Package: AntMAN 1.1.0

Bruno Bodin

AntMAN: Anthology of Mixture Analysis Tools

Fits finite Bayesian mixture models with a random number of components. The MCMC algorithm implemented is based on point processes as proposed by Argiento and De Iorio (2019) <arxiv:1904.09733> and offers a more computationally efficient alternative to reversible jump. Different mixture kernels can be specified: univariate Gaussian, multivariate Gaussian, univariate Poisson, and multivariate Bernoulli (latent class analysis). For the parameters characterising the mixture kernel, we specify conjugate priors, with possibly user specified hyper-parameters. We allow for different choices for the prior on the number of components: shifted Poisson, negative binomial, and point masses (i.e. mixtures with fixed number of components).

Authors:Priscilla Ong [aut, edt], Raffaele Argiento [aut], Bruno Bodin [aut, cre], Maria De Iorio [aut]

AntMAN_1.1.0.tar.gz
AntMAN_1.1.0.tar.gz(r-4.5-noble)AntMAN_1.1.0.tar.gz(r-4.4-noble)
AntMAN_1.1.0.tgz(r-4.4-emscripten)AntMAN_1.1.0.tgz(r-4.3-emscripten)
AntMAN.pdf |AntMAN.html✨
AntMAN/json (API)

# Install 'AntMAN' in R:
install.packages('AntMAN', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bbodin/antman/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • brain - Teen Brain Images from the National Institutes of Health, U.S.
  • carcinoma - Carcinoma dataset
  • galaxy - Galaxy velocities dataset
  • said - Usage frequency of the word "said" in the Brown corpus

openblascppopenmp

1.00 score 4 scripts 257 downloads 38 exports 64 dependencies

Last updated 3 years agofrom:5e4f4a093e. Checks:OK: 1 NOTE: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 30 2024
R-4.5-linux-x86_64NOTEDec 30 2024

Exports:AM_clusteringAM_coclusteringAM_demo_mvb_poiAM_demo_mvn_poiAM_demo_uvn_poiAM_demo_uvp_poiAM_emp_bayes_uninormAM_extractAM_find_gamma_DeltaAM_find_gamma_NegBinAM_find_gamma_PoisAM_mcmc_fitAM_mcmc_parametersAM_mcmc_refitAM_mix_components_prior_diracAM_mix_components_prior_negbinAM_mix_components_prior_poisAM_mix_hyperparams_multiberAM_mix_hyperparams_multinormAM_mix_hyperparams_uninormAM_mix_hyperparams_unipoisAM_mix_weights_prior_gammaAM_plot_chaincorAM_plot_densityAM_plot_mvb_cluster_frequencyAM_plot_pairsAM_plot_pmfAM_plot_similarity_matrixAM_plot_tracesAM_plot_valuesAM_prior_K_DeltaAM_prior_K_NegBinAM_prior_K_PoisAM_salsoAM_sample_multibinAM_sample_multinormAM_sample_uninormAM_sample_unipois

Dependencies:abindbackportsbayesplotcheckmateclicolorspacecpp11crayondistributionaldplyrfansifarverforcatsgenericsGGallyggplot2ggridgesggstatsgluegtablehmsisobandlabelinglatticelifecyclelpSolvemagrittrMASSMatrixmatrixStatsmcclustmgcvmunsellmvtnormnlmenumDerivpatchworkpillarpkgconfigplyrposteriorprettyunitsprogresspurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRdpackreshape2rlangsalsoscalesstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Return the clustering matrixAM_clustering
Return the co-clustering matrixAM_coclustering
Returns an example of 'AM_mcmc_fit' output produced by the multivariate bernoulli modelAM_demo_mvb_poi
Returns an example of 'AM_mcmc_fit' output produced by the multivariate gaussian modelAM_demo_mvn_poi
Returns an example of 'AM_mcmc_fit' output produced by the univariate Gaussian modelAM_demo_uvn_poi
Returns an example of 'AM_mcmc_fit' output produced by the univariate Poisson modelAM_demo_uvp_poi
compute the hyperparameters of an Normal-Inverse-Gamma distribution using an empirical Bayes approachAM_emp_bayes_uninorm
Extract values within a 'AM_mcmc_output' objectAM_extract
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-specifiedAM_find_gamma_Delta
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-specifiedAM_find_gamma_NegBin
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-specifiedAM_find_gamma_Pois
S3 class AM_mcmc_configurationAM_mcmc_configuration
Performs a Gibbs samplingAM_mcmc_fit
S3 class AM_mcmc_outputAM_mcmc_output
MCMC ParametersAM_mcmc_parameters
Performs a Gibbs sampling reusing previous configurationAM_mcmc_refit
S3 class AM_mix_components_priorAM_mix_components_prior
Generate a configuration object that contains a Point mass priorAM_mix_components_prior_dirac
Generate a configuration object for a Shifted Negative Binomial prior on the number of mixture componentsAM_mix_components_prior_negbin
Generate a configuration object for a Poisson prior on the number of mixture componentsAM_mix_components_prior_pois
S3 class AM_mix_hyperparamsAM_mix_hyperparams
multivariate Bernoulli mixture hyperparameters (Latent Class Analysis)AM_mix_hyperparams_multiber
multivariate Normal mixture hyperparametersAM_mix_hyperparams_multinorm
univariate Normal mixture hyperparametersAM_mix_hyperparams_uninorm
univariate Poisson mixture hyperparametersAM_mix_hyperparams_unipois
S3 class AM_mix_weights_priorAM_mix_weights_prior
specify a prior on the hyperparameter gamma for the Dirichlet mixture weights priorAM_mix_weights_prior_gamma
Plot the Autocorrelation functionAM_plot_chaincor
Plot the density of variables from 'AM_mcmc_output' objectAM_plot_density
Visualise the cluster frequency plot for the multivariate bernoulli modelAM_plot_mvb_cluster_frequency
Plot 'AM_mcmc_output' scatterplot matrixAM_plot_pairs
Plot the probability mass function of variables from 'AM_mcmc_output' objectAM_plot_pmf
Plot the Similarity MatrixAM_plot_similarity_matrix
Plot traces of variables from an 'AM_mcmc_output' objectAM_plot_traces
Plot posterior interval estimates obtained from MCMC drawsAM_plot_values
S3 class AM_priorAM_prior
Computes the prior on the number of clustersAM_prior_K_Delta
computes the prior number of clustersAM_prior_K_NegBin
Computes the prior number of clustersAM_prior_K_Pois
Sequentially Allocated Latent Structure OptimisationAM_salso
AntMAN: A package for fitting finite Bayesian Mixture models with a random number of componentsAntMAN
Teen Brain Images from the National Institutes of Health, U.S.brain
Carcinoma datasetcarcinoma
Galaxy velocities datasetgalaxy
plot AM_mcmc_outputplot.AM_mcmc_output
plot AM_priorplot.AM_prior
Usage frequency of the word "said" in the Brown corpussaid
summary information of the AM_mcmc_configuration objectsummary.AM_mcmc_configuration
summary information of the AM_mcmc_output objectsummary.AM_mcmc_output
summary information of the AM_mix_components_prior objectsummary.AM_mix_components_prior
summary information of the AM_mix_hyperparams objectsummary.AM_mix_hyperparams
summary information of the AM_mix_weights_prior objectsummary.AM_mix_weights_prior
summary information of the AM_prior objectsummary.AM_prior