Compositional Data Analysis
Estimation of the value of in the folded model
-generalised correlations between two compositional datasets
Tuning of the -generalised correlations between two compositio...
Energy test of equality of distributions using the -transforma...
The -IT transformation
Aitchison's test for two mean vectors and/or covariance matrices
The -IT-distance
Contour plot of the multivariate normal in
The -kernel regression with compositional response data
Cross validation for the -kernel regression with compositional...
The -k-NN regression for compositional response data
Cross validation for the -k-NN regression with compositional r...
All pairwise additive log-ratio transformations
The -k-NN regression with compositional predictor variables
LASSO with compositional predictors using the -transformation
Principal coordinate analysis using the -distance
Gaussian mixture models for compositional data using the -tran...
Naive Bayes classifiers for compositional data using the -tran...
Principal component analysis using the -transformation
Multivariate or univariate regression with compositional data in the c...
Projection pursuit regression with compositional predictor variables u...
Estimation of the value of via the alfa profile log-likelihoo...
The -transformation
Regularised and flexible discriminant analysis for compositional data ...
Regression with compositional data using the -transformation
Ridge regression with compositional data in the covariates side using ...
Fast estimation of the value of
The -distance
Inverse of the -transformation
Cross validation for the -k-NN regression with compositional p...
Cross-validation for LASSO with compositional predictors using the $al...
Cross-validation for the naive Bayes classifiers for compositional dat...
The k-nearest neighbours using the -distance
Tuning the number of PCs in the PCR with compositional data using the ...
Tuning of the projection pursuit regression with compositional predict...
Cross validation for the regularised and flexible discriminant analysi...
Tuning the value of in the -regression
Ridge regression plot
Cross validation for the ridge regression with compositional data as p...
MLE of the folded model for a given value of
The additive log-ratio transformation and its inverse
The -SCLS model for compositional responses and predictors
The -TFLR model for compositional responses and predictors
The Box-Cox transformation applied to ratios of components
MLE of distributions defined in the (0, 1) interval
Beta regression
Mixture model selection with the -transformation using BIC
Mixture model selection via BIC
Contour plot of the t distribution in
Naive Bayes classifiers for compositional data
Column-wise MLE of some univariate distributions
Estimating location and scatter parameters for compositional data
Multivariate kernel density estimation for compositional data
Contour plot of the kernel density estimate in
The k-NN algorithm for compositional data
Projection pursuit regression for compositional data
Multivariate regression with compositional data
Hypothesis testing for two or more compositional mean vectors
Tuning of the k-NN algorithm for compositional data
Contour plot of the normal distribution in
Compositional Data Analysis
Tuning of the projection pursuit regression for compositional data
Cross-validation for the -SCLS model
Cross-validation for the -TFLR model
Cross validation for some compositional regression models
Cross-validation for the naive Bayes classifiers for compositional dat...
Cross-validation for the Dirichlet discriminant analysis
Cross-validation for the LASSO log-ratio regression with compositional...
Cross-validation for the LASSO Kullback-Leibler divergence based regre...
Cross-validation for the SCLS model
Cross validation for the TFLR model
Dirichlet discriminant analysis
Density values of a Dirichlet distribution
Density of the Flexible Dirichlet distribution
Density of the folded model normal distribution
Density values of a generalised Dirichlet distribution
Contour plot of the Dirichlet distribution in
MLE of the a Dirichlet distribution
MLE of the Dirichlet distribution via Newton-Rapshon
Dirichlet regression
Log-likelihood ratio test for a Dirichlet mean vector
Divergence matrix of compositional data
Simulation of compositional data from Gaussian mixture models
Density values of a mixture of Dirichlet distributions
Projections based test for distributional equality of two groups
Principal coordinate analysis using the Jensen-Shannon divergence
The ESOV-distance
Contour plot of the Flexible Dirichlet distribution in
Contour plot of the -folded model in
The folded power transformation
The Frechet mean for compositional data
Helper Frechet mean for compositional data
Contour plot of the generalised Dirichlet distribution in
Log-contrast regression with compositional predictor variables
Principal component generalised linear models
Tuning the principal components with GLMs
Greenacre's power transformation
Two-sample test of high-dimensional means for compositional data
The Helmert sub-matrix
Log-contrast regression with multiple compositional predictors
ICE plot for the -kernel regression
ICE plot for the regression
ICE plot for univariate kernel regression
ICE plot for projection pursuit regression with compositional predicto...
Kernel regression with a numerical response vector or matrix
Generalised Dirichlet random values simulation
Cross validation for the kernel regression with Euclidean response dat...
Divergence based regression for compositional data with compositional ...
Divergence based regression for compositional data
Helper functions for the Kullback-Leibler regression
Minimized Kullback-Leibler divergence between Dirichlet and logistic n...
Kullback-Leibler divergence and Bhattacharyya distance between two Dir...
Tuning of the divergence based regression for compositional data with ...
LASSO log-ratio regression with compositional response
LASSO Kullback-Leibler divergence based regression
Plot of the LASSO coefficients
Log-contrast GLMS with compositional predictor variables
Log-contrast logistic or Poisson regression with with multiple composi...
Log-contrast quantile regression with compositional predictor variable...
Log-contrast quantile regression with with multiple compositional pred...
ANOVA for the log-contrast GLM versus the uncostrained GLM
ANOVA for the log-contrast regression versus the uncostrained linear r...
Principal component analysis
Generate random folds for cross-validation
Contour plot of the Gaussian mixture model in
Gaussian mixture models for compositional data
Contour plot of mixtures of Dirichlet distributions in
Multivariate kernel density estimation
Tuning of the bandwidth h of the kernel using the maximum likelihood c...
The multiplicative log-ratio transformation and its inverse
Multivariate linear regression
MLE for the multivariate t distribution
Non linear least squares regression for compositional data
Distance based regression models for proportions
Proportionality correlation coefficient matrix
Perturbation operation
The pivot coordinate transformation and its inverse
Power operation
Projection pursuit regression with compositional predictor variables
Tuning of the projection pursuit regression with compositional predict...
Estimation of the probability left outside the simplex when using the ...
Quasi binomial regression for proportions
Random values generation from some univariate distributions defined on...
Multivariate normal random values simulation on the simplex
Multivariate skew normal random values simulation on the simplex
Multivariate t random values simulation on the simplex
Dirichlet random values simulation
Simulation of compositional data from the Flexible Dirichlet distribut...
Simulation of compositional data from the folded model normal distribu...
Ridge regression plot
Ridge regression
Cross validation for the ridge regression
Simulation of compositional data from Gaussian mixture models
Simulation of compositional data from mixtures of Dirichlet distributi...
Permutation test for the matrix of coefficients in the SCLS model
Permutation linear independence test in the SCLS model
Simplicial constrained linear least squares (SCLS) for compositional r...
The SCLS model with multiple compositional predictors
Simplicial constrained median regression for compositional responses a...
Contour plot of the skew skew-normal distribution in
Spatial median regression
Log-likelihood ratio test for a symmetric Dirichlet distribution
Ternary diagram with the coefficients of the simplicial-simplicial reg...
Ternary diagram with confidence region for the matrix of coefficients ...
Ternary diagram with confidence region for the mean
Ternary diagram
Ternary diagram of regression models
Permutation test for the matrix of coefficients in the TFLR model
Permutation linear independence test in the TFLR model
Transformation-free linear regression (TFLR) for compositional respons...
The TFLR model with multiple compositional predictors
Total variability
Unconstrained GLMs with compositional predictor variables
Unconstrained logistic or Poisson regression with multiple composition...
Unconstrained linear regression with compositional predictor variables
Unconstrained linear regression with multiple compositional predictors
Unconstrained quantile regression with compositional predictor variabl...
Unconstrained quantile regression with multiple compositional predicto...
Unit-Weibull regression models for proportions
MLE of the zero adjusted Dirichlet distribution
Zero adjusted Dirichlet regression
Non-parametric zero replacement strategies
Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions). The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include: a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451> b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>. c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.1511.07600>. d) Tsagris M. (2015). "Regression analysis with compositional data containing zero values". Chilean Journal of Statistics, 6(2): 47--57. <https://soche.cl/chjs/volumes/06/02/Tsagris(2015).pdf>. e) Tsagris M., Preston S. and Wood A.T.A. (2016). "Improved supervised classification for compositional data using the alpha-transformation". Journal of Classification, 33(2): 243--261. <doi:10.1007/s00357-016-9207-5>. f) Tsagris M., Preston S. and Wood A.T.A. (2017). "Nonparametric hypothesis testing for equality of means on the simplex". Journal of Statistical Computation and Simulation, 87(2): 406--422. <doi:10.1080/00949655.2016.1216554>. g) Tsagris M. and Stewart C. (2018). "A Dirichlet regression model for compositional data with zeros". Lobachevskii Journal of Mathematics, 39(3): 398--412. <doi:10.1134/S1995080218030198>. h) Alenazi A. (2019). "Regression for compositional data with compositional data as predictor variables with or without zero values". Journal of Data Science, 17(1): 219--238. <doi:10.6339/JDS.201901_17(1).0010>. i) Tsagris M. and Stewart C. (2020). "A folded model for compositional data analysis". Australian and New Zealand Journal of Statistics, 62(2): 249--277. <doi:10.1111/anzs.12289>. j) Alenazi A. (2021). Alenazi, A. (2023). "A review of compositional data analysis and recent advances". Communications in Statistics--Theory and Methods, 52(16): 5535--5567. <doi:10.1080/03610926.2021.2014890>. k) Alenazi A.A. (2022). "f-divergence regression models for compositional data". Pakistan Journal of Statistics and Operation Research, 18(4): 867--882. <doi:10.18187/pjsor.v18i4.3969>. l) Tsagris M. and Stewart C. (2022). "A Review of Flexible Transformations for Modeling Compositional Data". In Advances and Innovations in Statistics and Data Science, pp. 225--234. <doi:10.1007/978-3-031-08329-7_10>. m) Tsagris M., Alenazi A. and Stewart C. (2023). "Flexible non-parametric regression models for compositional response data with zeros". Statistics and Computing, 33(106). <doi:10.1007/s11222-023-10277-5>. n) Tsagris. M. (2024). "Constrained least squares simplicial-simplicial regression". <doi:10.48550/arXiv.2403.19835>.