Package: NPflow 0.13.5

Boris P Hejblum

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 preprocessing applications. Method is detailed in: Hejblum, Alkhassimn, Gottardo, Caron & Thiebaut (2019) <doi:10.1214/18-AOAS1209>.

Authors:Boris P Hejblum [aut, cre], Chariff Alkhassim [aut], Francois Caron [aut]

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NEWS

# Install 'NPflow' in R:
install.packages('NPflow', repos = c('https://sistm.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sistm/npflow/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

64 exports 4 stars 1.40 score 64 dependencies 1 dependents 47 scripts 288 downloads

Last updated 8 months agofrom:c04585a4b5. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-win-x86_64OKSep 12 2024
R-4.5-linux-x86_64OKSep 12 2024
R-4.4-win-x86_64OKSep 12 2024
R-4.4-mac-x86_64OKSep 12 2024
R-4.4-mac-aarch64OKSep 12 2024
R-4.3-win-x86_64OKSep 12 2024
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Exports:burn.DPMMclustcluster_est_bindercluster_est_Fmeasurecluster_est_Mbinder_normcluster_est_pearcytoScatterDPMGibbsNDPMGibbsN_parallelDPMGibbsN_SeqPriorDPMGibbsSkewNDPMGibbsSkewN_parallelDPMGibbsSkewTDPMGibbsSkewT_parallelDPMGibbsSkewT_SeqPriorDPMGibbsSkewT_SeqPrior_parallelDPMpostevalClustLossFlimitedFmeasure_costCFmeasureCFmeasureC_no0invwishrndlgamma_mvMAP_sNiW_mmEMMAP_sNiW_mmEM_vagueMAP_sNiW_mmEM_weightedMLE_gammaMLE_NiW_mmEMMLE_sNiWMLE_sNiW_mmEMmmNiWpdfmmNiWpdfCmmsNiWlogpdfmmsNiWpdfCmmvnpdfCmmvsnpdfCmmvstpdfCmmvtpdfCmvnpdfmvnpdfCmvsnpdfmvstpdfmvtpdfNuMatParCplot_ConvDPMplot_DPMplot_DPMsnplot_DPMstpostProcess.DPMMclustpriormixrCRPrNiWrNNiWsample_alphasampleClassCsimilarityMatsimilarityMat_nocostCsimilarityMatCtraceEpsCupdate_SSupdate_SSsnupdate_SSstvclust2mcoclustCwishrnd

Dependencies:backportsbitbit64broombroom.helperscardsclicliprcolorspacecpp11crayondplyrellipsefansifarverfastclusterforcatsgenericsGGallyggplot2ggstatsgluegtablehavenhmsisobandlabelinglabelledlatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkpheatmappillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrreshape2rlangscalesstringistringrtibbletidyrtidyselecttruncnormtzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Bayesian Nonparametrics for Automatic Gating of Flow Cytometry dataNPflow-package NPflow
Burning MCMC iterations from a Dirichlet Process Mixture Model.burn.DPMMclust
Point estimate of the partition for the Binder loss functioncluster_est_binder
Point estimate of the partition using the F-measure as the cost function.cluster_est_Fmeasure
Point estimate of the partition using a modified Binder loss functioncluster_est_Mbinder_norm
Gets a point estimate of the partition using posterior expected adjusted Rand index (PEAR)cluster_est_pear
Scatterplot of flow cytometry datacytoScatter
Slice Sampling of the Dirichlet Process Mixture Model with a prior on alphaDPMGibbsN
Slice Sampling of the Dirichlet Process Mixture Model with a prior on alphaDPMGibbsN_parallel
Slice Sampling of Dirichlet Process Mixture of Gaussian distributionsDPMGibbsN_SeqPrior
Slice Sampling of Dirichlet Process Mixture of skew normal distributionsDPMGibbsSkewN
Parallel Implementation of Slice Sampling of Dirichlet Process Mixture of skew normal distributionsDPMGibbsSkewN_parallel
Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributionsDPMGibbsSkewT
Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributionsDPMGibbsSkewT_parallel
Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributionsDPMGibbsSkewT_SeqPrior
Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributionsDPMGibbsSkewT_SeqPrior_parallel
Posterior estimation for Dirichlet process mixture of multivariate (potentially skew) distributions modelsDPMpost
ELoss of a partition point estimate compared to a gold standardevalClustLoss
Compute a limited F-measureFlimited
Multiple cost computations with the F-measure as the loss functionFmeasure_costC
C++ implementation of the F-measure computationFmeasureC
C++ implementation of the F-measure computation without the reference class 0FmeasureC_no0
Multivariate log gamma functionlgamma_mv
EM MAP for mixture of sNiWMAP_sNiW_mmEM MAP_sNiW_mmEM_vague MAP_sNiW_mmEM_weighted
MLE for Gamma distributionMLE_gamma
EM MLE for mixture of NiWMLE_NiW_mmEM
MLE for sNiW distributed observationsMLE_sNiW
EM MLE for mixture of sNiWMLE_sNiW_mmEM
multivariate Normal inverse Wishart probability density function for multiple inputsmmNiWpdf
C++ implementation of multivariate Normal inverse Wishart probability density function for multiple inputsmmNiWpdfC
Probability density function of multiple structured Normal inverse WishartmmsNiWlogpdf
C++ implementation of multivariate structured Normal inverse Wishart probability density function for multiple inputsmmsNiWpdfC
C++ implementation of multivariate Normal probability density function for multiple inputsmmvnpdfC
C++ implementation of multivariate skew Normal probability density function for multiple inputsmmvsnpdfC
C++ implementation of multivariate Normal probability density function for multiple inputsmmvstpdfC
C++ implementation of multivariate Normal probability density function for multiple inputsmmvtpdfC
C++ implementation of multivariate Normal probability density function for multiple inputsmvnlikC
multivariate-Normal probability density functionmvnpdf
C++ implementation of multivariate normal probability density function for multiple inputsmvnpdfC
C++ implementation of multivariate skew normal likelihood function for multiple inputsmvsnlikC
multivariate Skew-Normal probability density functionmvsnpdf
C++ implementation of multivariate skew t likelihood function for multiple inputsmvstlikC
multivariate skew-t probability density functionmvstpdf
multivariate Student's t-distribution probability density functionmvtpdf
C++ implementation of similarity matrix computation using pre-computed distancesNuMatParC
Convergence diagnostic plotsplot_ConvDPM
Plot of a Dirichlet process mixture of gaussian distribution partitionplot_DPM
Plot of a Dirichlet process mixture of skew normal distribution partitionplot_DPMsn
Plot of a Dirichlet process mixture of skew t-distribution partitionplot_DPMst
Post-processing Dirichlet Process Mixture Models results to get a mixture distribution of the posterior locationspostProcess.DPMMclust
Methods for a summary of a 'DPMMclust' objectplot.summaryDPMMclust print.summaryDPMMclust summaryDPMMclust
Construction of an Empirical based priorpriormix
Generating cluster data from the Chinese Restaurant ProcessrCRP
Sampler for the concentration parameter of a Dirichlet processsample_alpha
Computes the co-clustering (or similarity) matrixsimilarityMat
C++ implementationsimilarityMat_nocostC
C++ implementationsimilarityMatC
Summarizing Dirichlet Process Mixture Modelssummary.DPMMclust
C++ implementationvclust2mcoclustC