Fitting, Diagnostics, and Plotting Functions for 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. (2017) . 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 and conducting posterior inference on parameters of interest.

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Infinite Mixture of Infinite Factor Analysers

Written by Keefe Murphy

The IMIFA package provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametric model-based clustering of high-dimensional data, introduced by Murphy et al. (2017) \href{}{arXiv:1701.07010}. The IMIFA model assumes factor analytic covariance structures within mixture components and simultaneously achieves dimension reduction and clustering 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 and conducting posterior inference on parameters of interest.

To install the development version of the package type:

# If required install devtools:
# install.packages('devtools')

To install the latest stable official release of the package from CRAN go to R and type:


In either case, you can then explore the package with:

help(mcmc_IMIFA) # Help on the main modelling function

To read the vignette guide to using the package, type the following within R:

vignette('IMIFA', package = 'IMIFA')


Infinite Mixtures of Infinite Factor Analysers

IMIFA v1.3.1 - (5th release [patch update]: 2017-07-07)

Bug Fixes

  • Fixed bug preventing M(I)FA models from being treated as (I)FA models when range.G contains 1.
  • Fixed bug preventing get_IMIFA_results from working properly when true labels are NOT supplied.

IMIFA v1.3.0 - (4th release [minor update]: 2017-06-22)

New Features

  • Added options "constrained" & "single" to mcmc_IMIFA's uni.type argument:
    as well as being either diagonal or isotropic (UUU / UUC), uniquenesses can now further be
    constrained across clusters (UCU / UCC), with appropriate warnings, defaults, checks,
    initialisations, computation of model choice penalties, and plotting behaviour in all 4 cases.
  • mcmc_IMIFA gains the tune.zeta argument, a list of heat, lambda & target parameters, to invoke
    diminishing adaptation for tuning the uniform proposal to achieve a target acceptance rate when alpha
    is learned via Metropolis-Hastings when the Pitman-Yor Process prior is employed for the IM(I)FA models.


  • (I)FA models sped up by considering uniquenesses under 1-cluster models as "constrained" or "single",
    rather than previously "unconstrained" or "isotropic", utilising pre-computation and empty assignment.
  • Previously hidden functions improved, exported and documented with examples:
    is.cols, Ledermann, Procrustes & shift_GA.
  • is.posi_def gains make argument, merging it with previously hidden function .make_posdef:
    Thus the 'nearest' positive-(semi)definite matrix and the usual check can be returned in a single call.
  • Sped-up sampling IM(I)FA labels, esp. when 'active' G falls to 1, or the dependent slice-sampler is used: arg. removed from gumbel_max; function stands alone, now only stored log-likelihoods computed.
  • psi argument added to sim_IMIFA_data to allow supplying true uniqueness parameter values directly.

Bug Fixes

  • Used bw="SJ" everywhere density is invoked for plotting (bw="nrd0" is invoked if this fails).
  • Fixed initialisation of uniquenesses for isotropic (I)FA models.
  • Fixed parallel coordinates plot axes and labels for all isotropic uniquenesses plots.
  • Fixed adaptation for MIFA/OMIFA/IMIFA models when all clusters simultaneously have zero factors.
  • Fixed storage bug in IM(I)FA models when learn.d is TRUE but learn.alpha is FALSE.
  • Fixed density plot for discount when mutation rate is too low (i.e. too many zeros).
  • Fixed simulation of loadings matrices for empty MIFA/OMIFA/IMIFA clusters using byrow=TRUE:
    loop to simulate loadings matrices now generally faster also for all models.
  • Fixed silly error re: way in which (I)FA models are treated as 1-cluster models to ensure they run:
    Related bug fixed for OM(I)FA/IM(I)FA models when starting number of clusters is actually supplied.

IMIFA v1.2.1 - (3rd release [patch update]: 2017-05-29)


  • Posterior mean scores can now also be plotted in the form of a heat map (previously loadings only).
    load.meth argument replaced by logical in plot.Results_IMIFA.
  • mat2cols gains compare argument to yield common palettes/breaks for heat maps of multiple matrices:
    Associated plot_cols function also fixed, and now unhidden.
  • Removed certain dependencies with faster personal code: e.g. Procrustes rotation now quicker:
    IMIFA no longer depends on the corpcor, gclus, MASS, matrixcalc, or MCMCpack libraries.

Bug Fixes

  • Used par()$bg (i.e. default "white") for plotting zero-valued entries of similarity matrix.
  • Range of data for labelling in heat_legend calculated correctly.
  • mcmc_IMIFA's verbose argument now governs printing of message & cat calls, but not stop or warning.
  • Fixed storage and plotting of loadings, particularly when some but not all clusters have zero factors.
  • Added to build.

IMIFA v1.2.0 - (2nd release [minor update]: 2017-05-09)

New Features

  • Learning the Pitman-Yor discount & alpha parameters via Metropolis-Hastings now implemented.
    Plotting function's param argument gains the option discount for posterior inference.
  • Sped up simulating cluster labels from unnormalised log probabilities using the Gumbel-Max trick (Yellott, 1977):
    gumbel_max replaces earlier function to sample cluster labels and is now unhidden/exported/documented.
  • Added new plot when plot.meth=GQ for OM(I)FA/IM(I)FA models depicting trace of #s of active/non-empty clusters.
  • Added function Zsimilarity to summarise posterior clustering by the sampled labels with minimum
    squared distance to a sparse similarity matrix constructed by averaging the adjacency matrices:
    when optionally called inside get_IMIFA_results, the similarity matrix can be plotted via plot.meth="zlabels".


  • Metropolis-Hastings updates implemented for alpha when discount is non-zero, rather than usual Gibbs.
    Mutation rate monitored rather than acceptance rate for Metropolis-Hastings updates of discount parameter.
  • Fixed calculation of # 'free' parameters for aic.mcmc & bic.mcmc criteria when uniquenesses are isotropic:
    PGMM_dfree, which calculates # 'free' parameters for finite factor analytic mixture models is exported/documented.
    This function is also used to add checks on the Dirichlet hyperparameter for OM(I)FA methods.
  • DIC model selection criterion now also available for infinite factor models (previously finite only).
  • G_priorDensity now better reflects discrete nature of the density, and plots for non-zero PY discount values.
  • Posterior mean loadings heatmaps now also display a colour key legend via new function heat_legend.
  • Avoided redundant simulation of stick-breaking/mixing proportions under both types of IM(I)FA slice sampler.
  • Simulated (finite) mixing proportions w/ Gamma(alpha, 1) trick (Devroye 1986, p.594) instead of MCMCpack:rdirichlet:
    rDirichlet replaces earlier function to sample mixing proportions and is now unhidden/exported/documented.
  • Deferred setting dimnames attributes in mcmc_IMIFA to get_IMIFA_results: lower memory burden/faster simulations.
  • Jettisoned superfluous duplicate material in object outputted from get_IMIFA_results to reduce size/simplify access.
  • IMFA/IMIFA trunc.G arg, the max allowable # active clusters, defaults to range.G and # active clusters now stored.
  • Code sped up when active G=1 by not simulating labels for IM(I)FA models.
  • Reduced chance of crash by exceeding memory capacity; score.switch defaults to FALSE if # models ran is large.

Bug Fixes

  • 2nd IM(I)FA label switching move sped up/properly weighted to ensure uniform sampling of neighbouring cluster pairs.
  • Offline label switching square assignment correction now permutes properly.
  • Fixed factor score trace plots by extracting indices of stored samples using Rfast::sort_unique and rotating properly.
  • Fixed adding of rnorm columns to scores matrix during adaptation, esp. when widest loadings matrix grows/shrinks.
  • Fixed initialisation (and upper limit) of number of clusters for OM(I)FA/IM(I)FA, esp. when N < P.
  • Updates of DP/PY alpha parameter now correctly depend on current # non-empty rather than active clusters.
  • Fixed density plots for parameters with bounded support, accounting for spike at zero for discount.
  • Slightly rearranged order Gibbs updates take place, esp. to ensure means enter simulation of uniquenesses properly.
  • Edited/robustified subsetting of large objects when storing mcmc_IMIFA output.
  • Tightened controls for when certain parameters are not stored for posterior inference.
  • Edited Ledermann upper bound stop(...) for finite factor models to warning(...).
  • Geometric rather than arithmetic mean used to derive single rate hyperparameter for PPCA's isotropic uniquenesses.
  • Uniquenesses now stored correctly for all clustering methods.
  • Indices of uncertain obs. returned (get_IMIFA_results)/printed (plot.Results_IMIFA) even when zlabels not supplied.
  • Fixed behaviour of progress bar when verbose=FALSE.
  • Fixed typos and expanded/clarified help documentation/vignette.

IMIFA v1.1.0 - (1st release: 2017-02-02)

Reference manual

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1.3.1 by Keefe Murphy, 8 months ago

Report a bug at

Browse source code at

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

Documentation:   PDF Manual  

Task views: Cluster Analysis & Finite Mixture Models

GPL (>= 2) license

Imports abind, e1071, graphics, grDevices, matrixStats, mclust, mvnfast, plotrix, Rfast, slam, stats, utils, viridis

Suggests Rmpfr, gmp, knitr, methods, rmarkdown

See at CRAN