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

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

Author
Boris P. Hejblum [aut, cre], Chariff Alkhassim [aut], Francois Caron [aut]
Date of publication
2016-05-03 18:35:17
Maintainer
Boris P. Hejblum <bhejblum@hsph.harvard.edu>
License
LGPL-3 | file LICENSE
Version
0.10.1

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