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.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 |
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 |
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 |
choose.pc |
Choose the number of principal components via reconstruction error |
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 |
compbn |
Bayesian network learning with compositional data |
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.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.olscompcomp |
Cross-validation for the constrained linear least squares for compositional responses and predictors |
cv.tflr |
Cross validation for the transformation-free linear regression for compositional responses and predictors |
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 |
kent.contour |
Contour plot of the Kent distribution in S^2 |
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 |
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 logistic or Poisson regression 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 |
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 |
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 |
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 |
pcc |
Proportionality correlation coefficient matrix |
pcr |
Principal component generalised linear models |
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 |
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 |
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 |