Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

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Documentation for package ‘NPflow’ version 0.13.5

• DESCRIPTION file.
• Package NEWS.

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NPflow-package	Bayesian Nonparametrics for Automatic Gating of Flow Cytometry data
burn.DPMMclust	Burning MCMC iterations from a Dirichlet Process Mixture Model.
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 cost function.
cluster_est_Mbinder_norm	Point estimate of the partition using a modified Binder loss function
cluster_est_pear	Gets a point estimate of the partition using posterior expected adjusted Rand index (PEAR)
cytoScatter	Scatterplot of flow cytometry data
DPMGibbsN	Slice Sampling of the Dirichlet Process Mixture Model with a prior on alpha
DPMGibbsN_parallel	Slice Sampling of the Dirichlet Process Mixture Model with a prior on alpha
DPMGibbsN_SeqPrior	Slice Sampling of Dirichlet Process Mixture of Gaussian distributions
DPMGibbsSkewN	Slice Sampling of Dirichlet Process Mixture of skew normal distributions
DPMGibbsSkewN_parallel	Parallel Implementation of Slice Sampling of Dirichlet Process Mixture of skew normal distributions
DPMGibbsSkewT	Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions
DPMGibbsSkewT_parallel	Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions
DPMGibbsSkewT_SeqPrior	Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions
DPMGibbsSkewT_SeqPrior_parallel	Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions
DPMpost	Posterior estimation for Dirichlet process mixture of multivariate (potentially skew) distributions models
evalClustLoss	ELoss of a partition point estimate compared to a gold standard
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 reference class 0
Fmeasure_costC	Multiple cost computations with the F-measure as the loss function
lgamma_mv	Multivariate log gamma function
MAP_sNiW_mmEM	EM MAP for mixture of sNiW
MAP_sNiW_mmEM_vague	EM MAP for mixture of sNiW
MAP_sNiW_mmEM_weighted	EM MAP for mixture of sNiW
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 function for multiple inputs
mmNiWpdfC	C++ implementation of multivariate Normal inverse Wishart probability density function for multiple inputs
mmsNiWlogpdf	Probability density function of multiple structured Normal inverse Wishart
mmsNiWpdfC	C++ implementation of multivariate structured Normal inverse Wishart probability density function for multiple inputs
mmvnpdfC	C++ implementation of multivariate Normal probability density function for multiple inputs
mmvsnpdfC	C++ implementation of multivariate skew Normal probability density function for multiple inputs
mmvstpdfC	C++ implementation of multivariate Normal probability density function for multiple inputs
mmvtpdfC	C++ implementation of multivariate Normal probability density function for multiple inputs
mvnlikC	C++ implementation of multivariate Normal probability density function for multiple inputs
mvnpdf	multivariate-Normal probability density function
mvnpdfC	C++ implementation of multivariate normal probability density function for multiple inputs
mvsnlikC	C++ implementation of multivariate skew normal likelihood function for multiple inputs
mvsnpdf	multivariate Skew-Normal probability density function
mvstlikC	C++ implementation of multivariate skew t likelihood function for multiple inputs
mvstpdf	multivariate skew-t probability density function
mvtpdf	multivariate Student's t-distribution probability density function
NPflow	Bayesian Nonparametrics for Automatic Gating of Flow Cytometry data
NuMatParC	C++ implementation of similarity matrix computation using pre-computed distances
plot.summaryDPMMclust	Methods for a summary of a 'DPMMclust' object
plot_ConvDPM	Convergence diagnostic plots
plot_DPM	Plot of a Dirichlet process mixture of gaussian distribution partition
plot_DPMsn	Plot of a Dirichlet process mixture of skew normal distribution partition
plot_DPMst	Plot of a Dirichlet process mixture of skew t-distribution partition
postProcess.DPMMclust	Post-processing Dirichlet Process Mixture Models results to get a mixture distribution of the posterior locations
print.summaryDPMMclust	Methods for a summary of a 'DPMMclust' object
priormix	Construction of an Empirical based prior
rCRP	Generating cluster data from the Chinese Restaurant Process
sample_alpha	Sampler for the concentration parameter of a Dirichlet process
similarityMat	Computes the co-clustering (or similarity) matrix
similarityMatC	C++ implementation
similarityMat_nocostC	C++ implementation
summary.DPMMclust	Summarizing Dirichlet Process Mixture Models
summaryDPMMclust	Methods for a summary of a 'DPMMclust' object
vclust2mcoclustC	C++ implementation