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 |