Man pages for BNPdensity
Ferguson-Klass Type Algorithm for Posterior Normalized Random Measures
| 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... |
| cens_data_check | Censoring data check |
| censor_code_rl | Censor code right-left |
| comment_on_NRMI_type | Comment on the NRMI process depending on the value of the... |
| comp1 | Ties function: univariate |
| comp2 | Ties function: bivariate |
| 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 | Conditional predictive ordinate function |
| cpo.default | Extract the Conditional Predictive Ordinates (CPOs) from a... |
| cpo.multNRMI | Extract the Conditional Predictive Ordinates (CPOs) from a... |
| cpo.NRMI1 | Extract the Conditional Predictive Ordinates (CPOs) from a... |
| cpo.NRMI2 | Extract the Conditional Predictive Ordinates (CPOs) from a... |
| dhalfcauchy | Density half Cauchy |
| dhalfnorm | Density half normal |
| dhalft | Density half Student-t |
| dist_name_k_index_converter | Convert distribution names to indices |
| dk | Kernel density function |
| dkcens2 | Density of the chosen kernel |
| dkcens2_1val | Density evaluation once |
| dt_ | Non-standard student-t density |
| dtnorm | Density truncated normal |
| 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... |
| expected_number_of_components_stable | Computes the expected number of components for a stable... |
| fcondXA | Conditional density evaluation in the semiparametric model |
| fcondXA2 | Conditional density evaluation in the fully nonparametric... |
| fcondXA2cens2 | Conditional density evaluation in the fully nonparametric... |
| fcondYXA | Conditional posterior distribution of the latents Y |
| fcondYXAcens2 | Conditional posterior distribution of the latents Y in the... |
| fcondYZXA | Conditional posterior distribution of the bivariate latents... |
| fcondYZXAcens2 | Conditional posterior distribution of the bivariate latents... |
| fill_sigmas | Repeat the common scale parameter of a semiparametric model... |
| 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. |
| gs3 | Conditional posterior distribution of latent U |
| gs3_adaptive3 | Conditional posterior distribution of latent U |
| gs3_log | Conditional posterior distribution of latent logU |
| gs4 | Resampling Ystar function |
| gs4cens2 | Resampling Ystar function in the case of censoring |
| gs5 | Conditional posterior distribution of sigma |
| gs5cens2 | Conditional posterior distribution of sigma in the case of... |
| gsHP | Updates the hyper-parameters of py0 |
| gsYZstar | Jointly resampling Ystar and Zstar function |
| gsYZstarcens2 | Jointly resampling Ystar and Zstar function in the case of... |
| is_censored | Test if the data is censored |
| is_semiparametric | Tests if a fit is a semi parametric or nonparametric model. |
| logacceptance_ratio_logu | Metropolis-Hastings ratio for the conditional of logU |
| logdprop_logu | Contribution of the proposal kernel logdensity to the... |
| logf_logu_cond_y | Contribution of the target logdensity of logU to the... |
| logf_u_cond_y | Target logdensity of U given the data |
| log_Vnk_PY | Calculate the Logarithm of the Vnk weights for the Pitman-Yor... |
| MixNRMI1 | Normalized Random Measures Mixture of Type I |
| MixNRMI1cens | Normalized Random Measures Mixture of Type I for censored... |
| MixNRMI2 | Normalized Random Measures Mixture of Type II |
| MixNRMI2cens | Normalized Random Measures Mixture of Type II for censored... |
| 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 |
| Mv | Continuous Jump heights function |
| MvInv | Invert jump heights function |
| p0 | Centering function |
| phalfcauchy | Distribution function half Cauchy |
| phalfnorm | Distribution function half Normal |
| phalft | Distribution function half Student-t |
| pk | Kernel distribution function |
| plotCDF_censored | Plot the Turnbull CDF and fitted CDF for censored data. |
| plotCDF_noncensored | Plot the empirical and fitted CDF for non censored data. |
| plot_clustering_and_CDF | Plot the clustering and the Cumulative Distribution Function |
| plotfit_censored | Plot the density estimate and the 95% credible interval for... |
| plotfit_noncensored | Plot the density estimate and the 95% credible interval for... |
| 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 |
| plotPDF_censored | Plot the density for censored data. |
| plotPDF_noncensored | Plot the density and a histogram for non censored data. |
| plot_prior_number_of_components | This plots the prior distribution on the number of components... |
| plot.PY1 | Plot the density estimate and the 95% credible interval |
| plot.PY2 | Plot the density estimate and the 95% credible interval |
| pp_plot_censored | Plot the percentile-percentile graph for non censored data,... |
| 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... |
| pt_ | Distribution function non-standard student-t |
| ptnorm | Distribution function truncated normal |
| qgeneric | Generic function to find quantiles of a distribution |
| qhalfcauchy | Quantile function half Cauchy |
| qhalfnorm | Quantile function half Normal |
| qhalft | Quantile function half Student-t |
| qq_plot_censored | Plot the quantile-quantile graph for censored data. |
| qq_plot_noncensored | Plot the quantile-quantile graph for non censored data. |
| qt_ | Quantile function non-standard Student-t |
| qtnorm | Quantile function truncated normal |
| rfystar | Conditional posterior distribution of the distinct Ystar |
| rfystarcens2 | Conditional posterior distribution of the distinct Ystar in... |
| rfyzstar | Conditional posterior distribution of the distinct vectors... |
| rfyzstarcens2 | Conditional posterior distribution of the distinct vectors... |
| rhalfcauchy | Random number generator half Cauchy |
| rhalfnorm | Random number generator half Normal |
| rhalft | Random number generator half Student-t |
| rk | Kernel density sampling function |
| rprop_logu | Proposal distribution for logU |
| rt_ | Random number generator non-standard Student-t |
| rtnorm | Random number generator for a truncated normal distribution |
| 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 |
| thresholdGG | Choosing the truncation level for the NGG process |
| traceplot | Draw a traceplot for multiple chains |
