NPflow: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Dirichlet process mixture of multivariate normal, skew normal or skew t-distributions modeling oriented towards flow-cytometry data pre-processing applications.

AuthorBoris P. Hejblum [aut, cre], Chariff Alkhassim [aut], Francois Caron [aut]
Date of publication2016-05-03 18:35:17
MaintainerBoris P. Hejblum <bhejblum@hsph.harvard.edu>
LicenseLGPL-3 | file LICENSE
Version0.10.1

View on CRAN

Man pages

burn.DPMMclust: Burning MCMC iterations from a Dirichlet Process Mixture...

cluster_est_binder: Point estimate of the partition for the Binder loss function

cluster_est_Fmeasure: Point estimate of the partition using the F-measure as the...

cluster_est_Mbinder_norm: Point estimate of the partition using a modified Binder loss...

cluster_est_pear: Gets a point estimate of the partition using posterior...

cytoScatter: Scatterplot of flow cytometry data

DPMGibbsN: Slice Sampling of the Dirichlet Process Mixture Model with a...

DPMGibbsN_parallel: Slice Sampling of the Dirichlet Process Mixture Model with a...

DPMGibbsN_SeqPrior: Slice Sampling of Dirichlet Process Mixture of Gaussian...

DPMGibbsSkewN: Slice Sampling of Dirichlet Process Mixture of skew normal...

DPMGibbsSkewN_parallel: Parallel Implementation of Slice Sampling of Dirichlet...

DPMGibbsSkewT: Slice Sampling of Dirichlet Process Mixture of skew...

DPMGibbsSkewT_parallel: Slice Sampling of Dirichlet Process Mixture of skew...

DPMGibbsSkewT_SeqPrior: Slice Sampling of Dirichlet Process Mixture of skew...

DPMGibbsSkewT_SeqPrior_parallel: Slice Sampling of Dirichlet Process Mixture of skew...

DPMpost: Posterior estimation for Dirichlet process mixture of...

evalClustLoss: ELoss of a partition point estimate compared to a gold...

Flimited: Compute a limited F-measure

FmeasureC: C++ implementation of the F-measure computation

FmeasureC_no0: C++ implementation of the F-measure computation without the...

Fmeasure_costC: Multiple cost computations with Fmeasure as the loss function

invwishrnd: Sample from a inverse-Wishart distribution

lgamma_mv: Multivariate log gamma function

MAP_sNiW_mmEM: EM MAP for mixture of sNiW

methods.summaryDPMMclust: Methods for a summary of a 'DPMMclust' object

MLE_gamma: MLE for Gamma distribution

MLE_NiW_mmEM: EM MLE for mixture of NiW

MLE_sNiW: MLE for sNiW distributed observations

MLE_sNiW_mmEM: EM MLE for mixture of sNiW

mmNiWpdf: multivariate Normal inverse Wishart probability density...

mmNiWpdfC: C++ implementation of multivariate Normal inverse Wishart...

mmsNiWlogpdf: Probability density function of multiple structured Normal...

mmsNiWpdfC: C++ implementation of multivariate structured Normal inverse...

mmvnpdfC: C++ implementation of multivariate Normal probability density...

mmvsnpdfC: C++ implementation of multivariate skew Normal probability...

mmvstpdfC: C++ implementation of multivariate Normal probability density...

mmvtpdfC: C++ implementation of multivariate Normal probability density...

mvnlikC: C++ implementation of multivariate Normal probability density...

mvnpdf: multivariate-Normal probability density function

mvnpdfC: C++ implementation of multivariate normal likelihood function...

mvsnlikC: C++ implementation of multivariate skew normal likelihood...

mvsnpdf: multivariate Skew-Normal probability density function

mvstlikC: C++ implementation of multivariate skew t likelihood function...

mvstpdf: multivariate skew-t probability density function

mvtpdf: multivariate Student's t-distribution probability density...

NPflow-package: Bayesian Nonparametrics for Automatic Gating of Flow...

NuMatParC: C++ implementation of similarity matrix computation using...

plot_ConvDPM: Convergence diagnostic plots

plot_DPM: Plot of a Dirichlet process mixture of gaussian distribution...

plot_DPMsn: Plot of a Dirichlet process mixture of skew normal...

plot_DPMst: Plot of a Dirichlet process mixture of skew t-distribution...

postProcess.DPMMclust: Post-processing Dirichlet Process Mixture Models results to...

priormix: Construction of an Empirical based prior

rCRP: Generating cluster data from the Chinese Restaurant Process

rNiW: Sample from a Normal inverse-Wishart distribution whose...

rNNiW: Sample from a normal inverse Wishart distribution whose...

sample_alpha: Sampler for the concentration parameter of a Dirichlet...

sampleClassC: C++ implementation of the multinomial sampling from a matrix...

similarityMat: Computes the coclustering (or similarity) matrix

similarityMatC: C++ implementation

similarityMat_nocostC: C++ implementation

summary.DPMMclust: Summarizing Dirichlet Process Mixture Models

traceEpsC: C++ implementation of residual trace computation step used...

update_SS: Return updated sufficient statistics S with new data matrix z

update_SSsn: Return updated sufficient statistics S with new data matrix z

update_SSst: Return updated sufficient statistics S for skew...

vclust2mcoclustC: C++ implementation

wishrnd: Sample from a Wishart distribution

Files in this package

NPflow
NPflow/inst
NPflow/inst/CITATION
NPflow/src
NPflow/src/Makevars
NPflow/src/mmsNiWpdfC.cpp
NPflow/src/mmvsnpdfC.cpp
NPflow/src/mmvtpdfC.cpp
NPflow/src/NuMatParC.cpp
NPflow/src/mmNiWpdfC.cpp
NPflow/src/sampleClassC.cpp
NPflow/src/mvnlikC.cpp
NPflow/src/mvnpdfC.cpp
NPflow/src/mvstlikC.cpp
NPflow/src/TraceEpsC.cpp
NPflow/src/FmeasureC.cpp
NPflow/src/mvsnlikC.cpp
NPflow/src/vclust2mcoclustC.cpp
NPflow/src/similarityMatC.cpp
NPflow/src/mmvstpdfC.cpp
NPflow/src/lgamma_mvC.h
NPflow/src/lgamma_mvC.cpp
NPflow/src/similarityMat_nocostC.cpp
NPflow/src/Makevars.win
NPflow/src/RcppExports.cpp
NPflow/src/mmvnpdfC.cpp
NPflow/NAMESPACE
NPflow/NEWS
NPflow/R
NPflow/R/cluster_est_Fmeasure.R NPflow/R/DPMGibbsSkewT_SeqPrior_parallel.R NPflow/R/DPMpost.R NPflow/R/sliceSampler_N_SeqPrior.R NPflow/R/DPMGibbsN_parallel.R NPflow/R/evalClustLoss.R NPflow/R/MLE_sNiW.R NPflow/R/SliceSampler_SkewN_parallel.R NPflow/R/sample_alpha.R NPflow/R/sliceSampler_N_parallel.R NPflow/R/MLE_gamma.R NPflow/R/MAP_sNiW_mmEM.R NPflow/R/logposterior_DPMG.R NPflow/R/SliceSampler_SkewN.R NPflow/R/plot_ConvDPM.R NPflow/R/postProcess.DPMMclust.R NPflow/R/sliceSampler_skewT_SeqPrior_parallel.R NPflow/R/DPMGibbsSkewT_parallel.R NPflow/R/cluster_est_pear.R NPflow/R/mvtpdf.R NPflow/R/sliceSampler_skewT_SeqPrior.R NPflow/R/wishrnd.R NPflow/R/sliceSampler_skewT_parallel.R NPflow/R/NPflow-package.R NPflow/R/dNNiW.R NPflow/R/rCRP.R NPflow/R/DPMGibbsSkewT_SeqPrior.R NPflow/R/update_SSsn.R NPflow/R/plot_DPM.R NPflow/R/mvstpdf.R NPflow/R/sliceSampler_N.R NPflow/R/NPflow-internal.R NPflow/R/logposterior_DPMST.R NPflow/R/summary.DPMMclust.R NPflow/R/RcppExports.R NPflow/R/DPMGibbsN.R NPflow/R/sample_scale.R NPflow/R/similarityMat.R NPflow/R/DPMGibbsN_SeqPrior.R NPflow/R/DPMGibbsSkewT.R NPflow/R/cytoScatter.R NPflow/R/Flimited.R NPflow/R/logposterior_DPMSN.R NPflow/R/MLE_sNiW_mmEM.R NPflow/R/update_SSst.R NPflow/R/invwishrnd.R NPflow/R/rNNiW.R NPflow/R/plot_DPMst.R NPflow/R/cluster_est_Mbinder_norm.R NPflow/R/plot_DPMsn.R NPflow/R/cluster_est_binder.R NPflow/R/mmNiWpdf.R NPflow/R/mvsnpdf.R NPflow/R/mvnpdf.R NPflow/R/pred.R NPflow/R/update_SS.R NPflow/R/burn.DPMM.R NPflow/R/sliceSampler_skewT.R NPflow/R/rNiW.R NPflow/R/DPMGibbsSkewN_parallel.R NPflow/R/DPMGibbsSkewN.R NPflow/R/mmsNiWlogpdf.R NPflow/R/priormix.R NPflow/R/dNiW.R
NPflow/MD5
NPflow/README
NPflow/DESCRIPTION
NPflow/man
NPflow/man/rCRP.Rd NPflow/man/mvnpdfC.Rd NPflow/man/postProcess.DPMMclust.Rd NPflow/man/FmeasureC.Rd NPflow/man/mvstlikC.Rd NPflow/man/update_SSst.Rd NPflow/man/mvsnlikC.Rd NPflow/man/evalClustLoss.Rd NPflow/man/DPMpost.Rd NPflow/man/plot_DPMst.Rd NPflow/man/cytoScatter.Rd NPflow/man/traceEpsC.Rd NPflow/man/cluster_est_pear.Rd NPflow/man/vclust2mcoclustC.Rd NPflow/man/similarityMatC.Rd NPflow/man/rNiW.Rd NPflow/man/DPMGibbsN_SeqPrior.Rd NPflow/man/DPMGibbsSkewT.Rd NPflow/man/lgamma_mv.Rd NPflow/man/burn.DPMMclust.Rd NPflow/man/MLE_sNiW.Rd NPflow/man/DPMGibbsN_parallel.Rd NPflow/man/mmvsnpdfC.Rd NPflow/man/invwishrnd.Rd NPflow/man/mmNiWpdfC.Rd NPflow/man/cluster_est_Fmeasure.Rd NPflow/man/Fmeasure_costC.Rd NPflow/man/sampleClassC.Rd NPflow/man/update_SSsn.Rd NPflow/man/DPMGibbsSkewN_parallel.Rd NPflow/man/NPflow-package.Rd NPflow/man/mvnlikC.Rd NPflow/man/DPMGibbsSkewT_SeqPrior_parallel.Rd NPflow/man/mmsNiWpdfC.Rd NPflow/man/mvnpdf.Rd NPflow/man/update_SS.Rd NPflow/man/sample_alpha.Rd NPflow/man/Flimited.Rd NPflow/man/wishrnd.Rd NPflow/man/summary.DPMMclust.Rd NPflow/man/DPMGibbsSkewT_SeqPrior.Rd NPflow/man/cluster_est_Mbinder_norm.Rd NPflow/man/DPMGibbsN.Rd NPflow/man/cluster_est_binder.Rd NPflow/man/priormix.Rd NPflow/man/DPMGibbsSkewT_parallel.Rd NPflow/man/plot_DPMsn.Rd NPflow/man/NuMatParC.Rd NPflow/man/mmNiWpdf.Rd NPflow/man/FmeasureC_no0.Rd NPflow/man/MLE_sNiW_mmEM.Rd NPflow/man/mmvtpdfC.Rd NPflow/man/similarityMat.Rd NPflow/man/MAP_sNiW_mmEM.Rd NPflow/man/mvstpdf.Rd NPflow/man/mvsnpdf.Rd NPflow/man/MLE_gamma.Rd NPflow/man/mmsNiWlogpdf.Rd NPflow/man/DPMGibbsSkewN.Rd NPflow/man/similarityMat_nocostC.Rd NPflow/man/methods.summaryDPMMclust.Rd NPflow/man/rNNiW.Rd NPflow/man/mmvnpdfC.Rd NPflow/man/mvtpdf.Rd NPflow/man/mmvstpdfC.Rd NPflow/man/plot_ConvDPM.Rd NPflow/man/MLE_NiW_mmEM.Rd NPflow/man/plot_DPM.Rd
NPflow/LICENSE

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