| acor | alpha-generalised correlations between two compositional... |
| acor.tune | Tuning of the alpha-generalised correlations between two... |
| aeqdist.etest | Energy test of equality of distributions using the... |
| a.est | Estimation of the value of alpha in the folded model |
| ait | The alpha-IT transformation |
| aitdist | The alpha-IT-distance |
| ait.test | Aitchison's test for two mean vectors and/or covariance... |
| akern.reg | The alpha-kernel regression with compositional response data |
| akernreg.tune | cross-validation for the alpha-kernel regression with... |
| aknn.reg | The alpha-k-NN regression for compositional response data |
| aknnreg.tune | cross-validation for the alpha-k-NN regression with... |
| alfa | The alpha-transformation |
| alfa.contour | Contour plot of the alpha multivariate normal in S^2 |
| alfadist | The alpha-distance |
| alfainv | Inverse of the alpha-transformation |
| alfa.knn.reg | The alpha-k-NN regression with compositional predictor... |
| alfaknnreg.tune | cross-validation for the alpha-k-NN regression with... |
| alfa.lasso | LASSO with compositional predictors using the... |
| alfalasso.tune | Cross-validation for LASSO with compositional predictors... |
| alfa.mds | Principal coordinate analysis using the alpha-distance |
| alfa.mix.norm | Gaussian mixture models for compositional data using the... |
| alfa.nb | Naive Bayes classifiers for compositional data using the... |
| alfanb.tune | Cross-validation for the naive Bayes classifiers for... |
| alfann | The k-nearest neighbours using the alpha-distance |
| alfa.pca | Principal component analysis using the alpha-transformation |
| alfa.pcr | Multivariate or univariate regression with compositional data... |
| alfapcr.tune | Tuning the number of PCs in the PCR with compositional data... |
| alfa.pprcomp | Projection pursuit regression with compositional predictor... |
| alfapprcomp.tune | Tuning of the projection pursuit regression with... |
| alfa.profile | Estimation of the value of alpha via the alfa profile... |
| alfa.rda | Regularised and flexible discriminant analysis for... |
| alfarda.tune | cross-validation for the regularised and flexible... |
| alfa.reg | Regression with compositional data using the... |
| alfareg.tune | Tuning the value of alpha in the alpha-regression |
| alfa.ridge | Ridge regression with compositional data in the covariates... |
| alfaridge.plot | Ridge regression plot |
| alfaridge.tune | cross-validation for the ridge regression with compositional... |
| alfa.tune | Fast estimation of the value of alpha |
| 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... |
| atflr | The alpha-TFLR model for compositional responses and... |
| 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.mixcompnorm | Mixture model selection via BIC |
| bivt.contour | Contour plot of the t distribution in S^2 |
| colbeta.mle | Column-wise MLE of some univariate distributions |
| comp.den | Estimating location and scatter parameters for compositional... |
| 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 |
| compknn.tune | Tuning of the k-NN algorithm for compositional data |
| comp.nb | Naive Bayes classifiers for compositional data |
| compnorm.contour | Contour plot of the normal distribution in S^2 |
| Compositional-package | Compositional Data Analysis |
| comp.ppr | Projection pursuit regression for compositional data |
| compppr.tune | Tuning of the projection pursuit regression for compositional... |
| comp.reg | Multivariate regression with compositional data |
| comp.test | Hypothesis testing for two or more compositional mean vectors |
| cv.ascls | Cross-validation for the alpha-SCLS model |
| cv.atflr | Cross-validation for the alpha-TFLR model |
| cv.compnb | Cross-validation for the naive Bayes classifiers for... |
| cv.comp.reg | cross-validation for some compositional regression models |
| cv.dda | Cross-validation for the Dirichlet discriminant analysis |
| cv.lasso.compreg | Cross-validation for the LASSO log-ratio regression with... |
| cv.lasso.klcompreg | Cross-validation for the LASSO Kullback-Leibler divergence... |
| 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 |
| dirimean.test | Log-likelihood ratio test for a Dirichlet mean vector |
| diri.nr | MLE of the Dirichlet distribution via Newton-Rapshon |
| diri.reg | Dirichlet regression |
| 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... |
| eel.test2 | Exponential empirical likelihood hypothesis testing for two... |
| 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... |
| 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 |
| glmpcr.tune | Tuning the principal components with GLMs |
| green | Greenacre's power transformation |
| hd.meantest2 | Two-sample test of high-dimensional means for compositional... |
| helm | The Helmert sub-matrix |
| hotel2T2 | Hotelling's multivariate version of the 2 sample t-test for... |
| 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... |
| 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... |
| kl.alfapcr | Divergence based regression for compositional data with... |
| klalfapcr.tune | Tuning of the divergence based regression for compositional... |
| 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... |
| kl.diri.normal | Minimized Kullback-Leibler divergence between Dirichlet and... |
| lassocoef.plot | Plot of the LASSO coefficients |
| lasso.compreg | LASSO log-ratio regression with compositional response |
| lasso.klcompreg | LASSO Kullback-Leibler divergence based regression |
| lc.glm | Log-contrast GLMS with compositional predictor variables |
| lc.glm2 | Log-contrast logistic or Poisson regression with with... |
| lcglm.aov | ANOVA for the log-contrast GLM versus the uncostrained GLM |
| lc.reg | Log-contrast regression with compositional predictor... |
| lc.reg2 | Log-contrast regression with multiple compositional... |
| lcreg.aov | ANOVA for the log-contrast regression versus the uncostrained... |
| lc.rq | Log-contrast quantile regression with compositional predictor... |
| lc.rq2 | Log-contrast quantile regression with with multiple... |
| logpca | Principal component analysis |
| makefolds | Generate random folds for cross-validation |
| maov | Multivariate analysis of variance assuming equality of the... |
| 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... |
| 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 |
| perturbation | Perturbation operation |
| pivot | The pivot coordinate transformation and its inverse |
| pow | Power operation |
| pprcomp | Projection pursuit regression with compositional predictor... |
| pprcomp.tune | Tuning of the projection pursuit regression with... |
| probout | Estimation of the probability left outside the simplex when... |
| propreg | Quasi binomial regression for proportions |
| rbeta1 | Random values generation from some univariate distributions... |
| rcompnorm | Multivariate normal random values simulation on the simplex |
| rcompsn | Multivariate skew normal random values simulation on the... |
| 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... |
| rdiri | Dirichlet random values simulation |
| read.fbm | Read a file as a Filebacked Big Matrix |
| rfd | Simulation of compositional data from the Flexible Dirichlet... |
| rfolded | Simulation of compositional data from the folded model normal... |
| 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... |
| scls | Simplicial constrained linear least squares (SCLS) for... |
| scls2 | The SCLS model with multiple compositional predictors |
| scls.betest | Permutation test for the matrix of coefficients in the SCLS... |
| scls.indeptest | Permutation linear independence test in the SCLS model |
| scrq | Simplicial constrained median regression for compositional... |
| 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... |
| ternary | Ternary diagram |
| ternary.coef | Ternary diagram with the coefficients of the... |
| ternary.coefcr | Ternary diagram with confidence region for the matrix of... |
| ternary.mcr | Ternary diagram with confidence region for the mean |
| ternary.reg | Ternary diagram of regression models |
| tflr | Transformation-free linear regression (TFLR) for... |
| tflr2 | The TFLR model with multiple compositional predictors |
| tflr.betest | Permutation test for the matrix of coefficients in the TFLR... |
| tflr.indeptest | Permutation linear independence test in the TFLR model |
| totvar | Total variability |
| ulc.glm | Unconstrained GLMs with compositional predictor variables |
| ulc.glm2 | Unconstrained logistic or Poisson regression with multiple... |
| ulc.reg | Unconstrained linear regression with compositional predictor... |
| ulc.reg2 | Unconstrained linear regression with multiple compositional... |
| ulc.rq | Unconstrained quantile regression with compositional... |
| ulc.rq2 | Unconstrained quantile regression with multiple compositional... |
| 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 |
