Compositional Data Analysis


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Documentation for package ‘Compositional’ version 5.0

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A B C D E F G H I J K L M N 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
akern.reg The alpha-kernel regression for compositional response data
akernreg.tune Cross validation for the alpha-kernel regression for compositional response data
aknn.reg The alpha-k-NN regression for compositional response data
aknnreg.tune Cross validation for the alpha-k-NN regression for 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.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
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

-- 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 --

choose.pc Choose the number of principal components via reconstruction error
comp.den Estimating location and scatter parameters 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
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

-- D --

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
diri.nr Fitting a Dirichlet distribution via Newton-Rapshon
diri.reg Dirichlet regression
diri.reg2 Dirichlet regression
dirimean.test Log-likelihood ratio test for a Dirichlet mean vector
divergence Divergence matrix of compositional data

-- E --

eel.test1 Exponential empirical likelihood for a one sample mean vector hypothesis testing
eel.test2 Exponential empirical likelihood hypothesis testing for two mean vectors
el.test1 Empirical likelihood for a one sample mean vector hypothesis testing
el.test2 Empirical likelihood hypothesis testing for two mean vectors
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
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

-- G --

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
hotel1T2 Hotelling's multivariate version of the 1 sample t-test for Euclidean data
hotel2T2 Hotelling's multivariate version of the 2 sample t-test for Euclidean data
hsecant01.est MLE of distributions defined in the (0, 1) interval

-- I --

ibeta.est MLE of distributions defined in the (0, 1) interval
ice.pprcomp ICE plot for projection pursuit regression with compositional predictor variables

-- J --

james James multivariate version of the t-test
js.compreg Divergence based regression for compositional data

-- K --

kent.contour Contour plot of the Kent distribution in S^2
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
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 logistic or Poisson regression with compositional predictor variables
lc.reg Log-contrast regression with compositional predictor variables
lc.reg2 Log-contrast regression with multiple compositional predictors
lcreg.aov ANOVA for the log-contrast regression versus the uncostrained log-contrast regression
logitnorm.est MLE of distributions defined in the (0, 1) interval
logpca Principal component analysis

-- M --

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
mixreg Zero adjusted Dirichlet regression
mkde Multivariate kernel density estimation
mkde.tune Tuning of the bandwidth h of the kernel using the maximum likelihood cross validation
multinompcr.tune Tuning the principal components with GLMs
multivreg Multivariate linear regression
multivt MLE for the multivariate t distribution

-- N --

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

-- O --

ols.compcomp Constrained linear least squares for compositional responses and predictors
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 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

-- R --

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
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

-- S --

simplex.est MLE of distributions defined in the (0, 1) interval
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.reg Ternary diagram of regression models
tflr Transformation-free linear regression for compositional responses and predictors
totvar Total variability
tv.compreg Divergence based regression for compositional data

-- U --

ulc.glm Unconstrained log-contrast logistic or Poisson regression with compositional predictor variables
ulc.reg Unconstrained log-contrast regression with compositional predictor variables
ulc.reg2 Unconstrained log-contrast 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 --

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