Compositional Data Analysis


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Documentation for package ‘Compositional’ version 6.9

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A B C D E F G H I J K L M O P R S T U Z

Compositional-package Compositional Data Analysis

-- A --

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.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.reg2 Regression with compositional data using the alpha-transformation
alfa.reg3 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
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
alrinv The additive log-ratio transformation and its inverse
ascls The alpha-SCLS model for compositional responses and predictors
atflr The alpha-TFLR model for compositional responses and predictors

-- B --

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

-- C --

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
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.tflr Cross validation for the TFLR model

-- D --

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

-- E --

es The ESOV-distance
esov The ESOV-distance
esov.mds Principal coordinate analysis using the Jensen-Shannon divergence
esova The ESOV-distance

-- F --

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

-- G --

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

-- H --

hd.meantest2 Two-sample test of high-dimensional means for compositional data
helling.prop.reg Distance based regression models for proportions
helm The Helmert sub-matrix
hsecant01.est MLE of distributions defined in the (0, 1) interval

-- I --

ibeta.est MLE of distributions defined in the (0, 1) interval
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

-- J --

js.compreg Divergence based regression for compositional data

-- K --

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

-- L --

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
logitnorm.est MLE of distributions defined in the (0, 1) interval
logpca Principal component analysis

-- M --

makefolds Generate random folds for cross-validation
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

-- O --

ols.compreg Non linear least squares regression for compositional data
ols.prop.reg Distance based regression models for proportions

-- P --

pcc Proportionality correlation coefficient matrix
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

-- R --

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
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

-- S --

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
symkl.compreg Divergence based regression for compositional data

-- T --

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
tv.compreg Divergence based regression for compositional data

-- U --

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
unitweibull.est MLE of distributions defined in the (0, 1) interval

-- Z --

zad.est MLE of the zero adjusted Dirichlet distribution
zadr Zero adjusted Dirichlet regression
zadr2 Zero adjusted Dirichlet regression
zeroreplace Non-parametric zero replacement strategies
zilogitnorm.est MLE of distributions defined in the (0, 1) interval