alfapprcomp.tune |
| Tuning the number of PCs in the PCR with compositional data using the alpha-transformation | alfapcr.tune |
| Tuning the parameters of the regularised discriminant analysis | rda.tune |
| Tuning the principal components with GLMs | glmpcr.tune multinompcr.tune pcr.tune |
| Tuning the value of alpha in the alpha-regression | alfareg.tune |
| Two-sample test of high-dimensional means for compositional data | hd.meantest2 |
| Unconstrained GLMs with compositional predictor variables | ulc.glm |
| Unconstrained linear regression with compositional predictor variables | ulc.reg |
| Unconstrained linear regression with multiple compositional predictors | ulc.reg2 |
| Unconstrained logistic or Poisson regression with multiple compositional predictors | ulc.glm2 |
| Unconstrained quantile regression with compositional predictor variables | ulc.rq |
| Unconstrained quantile regression with multiple compositional predictors | ulc.rq2 |
| Unit-Weibull regression models for proportions | unitweib.reg |
| Zero adjusted Dirichlet regression | zadr zadr2 |
