Compositional Data Analysis

acor | Alpha generalised correlations between two compositional... |

acor.tune | Tuning of the alpha generalised correlations between two... |

a.est | Estimation of the value of alpha in the folded model |

akern.reg | The alpha-kernel regression for compositional response data |

akernreg.tune | Cross validation for the alpha-kernel regression for... |

aknn.reg | The alpha-k-NN regression for compositional response data |

aknnreg.tune | Cross validation for the alpha-k-NN regression for... |

alfa | The alpha-transformation |

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.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.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 |

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.mixcompnorm | Mixture model selection via BIC |

bivt.contour | Contour plot of the t distribution in S^2 |

choose.pc | Choose the number of principal components via reconstruction... |

compbn | Bayesian network learning with compositional data |

comp.den | Estimating location and scatter parameters for compositional... |

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 |

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.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.klcompreg | Cross-validation for the LASSO Kullback-Leibler divergence... |

cv.olscompcomp | Cross-validation for the constrained linear least squares for... |

cv.tflr | Cross validation for the transformation-free linear... |

dda | Dirichlet discriminant analysis |

ddiri | Density values of a Dirichlet distribution |

diri.contour | Contour plot of the Dirichlet distribution in S^2 |

diri.est | Fitting a Dirichlet distribution |

dirimean.test | Log-likelihood ratio test for a Dirichlet mean vector |

diri.nr | Fitting a Dirichlet distribution via Newton-Rapshon |

diri.reg | Dirichlet regression |

divergence | Divergence matrix of compositional data |

eel.test1 | Exponential empirical likelihood for a one sample mean vector... |

eel.test2 | Exponential empirical likelihood hypothesis testing for two... |

el.test1 | Empirical likelihood for a one sample mean vector hypothesis... |

el.test2 | Empirical likelihood hypothesis testing for two mean vectors |

esov | The ESOV-distance |

fd.contour | Contour plot of the Flexible Dirichlet distribution in S^2 |

fd.density | Density of the Flexible Dirichlet distribution |

fd.est | Fitting a Flexible Dirichlet distribution |

fold.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 |

glm.pcr | Principal component generalised linear models |

glmpcr.tune | Tuning the principal components with GLMs |

green | Greenacre's power transformation |

helm | The Helmert sub-matrix |

hotel1T2 | Hotelling's multivariate version of the 1 sample t-test for... |

hotel2T2 | Hotelling's multivariate version of the 2 sample t-test for... |

james | James multivariate version of the t-test |

kent.contour | Contour plot of the Kent distribution in S^2 |

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... |

lassocoef.plot | Plot of the LASSO coefficients |

lasso.klcompreg | LASSO Kullback-Leibler divergence based regression |

lc.reg | Log-contrast regression with compositional predictor... |

logpca | Principal component analysis |

makefolds | Generate random folds for cross-validation |

maov | Multivariate analysis of variance |

maovjames | Multivariate analysis of variance (James test) |

mix.compnorm | Gaussian mixture models for compositional data |

mixnorm.contour | Contour plot of the Gaussian mixture model in S^2 |

mkde | Multivariate kernel density estimation |

mkde.tune | Tuning of the bandwidth h of the kernel using the maximum... |

multivreg | Multivariate linear regression |

multivt | MLE for the multivarite t distribution |

norm.contour | Contour plot of the normal distribution in S^2 |

ols.compcomp | Constrained linear least squares for compositional responses... |

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 |

pow | Power operation |

probout | Estimation of the probability left outside the simplex when... |

propreg | Quasi binomial regression for proportions |

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 |

rfd | Simulation of compositional data from the Flexible Dirichlet... |

rfolded | Simulation of compositional data from the folded model normal... |

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 |

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.reg | Ternary diagram of regression models |

tflr | Transformation-free linear regression for compositional... |

totvar | Total variability |

unitweib.reg | Unit-Weibull regression models for proportions |

zadr | Zero adjusted Dirichlet regression |

zeroreplace | Non parametric zero replacement strategies |

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