Package: IMIFA 2.2.0

IMIFA: Infinite Mixtures of Infinite Factor Analysers and Related Models

Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2020) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.

Authors:Keefe Murphy [aut, cre], Cinzia Viroli [ctb], Isobel Claire Gormley [ctb]

IMIFA_2.2.0.tar.gz
IMIFA_2.2.0.zip(r-4.5)IMIFA_2.2.0.zip(r-4.4)IMIFA_2.2.0.zip(r-4.3)
IMIFA_2.2.0.tgz(r-4.4-any)IMIFA_2.2.0.tgz(r-4.3-any)
IMIFA_2.2.0.tar.gz(r-4.5-noble)IMIFA_2.2.0.tar.gz(r-4.4-noble)
IMIFA_2.2.0.tgz(r-4.4-emscripten)IMIFA_2.2.0.tgz(r-4.3-emscripten)
IMIFA.pdf |IMIFA.html
IMIFA/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/keefe-murphy/imifa/issues

Datasets:
  • USPSdigits - USPS handwritten digits
  • coffee - Chemical composition of Arabica and Robusta coffee samples
  • olive - Fatty acid composition of Italian olive oils

On CRAN:

bayesian-nonparametricsdimension-reductionfactor-analysisgaussian-mixture-modelmodel-based-clustering

5.29 score 7 stars 56 scripts 584 downloads 34 exports 12 dependencies

Last updated 12 months agofrom:bb2611691c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:bnpControlexp_ltrgammaG_calibrateG_expectedG_priorDensityG_varianceget_IMIFA_resultsgumbel_maxheat_legendIMIFA_newsis.colsis.posi_defLedermannmat2colsmcmc_IMIFAMGP_checkmgpControlmixfaControlpareto_scalePGMM_dfreeplot_colspost_conf_matProcrustespsi_hyperrDirichletrltrgammascores_MAPshift_GAshow_digitshow_IMIFA_digitsim_IMIFA_datasim_IMIFA_modelstoreControlZsimilarity

Dependencies:BHmatrixStatsmclustmvnfastRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRfastslamviridisLite

IMIFA: Infinite Mixtures of Infinite Factor Analysers and Related Models

Rendered fromIMIFA.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-12-12
Started: 2017-01-30

Readme and manuals

Help Manual

Help pageTopics
IMIFA: Infinite Mixtures of Infinite Factor Analysers and Related ModelsIMIFA-package IMIFA
Control settings for the Bayesian Nonparametric priors for infinite mixture models (or shrinkage priors for overfitted mixtures)bnpControl
Chemical composition of Arabica and Robusta coffee samplescoffee
1st & 2nd Moments of the Pitman-Yor / Dirichlet ProcessesG_calibrate G_expected G_moments G_variance
Plot Pitman-Yor / Dirichlet Process PriorsG_priorDensity
Extract results, conduct posterior inference and compute performance metrics for MCMC samples of models from the IMIFA familyget_IMIFA_results print.Results_IMIFA summary.Results_IMIFA
Simulate Cluster Labels from Unnormalised Log-Probabilities using the Gumbel-Max Trickgumbel_max
Add a colour key legend to heatmap plotsheat_legend
Show the NEWS fileIMIFA_news
Check for Valid Coloursis.cols
Check Positive-(Semi)definiteness of a matrixis.posi_def
Ledermann BoundLedermann
Left Truncated Gamma Distributionsexp_ltrgamma ltrgamma rltrgamma
Convert a numeric matrix to coloursmat2cols
Adaptive Gibbs Sampler for Nonparametric Model-based Clustering using models from the IMIFA familymcmc_IMIFA print.IMIFA summary.IMIFA
Check the validity of Multiplicative Gamma Process (MGP) hyperparametersMGP_check
Control settings for the MGP prior and AGS for infinite factor modelsmgpControl
Control settings for the IMIFA family of factor analytic mixturesmixfaControl
Fatty acid composition of Italian olive oilsolive
Pareto Scalingpareto_scale
Estimate the Number of Free Parameters in Finite Factor Analytic Mixture Models (PGMM)PGMM_dfree
Plots a matrix of coloursplot_cols
Plotting output and parameters of inferential interest for IMIFA and related modelsplot.Results_IMIFA
Posterior Confusion Matrixpost_conf_mat
Procrustes TransformationProcrustes
Find sensible inverse gamma hyperparameters for variance/uniqueness parameterspsi_hyper
Simulate Mixing Proportions from a Dirichlet DistributionrDirichlet
Decompose factor scores by clusterscores_MAP
Moment Matching Parameters of Shifted Gamma Distributionsshift_GA
Show image of grayscale gridshow_digit
Plot the posterior mean imageshow_IMIFA_digit
Simulate Data from a Mixture of Factor Analysers Structuresim_IMIFA sim_IMIFA_data sim_IMIFA_model
Set storage values for use with the IMIFA family of modelsstoreControl
USPS handwritten digitsUSPSdigits
Summarise MCMC samples of clustering labels with a similarity matrix and find the 'average' clusteringZsimilarity