# Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

## Documentation for package ‘NPflow’ version 0.13.1

- DESCRIPTION file.

## Help Pages

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 distibutions
DPMGibbsSkewN | Slice Sampling of Dirichlet Process Mixture of skew normal ditributions
DPMGibbsSkewN_parallel | Parallel Implementation of Slice Sampling of Dirichlet Process Mixture of skew Normals
DPMGibbsSkewT | Slice Sampling of Dirichlet Process Mixture of skew Students's t-distibutions
DPMGibbsSkewT_parallel | Slice Sampling of Dirichlet Process Mixture of skew Students's t-distibutions
DPMGibbsSkewT_SeqPrior | Slice Sampling of Dirichlet Process Mixture of skew Students's t-distibutions
DPMGibbsSkewT_SeqPrior_parallel | Slice Sampling of Dirichlet Process Mixture of skew Students's t-distibutions
DPMpost | Posterior estimation for Dirichlet process mixture of multivariate (potentially skew) distibutions 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 ref classe 0
Fmeasure_costC | Multiple cost computations with Fmeasure 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 precomputed 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 coclustering (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