Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures

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Documentation for package ‘BNPdensity’ version 2023.3.8

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BNPdensity-package Bayesian nonparametric density estimation
acidity Acidity Index Dataset
add Add x and y
as.mcmc.multNRMI Convert the output of multMixNRMI into a coda mcmc object
asNumeric_no_warning If the function Rmpfr::asNumeric returns a warning about inefficiency, silence it.
BNPdensity Bayesian nonparametric density estimation
comment_on_NRMI_type Comment on the NRMI process depending on the value of the parameters
compute_optimal_clustering Compute the optimal clustering from an MCMC sample
compute_thinning_grid Compute the grid for thinning the MCMC chain
convert_to_mcmc Convert the output of multMixNRMI into a coda mcmc object
cpo.multNRMI Extract the Conditional Predictive Ordinates (CPOs) from a list of fitted objects
cpo.NRMI1 Extract the Conditional Predictive Ordinates (CPOs) from a fitted object
cpo.NRMI2 Extract the Conditional Predictive Ordinates (CPOs) from a fitted object
dist_name_k_index_converter Convert distribution names to indices
dt_ Non-standard student-t density
enzyme Enzyme Dataset
Enzyme1.out Fit of MixNRMI1 function to the enzyme dataset
Enzyme2.out Fit of MixNRMI2 function to the enzyme dataset
expected_number_of_components_Dirichlet Computes the expected number of components for a Dirichlet process.
expected_number_of_components_stable Computes the expected number of components for a stable process.
fill_sigmas Repeat the common scale parameter of a semiparametric model to match the dimension of the location parameters.
galaxy Galaxy Data Set
Galaxy1.out Fit of MixNRMI1 function to the galaxy dataset
Galaxy2.out Fit of MixNRMI2 function to the galaxy dataset
give_kernel_name Gives the kernel name from the integer code
GOFplots Plot Goodness of fits graphical checks for censored data
GOFplots_censored Plot Goodness of fits graphical checks for censored data
GOFplots_noncensored Plot Goodness of fits graphical checks for non censored data
grid_from_data Create a plotting grid from censored or non-censored data.
grid_from_data_censored Create a plotting grid from censored data.
grid_from_data_noncensored Create a plotting grid from non-censored data.
is_censored Test if the data is censored
is_semiparametric Tests if a fit is a semi parametric or nonparametric model.
MixNRMI1 Normalized Random Measures Mixture of Type I
MixNRMI1cens Normalized Random Measures Mixture of Type I for censored data
MixNRMI2 Normalized Random Measures Mixture of Type II
MixNRMI2cens Normalized Random Measures Mixture of Type II for censored data
MixPY1 Pitman-Yor process mixture of Type I
MixPY2 Pitman-Yor process mixture of Type II
multMixNRMI1 Multiple chains of MixNRMI1
multMixNRMI1cens Multiple chains of MixNRMI1cens
multMixNRMI2 Multiple chains of MixNRMI2
multMixNRMI2cens Multiple chains of MixNRMI2cens
MvInv Invert jump heights function
plot.multNRMI Plot the density estimate and the 95% credible interval
plot.NRMI1 Plot the density estimate and the 95% credible interval
plot.NRMI2 Plot the density estimate and the 95% credible interval
plot.PY1 Plot the density estimate and the 95% credible interval
plot.PY2 Plot the density estimate and the 95% credible interval
plotCDF_censored Plot the Turnbull CDF and fitted CDF for censored data.
plotCDF_noncensored Plot the empirical and fitted CDF for non censored data.
plotfit_censored Plot the density estimate and the 95% credible interval for censored data
plotfit_noncensored Plot the density estimate and the 95% credible interval for noncensored data
plotPDF_censored Plot the density for censored data.
plotPDF_noncensored Plot the density and a histogram for non censored data.
plot_clustering_and_CDF Plot the clustering and the Cumulative Distribution Function
plot_prior_number_of_components This plots the prior distribution on the number of components for the stable process. The Dirichlet process is provided for comparison.
pp_plot_censored Plot the percentile-percentile graph for non censored data, using the Turnbull estimator the position of the percentiles.
pp_plot_noncensored Plot the percentile-percentile graph for non censored data.
print.multNRMI S3 method for class 'multNRMI'
print.NRMI1 S3 method for class 'MixNRMI1'
print.NRMI2 S3 method for class 'MixNRMI2'
print.PY1 S3 method for class 'PY1'
print.PY2 S3 method for class 'PY2'
process_dist_name Process the distribution name argument into a distribution index
qq_plot_censored Plot the quantile-quantile graph for censored data.
qq_plot_noncensored Plot the quantile-quantile graph for non censored data.
salinity Salinity tolerance
summary.multNRMI S3 method for class 'multNRMI'
summary.NRMI1 S3 method for class 'MixNRMI1'
summary.NRMI2 S3 method for class 'MixNRMI2'
summary.PY1 S3 method for class 'PY1'
summary.PY2 S3 method for class 'PY2'
summarytext Common text for the summary S3 methods
traceplot Draw a traceplot for multiple chains