DESCRIPTION

Package: hdp
Title: Hierarchical Dirichlet Process for categorical count data
Version: 0.1.3
Authors@R: c(person("Nicola", "Roberts",
  email="nr3@sanger.ac.uk", role=c("aut", "cre")),
  person("Yee Whye", "Teh", role=c("aut", "cph"),
  comment="MATLAB and C original, http://www.stats.ox.ac.uk/~teh/research/npbayes/npbayes-r21.tgz"))
Depends:
    R(>= 3.2)
Imports:
    lsa,
    methods,
    flexclust,
    coda,
    clue,
    Matrix
LazyData: true
Description: Model categorical count data with a hierarchical Dirichlet
    Process. Includes functions to initialise a HDP with a custom tree
    structure, perform Gibbs sampling of the posterior distribution,
    and analyse the output. The underlying mathematical theory is
    described by Teh et al. (Hierarchical Dirichlet Processes,
    Journal of the American Statistical Association, 2006, 101:476). This R
    package was adapted from open source MATLAB and C code written by Yee Whye
    Teh and available here
    http://www.stats.ox.ac.uk/~teh/research/npbayes/npbayes-r21.tgz.
License: file LICENSE
URL: https://github.com/nicolaroberts/hdp
BugReports: https://github.com/nicolaroberts/hdp/issues
Suggests:
    testthat,
    SomaticCancerAlterations,
    GenomicRanges,
    Biostrings,
    RColorBrewer,
    knitr,
    rmarkdown,
    BiocStyle,
    devtools
Collate:
    'aaa-classes-input.R'
    'aaa-classes-output.R'
    'aaa-generics-input.R'
    'hdp_extract_comp_multi.R'
    'hdp_extract_comp_single.R'
    'aaa-generics-output.R'
    'cull_posterior_samples.R'
    'dp_activate.R'
    'dp_freeze.R'
    'hdp.R'
    'hdp_addconparam.R'
    'hdp_adddp.R'
    'hdp_getstate.R'
    'hdp_init.R'
    'hdp_multi_chain.R'
    'hdp_posterior.R'
    'hdp_prior_init.R'
    'hdp_quick_init.R'
    'hdp_setdata.R'
    'iterate.R'
    'plot_chain.R'
    'plot_components.R'
    'stirling.R'
    'utilities.R'
    'utilities_nr3.R'
    'zzz.R'
VignetteBuilder: knitr
RoxygenNote: 6.0.1