# Anthology of Mixture Analysis Tools

## Documentation for package ‘AntMAN’ version 1.1.0

- DESCRIPTION file.

## Help Pages

AM_clustering | Return the clustering matrix
AM_coclustering | Return the co-clustering matrix
AM_demo_mvb_poi | Returns an example of 'AM_mcmc_fit' output produced by the multivariate bernoulli model
AM_demo_mvn_poi | Returns an example of 'AM_mcmc_fit' output produced by the multivariate gaussian model
AM_demo_uvn_poi | Returns an example of 'AM_mcmc_fit' output produced by the univariate Gaussian model
AM_demo_uvp_poi | Returns an example of 'AM_mcmc_fit' output produced by the univariate Poisson model
AM_emp_bayes_uninorm | compute the hyperparameters of an Normal-Inverse-Gamma distribution using an empirical Bayes approach
AM_extract | Extract values within a 'AM_mcmc_output' object
AM_find_gamma_Delta | Given that the prior on M is a dirac delta, find the gamma hyperparameter of the weights prior to match E(K)=K*, where K* is user-specified
AM_find_gamma_NegBin | Given that the prior on M is a Negative Binomial, find the gamma hyperparameter of the weights prior to match E(K)=K*, where K* is user-specified
AM_find_gamma_Pois | Given that the prior on M is a shifted Poisson, find the gamma hyperparameter of the weights prior to match E(K)=K^{*}, where K^{*} is user-specified
AM_mcmc_configuration | S3 class AM_mcmc_configuration
AM_mcmc_fit | Performs a Gibbs sampling
AM_mcmc_output | S3 class AM_mcmc_output
AM_mcmc_parameters | MCMC Parameters
AM_mcmc_refit | Performs a Gibbs sampling reusing previous configuration
AM_mix_components_prior | S3 class AM_mix_components_prior
AM_mix_components_prior_dirac | Generate a configuration object that contains a Point mass prior
AM_mix_components_prior_negbin | Generate a configuration object for a Shifted Negative Binomial prior on the number of mixture components
AM_mix_components_prior_pois | Generate a configuration object for a Poisson prior on the number of mixture components
AM_mix_hyperparams | S3 class AM_mix_hyperparams
AM_mix_hyperparams_multiber | multivariate Bernoulli mixture hyperparameters (Latent Class Analysis)
AM_mix_hyperparams_multinorm | multivariate Normal mixture hyperparameters
AM_mix_hyperparams_uninorm | univariate Normal mixture hyperparameters
AM_mix_hyperparams_unipois | univariate Poisson mixture hyperparameters
AM_mix_weights_prior | S3 class AM_mix_weights_prior
AM_mix_weights_prior_gamma | specify a prior on the hyperparameter gamma for the Dirichlet mixture weights prior
AM_plot_chaincor | Plot the Autocorrelation function
AM_plot_density | Plot the density of variables from 'AM_mcmc_output' object
AM_plot_mvb_cluster_frequency | Visualise the cluster frequency plot for the multivariate bernoulli model
AM_plot_pairs | Plot 'AM_mcmc_output' scatterplot matrix
AM_plot_pmf | Plot the probability mass function of variables from 'AM_mcmc_output' object
AM_plot_similarity_matrix | Plot the Similarity Matrix
AM_plot_traces | Plot traces of variables from an 'AM_mcmc_output' object
AM_plot_values | Plot posterior interval estimates obtained from MCMC draws
AM_prior | S3 class AM_prior
AM_prior_K_Delta | Computes the prior on the number of clusters
AM_prior_K_NegBin | computes the prior number of clusters
AM_prior_K_Pois | Computes the prior number of clusters
AM_salso | Sequentially Allocated Latent Structure Optimisation
AntMAN | AntMAN: A package for fitting finite Bayesian Mixture models with a random number of components
brain | Teen Brain Images from the National Institutes of Health, U.S.
carcinoma | Carcinoma dataset
galaxy | Galaxy velocities dataset
plot.AM_mcmc_output | plot AM_mcmc_output
plot.AM_prior | plot AM_prior
said | Usage frequency of the word "said" in the Brown corpus
summary.AM_mcmc_configuration | summary information of the AM_mcmc_configuration object
summary.AM_mcmc_output | summary information of the AM_mcmc_output object
summary.AM_mix_components_prior | summary information of the AM_mix_components_prior object
summary.AM_mix_hyperparams | summary information of the AM_mix_hyperparams object
summary.AM_mix_weights_prior | summary information of the AM_mix_weights_prior object
summary.AM_prior | summary information of the AM_prior object