R: Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures

# Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures

## Documentation for package ‘BNPdensity’ version 2023.3.8

- DESCRIPTION file.

## Help Pages

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