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

Functions

burn.DPMMclust Man page
cluster_est_binder Man page
cluster_est_Fmeasure Man page
cluster_est_Mbinder_norm Man page
cluster_est_pear Man page
cytoScatter Man page
DPMGibbsN Man page
DPMGibbsN_parallel Man page
DPMGibbsN_SeqPrior Man page
DPMGibbsSkewN Man page
DPMGibbsSkewN_parallel Man page
DPMGibbsSkewT Man page
DPMGibbsSkewT_parallel Man page
DPMGibbsSkewT_SeqPrior Man page
DPMGibbsSkewT_SeqPrior_parallel Man page
DPMpost Man page
evalClustLoss Man page
Flimited Man page
FmeasureC Man page
FmeasureC_no0 Man page
Fmeasure_costC Man page
invwishrnd Man page
lgamma_mv Man page
MAP_sNiW_mmEM Man page
MAP_sNiW_mmEM_vague Man page
MAP_sNiW_mmEM_weighted Man page
MLE_gamma Man page
MLE_NiW_mmEM Man page
MLE_sNiW Man page
MLE_sNiW_mmEM Man page
mmNiWpdf Man page
mmNiWpdfC Man page
mmsNiWlogpdf Man page
mmsNiWpdfC Man page
mmvnpdfC Man page
mmvsnpdfC Man page
mmvstpdfC Man page
mmvtpdfC Man page
mvnlikC Man page
mvnpdf Man page
mvnpdfC Man page
mvsnlikC Man page
mvsnpdf Man page
mvstlikC Man page
mvstpdf Man page
mvtpdf Man page
NPflow Man page
NPflow-package Man page
NuMatParC Man page
plot_ConvDPM Man page
plot_DPM Man page
plot_DPMsn Man page
plot_DPMst Man page
plot.summaryDPMMclust Man page
postProcess.DPMMclust Man page
print.summaryDPMMclust Man page
priormix Man page
rCRP Man page
rNiW Man page
rNNiW Man page
sample_alpha Man page
sampleClassC Man page
similarityMat Man page
similarityMatC Man page
similarityMat_nocostC Man page
summaryDPMMclust Man page
summary.DPMMclust Man page
traceEpsC Man page
update_SS Man page
update_SSsn Man page
update_SSst Man page
vclust2mcoclustC Man page
wishrnd Man page

Files

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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