r_bindings.cpp File Reference

#include "Rcpp/XPtr.h"
#include "params/DP-params.hpp"
#include "params/GaussianMixtureModel-params.hpp"
#include "params/NGGP-params.hpp"
#include "params/Natarajan-params.hpp"
#include "params/utils-params.hpp"
#include "utils/Data.hpp"
#include "utils/Datax.hpp"
#include "utils/Params.hpp"
#include <RcppEigen.h>
#include <memory>
#include "likelihoods/Gamma_likelihood_distances.hpp"
#include "likelihoods/GaussianMixtureModel_likelihood.hpp"
#include "likelihoods/Natarajan_likelihood.hpp"
#include "likelihoods/Natarajan_likelihood_summaryStats.hpp"
#include "likelihoods/Null_likelihood.hpp"
#include "utils/Likelihood.hpp"
#include "processes/DP.hpp"
#include "processes/DPx.hpp"
#include "processes/NGGP.hpp"
#include "processes/NGGPx.hpp"
#include "utils/Process.hpp"
#include "processes/module/binary_covariate_module.hpp"
#include "processes/module/binary_covariate_module_cache.hpp"
#include "processes/module/categorical_covariate_module.hpp"
#include "processes/module/continuos_covariate_module.hpp"
#include "processes/module/continuos_covariate_module_cache.hpp"
#include "processes/module/spatial_module.hpp"
#include "processes/module/spatial_module_cache.hpp"
#include "processes/module/spatial_module_continuous.hpp"
#include "processes/caches/binary_cache.hpp"
#include "processes/caches/continuos_cache.hpp"
#include "processes/caches/spatial_cache.hpp"
#include "utils/ClusterInfo.hpp"
#include "samplers/U_sampler/MALA.hpp"
#include "samplers/U_sampler/RWMH.hpp"
#include "samplers/U_sampler/U_sampler.hpp"
#include "samplers/neal.hpp"
#include "samplers/neal_ZDNAM.hpp"
#include "samplers/splitmerge.hpp"
#include "samplers/splitmerge_LSS.hpp"
#include "samplers/splitmerge_LSS_SDDS.hpp"
#include "samplers/splitmerge_SAMS.hpp"
#include "utils/Sampler.hpp"

Functions
Data *	get_data_ptr (SEXP sexp)
ClusterInfo *	get_cluster_info_ptr (SEXP sexp)
Rcpp::XPtr< Params >	create_Params (double delta1, double alpha, double beta, double delta2, double gamma, double zeta, int BI, int NI, double a, double sigma, double tau, Eigen::MatrixXd D)
Rcpp::XPtr< utils_params >	create_utils_params (int BI, int NI, Eigen::MatrixXd D)
Rcpp::XPtr< NGGP_params >	create_NGGP_params (double a, double sigma, double tau)
Rcpp::XPtr< DP_params >	create_DP_params (double a)
Rcpp::XPtr< Natarajan_params >	create_Natarajan_params (double delta1, double alpha, double beta, double delta2, double gamma, double zeta)
Rcpp::XPtr< GaussianMixtureModel_params >	create_GaussianMixtureModel_params (double m0, double kappa0, double alpha0, double beta0)
Rcpp::XPtr< Data >	create_Data (Rcpp::XPtr< utils_params > params, Eigen::VectorXi initial_allocations)
Rcpp::XPtr< ContinuosCache >	create_Continuos_cache (Eigen::VectorXi &initial_allocations, Eigen::VectorXd continuos_covariates)
Rcpp::XPtr< BinaryCache >	create_Binary_cache (Eigen::VectorXi &initial_allocations, Eigen::VectorXi binary_covariates)
Rcpp::XPtr< SpatialCache >	create_Spatial_cache (Eigen::VectorXi &initial_allocations, Eigen::MatrixXi W)
Rcpp::XPtr< Datax >	create_Datax (Rcpp::XPtr< utils_params > params, Rcpp::List modules_list, Eigen::VectorXi initial_allocations)
Rcpp::XPtr< Natarajan_likelihood >	create_Natarajan_likelihood (SEXP data_sexp, Rcpp::XPtr< Natarajan_params > params, Rcpp::XPtr< utils_params > utils)
Rcpp::XPtr< Natarajan_likelihood_summaryStats >	create_Natarajan_likelihood_summaryStats (SEXP data_sexp, Rcpp::XPtr< Natarajan_params > params, Rcpp::XPtr< utils_params > utils)
Rcpp::XPtr< Null_likelihood >	create_Null_likelihood (SEXP data_sexp)
Rcpp::XPtr< Gamma_likelihood_distances >	create_Gamma_likelihood_distances (SEXP data_sexp, Rcpp::XPtr< Natarajan_params > params, Rcpp::XPtr< utils_params > utils)
Rcpp::XPtr< GaussianMixtureModel_likelihood >	create_GaussianMixtureModel_likelihood (SEXP data_sexp, Rcpp::XPtr< GaussianMixtureModel_params > params)
Rcpp::XPtr< RWMH >	create_RWMH (Rcpp::XPtr< NGGP_params > params, SEXP data_sexp, bool use_V, double proposal_sd, bool tuning_enabled)
Rcpp::XPtr< MALA >	create_MALA (Rcpp::XPtr< NGGP_params > params, SEXP data_sexp, bool use_V, double proposal_sd, bool tuning_enabled)
Rcpp::XPtr< DP >	create_DP (SEXP data_sexp, Rcpp::XPtr< DP_params > params)
Rcpp::XPtr< NGGP >	create_NGGP (SEXP data_sexp, Rcpp::XPtr< NGGP_params > params, Rcpp::XPtr< U_sampler > u_sampler)
Rcpp::XPtr< std::shared_ptr< Module > >	create_SpatialModule (SEXP data_sexp, Eigen::MatrixXi W, double spatial_coefficient)
Rcpp::XPtr< std::shared_ptr< Module > >	create_SpatialModuleContinuous (SEXP data_sexp, Eigen::MatrixXd W, double spatial_coefficient)
Rcpp::XPtr< std::shared_ptr< Module > >	create_SpatialModuleCache (SEXP data_sexp, Rcpp::XPtr< SpatialCache > cache, double spatial_coefficient)
Rcpp::XPtr< std::shared_ptr< Module > >	create_ContinuosCovariatesModule (SEXP data_sexp, Eigen::VectorXd covariates, bool fixed_v, double m=0, double B=1, double v=1, double nu=1, double S0=1)
Rcpp::XPtr< std::shared_ptr< Module > >	create_ContinuosCovariatesModuleCache (SEXP data_sexp, Rcpp::XPtr< ContinuosCache > cache, bool fixed_v, double m=0, double B=1, double v=1, double nu=1, double S0=1)
Rcpp::XPtr< std::shared_ptr< Module > >	create_BinaryCovariatesModule (SEXP data_sexp, Eigen::VectorXi covariates, double prior_a=1.0, double prior_b=1.0)
Rcpp::XPtr< std::shared_ptr< Module > >	create_BinaryCovariatesModuleCache (SEXP data_sexp, Rcpp::XPtr< BinaryCache > cache, double beta_prior_alpha=1.0, double beta_prior_beta=1.0)
Rcpp::XPtr< std::shared_ptr< Module > >	create_CategoricalCovariatesModule (SEXP data_sexp, Eigen::VectorXi categorical_covariate, std::vector< double > prior_alpha)
Rcpp::XPtr< DPx >	create_DPx (SEXP data_sexp, Rcpp::XPtr< DP_params > params, Rcpp::List modules_list)
Rcpp::XPtr< NGGPx >	create_NGGPx (SEXP data_sexp, Rcpp::XPtr< NGGP_params > params, Rcpp::XPtr< U_sampler > u_sampler, Rcpp::List modules_list)
Rcpp::XPtr< Neal3 >	create_Neal3 (SEXP data_sexp, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process)
Rcpp::XPtr< Neal3ZDNAM >	create_Neal3ZDNAM (SEXP data_sexp, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process)
Rcpp::XPtr< SplitMerge >	create_SplitMerge (SEXP data_sexp, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process, bool shuffle)
Rcpp::XPtr< SplitMerge_SAMS >	create_SplitMerge_SAMS (SEXP data_sexp, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process, bool shuffle)
Rcpp::XPtr< SplitMerge_LSS >	create_SplitMerge_LSS (SEXP data_sexp, Rcpp::XPtr< utils_params > params, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process, bool shuffle)
Rcpp::XPtr< SplitMerge_LSS_SDDS >	create_SplitMerge_LSS_SDDS (SEXP data_sexp, Rcpp::XPtr< utils_params > params, Rcpp::XPtr< Likelihood > likelihood, Rcpp::XPtr< Process > process, bool shuffle)
void	process_update_params (Rcpp::XPtr< Process > process)
void	sampler_step (Rcpp::XPtr< Sampler > sampler)
Eigen::VectorXi	data_get_allocations (SEXP data_sexp)
int	data_get_K (SEXP data_sexp)
double	u_sampler_get_U (Rcpp::XPtr< U_sampler > u_sampler)
double	u_sampler_get_acceptance_rate (Rcpp::XPtr< U_sampler > u_sampler)
int	params_get_BI (Rcpp::XPtr< utils_params > params)
int	params_get_NI (Rcpp::XPtr< utils_params > params)
double	NGGP_params_get_a (Rcpp::XPtr< NGGP_params > params)
double	params_get_sigma (Rcpp::XPtr< NGGP_params > params)
double	params_get_tau (Rcpp::XPtr< NGGP_params > params)
std::string	params_get_name (Rcpp::XPtr< Process_params > params)
double	DP_params_get_a (Rcpp::XPtr< DP_params > params)
void	cluster_info_set_allocation (Rcpp::XPtr< ClusterInfo > cluster_info, int index, int cluster, int old_cluster)
void	cluster_info_recompute (Rcpp::XPtr< ClusterInfo > cluster_info, int K, Eigen::VectorXi allocations)
void	datax_set_allocation (Rcpp::XPtr< Datax > data, int index, int cluster)
void	datax_set_allocations (Rcpp::XPtr< Datax > data, Eigen::VectorXi new_allocations)
void	lss_sdds_accepted_moves (Rcpp::XPtr< SplitMerge_LSS_SDDS > sampler)
	RCPP_MODULE (bnpclust_module)

Function Documentation

cluster_info_recompute()

void cluster_info_recompute	(	Rcpp::XPtr< ClusterInfo >	cluster_info,
		int	K,
		Eigen::VectorXi	allocations )

cluster_info_set_allocation()

void cluster_info_set_allocation	(	Rcpp::XPtr< ClusterInfo >	cluster_info,
		int	index,
		int	cluster,
		int	old_cluster )

create_Binary_cache()

Rcpp::XPtr< BinaryCache > create_Binary_cache	(	Eigen::VectorXi &	initial_allocations,
		Eigen::VectorXi	binary_covariates )

create_BinaryCovariatesModule()

Rcpp::XPtr< std::shared_ptr< Module > > create_BinaryCovariatesModule	(	SEXP	data_sexp,
		Eigen::VectorXi	covariates,
		double	prior_a = 1.0,
		double	prior_b = 1.0 )

create_BinaryCovariatesModuleCache()

Rcpp::XPtr< std::shared_ptr< Module > > create_BinaryCovariatesModuleCache	(	SEXP	data_sexp,
		Rcpp::XPtr< BinaryCache >	cache,
		double	beta_prior_alpha = 1.0,
		double	beta_prior_beta = 1.0 )

create_CategoricalCovariatesModule()

Rcpp::XPtr< std::shared_ptr< Module > > create_CategoricalCovariatesModule	(	SEXP	data_sexp,
		Eigen::VectorXi	categorical_covariate,
		std::vector< double >	prior_alpha )

create_Continuos_cache()

Rcpp::XPtr< ContinuosCache > create_Continuos_cache	(	Eigen::VectorXi &	initial_allocations,
		Eigen::VectorXd	continuos_covariates )

create_ContinuosCovariatesModule()

Rcpp::XPtr< std::shared_ptr< Module > > create_ContinuosCovariatesModule	(	SEXP	data_sexp,
		Eigen::VectorXd	covariates,
		bool	fixed_v,
		double	m = 0,
		double	B = 1,
		double	v = 1,
		double	nu = 1,
		double	S0 = 1 )

create_ContinuosCovariatesModuleCache()

Rcpp::XPtr< std::shared_ptr< Module > > create_ContinuosCovariatesModuleCache	(	SEXP	data_sexp,
		Rcpp::XPtr< ContinuosCache >	cache,
		bool	fixed_v,
		double	m = 0,
		double	B = 1,
		double	v = 1,
		double	nu = 1,
		double	S0 = 1 )

create_Data()

Rcpp::XPtr< Data > create_Data	(	Rcpp::XPtr< utils_params >	params,
		Eigen::VectorXi	initial_allocations )

create_Datax()

Rcpp::XPtr< Datax > create_Datax	(	Rcpp::XPtr< utils_params >	params,
		Rcpp::List	modules_list,
		Eigen::VectorXi	initial_allocations )

create_DP()

Rcpp::XPtr< DP > create_DP	(	SEXP	data_sexp,
		Rcpp::XPtr< DP_params >	params )

create_DP_params()

Rcpp::XPtr< DP_params > create_DP_params

(

double

a

)

create_DPx()

Rcpp::XPtr< DPx > create_DPx	(	SEXP	data_sexp,
		Rcpp::XPtr< DP_params >	params,
		Rcpp::List	modules_list )

create_Gamma_likelihood_distances()

Rcpp::XPtr< Gamma_likelihood_distances > create_Gamma_likelihood_distances	(	SEXP	data_sexp,
		Rcpp::XPtr< Natarajan_params >	params,
		Rcpp::XPtr< utils_params >	utils )

create_GaussianMixtureModel_likelihood()

Rcpp::XPtr< GaussianMixtureModel_likelihood > create_GaussianMixtureModel_likelihood	(	SEXP	data_sexp,
		Rcpp::XPtr< GaussianMixtureModel_params >	params )

create_GaussianMixtureModel_params()

Rcpp::XPtr< GaussianMixtureModel_params > create_GaussianMixtureModel_params	(	double	m0,
		double	kappa0,
		double	alpha0,
		double	beta0 )

create_MALA()

Rcpp::XPtr< MALA > create_MALA	(	Rcpp::XPtr< NGGP_params >	params,
		SEXP	data_sexp,
		bool	use_V,
		double	proposal_sd,
		bool	tuning_enabled )

create_Natarajan_likelihood()

Rcpp::XPtr< Natarajan_likelihood > create_Natarajan_likelihood	(	SEXP	data_sexp,
		Rcpp::XPtr< Natarajan_params >	params,
		Rcpp::XPtr< utils_params >	utils )

create_Natarajan_likelihood_summaryStats()

Rcpp::XPtr< Natarajan_likelihood_summaryStats > create_Natarajan_likelihood_summaryStats	(	SEXP	data_sexp,
		Rcpp::XPtr< Natarajan_params >	params,
		Rcpp::XPtr< utils_params >	utils )

create_Natarajan_params()

Rcpp::XPtr< Natarajan_params > create_Natarajan_params	(	double	delta1,
		double	alpha,
		double	beta,
		double	delta2,
		double	gamma,
		double	zeta )

create_Neal3()

Rcpp::XPtr< Neal3 > create_Neal3	(	SEXP	data_sexp,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process )

create_Neal3ZDNAM()

Rcpp::XPtr< Neal3ZDNAM > create_Neal3ZDNAM	(	SEXP	data_sexp,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process )

create_NGGP()

Rcpp::XPtr< NGGP > create_NGGP	(	SEXP	data_sexp,
		Rcpp::XPtr< NGGP_params >	params,
		Rcpp::XPtr< U_sampler >	u_sampler )

create_NGGP_params()

Rcpp::XPtr< NGGP_params > create_NGGP_params	(	double	a,
		double	sigma,
		double	tau )

create_NGGPx()

Rcpp::XPtr< NGGPx > create_NGGPx	(	SEXP	data_sexp,
		Rcpp::XPtr< NGGP_params >	params,
		Rcpp::XPtr< U_sampler >	u_sampler,
		Rcpp::List	modules_list )

create_Null_likelihood()

Rcpp::XPtr< Null_likelihood > create_Null_likelihood

(

SEXP

data_sexp

)

create_Params()

Rcpp::XPtr< Params > create_Params	(	double	delta1,
		double	alpha,
		double	beta,
		double	delta2,
		double	gamma,
		double	zeta,
		int	BI,
		int	NI,
		double	a,
		double	sigma,
		double	tau,
		Eigen::MatrixXd	D )

create_RWMH()

Rcpp::XPtr< RWMH > create_RWMH	(	Rcpp::XPtr< NGGP_params >	params,
		SEXP	data_sexp,
		bool	use_V,
		double	proposal_sd,
		bool	tuning_enabled )

create_Spatial_cache()

Rcpp::XPtr< SpatialCache > create_Spatial_cache	(	Eigen::VectorXi &	initial_allocations,
		Eigen::MatrixXi	W )

create_SpatialModule()

Rcpp::XPtr< std::shared_ptr< Module > > create_SpatialModule	(	SEXP	data_sexp,
		Eigen::MatrixXi	W,
		double	spatial_coefficient )

create_SpatialModuleCache()

Rcpp::XPtr< std::shared_ptr< Module > > create_SpatialModuleCache	(	SEXP	data_sexp,
		Rcpp::XPtr< SpatialCache >	cache,
		double	spatial_coefficient )

create_SpatialModuleContinuous()

Rcpp::XPtr< std::shared_ptr< Module > > create_SpatialModuleContinuous	(	SEXP	data_sexp,
		Eigen::MatrixXd	W,
		double	spatial_coefficient )

create_SplitMerge()

Rcpp::XPtr< SplitMerge > create_SplitMerge	(	SEXP	data_sexp,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process,
		bool	shuffle )

create_SplitMerge_LSS()

Rcpp::XPtr< SplitMerge_LSS > create_SplitMerge_LSS	(	SEXP	data_sexp,
		Rcpp::XPtr< utils_params >	params,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process,
		bool	shuffle )

create_SplitMerge_LSS_SDDS()

Rcpp::XPtr< SplitMerge_LSS_SDDS > create_SplitMerge_LSS_SDDS	(	SEXP	data_sexp,
		Rcpp::XPtr< utils_params >	params,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process,
		bool	shuffle )

create_SplitMerge_SAMS()

Rcpp::XPtr< SplitMerge_SAMS > create_SplitMerge_SAMS	(	SEXP	data_sexp,
		Rcpp::XPtr< Likelihood >	likelihood,
		Rcpp::XPtr< Process >	process,
		bool	shuffle )

create_utils_params()

Rcpp::XPtr< utils_params > create_utils_params	(	int	BI,
		int	NI,
		Eigen::MatrixXd	D )

data_get_allocations()

Eigen::VectorXi data_get_allocations

(

SEXP

data_sexp

)

data_get_K()

int data_get_K

(

SEXP

data_sexp

)

datax_set_allocation()

void datax_set_allocation	(	Rcpp::XPtr< Datax >	data,
		int	index,
		int	cluster )

datax_set_allocations()

void datax_set_allocations	(	Rcpp::XPtr< Datax >	data,
		Eigen::VectorXi	new_allocations )

DP_params_get_a()

double DP_params_get_a

(

Rcpp::XPtr< DP_params >

params

)

get_cluster_info_ptr()

ClusterInfo * get_cluster_info_ptr

(

SEXP

sexp

)

get_data_ptr()

Data * get_data_ptr

(

SEXP

sexp

)

lss_sdds_accepted_moves()

void lss_sdds_accepted_moves

(

Rcpp::XPtr< SplitMerge_LSS_SDDS >

sampler

)

NGGP_params_get_a()

double NGGP_params_get_a

(

Rcpp::XPtr< NGGP_params >

params

)

params_get_BI()

int params_get_BI

(

Rcpp::XPtr< utils_params >

params

)

params_get_name()

std::string params_get_name

(

Rcpp::XPtr< Process_params >

params

)

params_get_NI()

int params_get_NI

(

Rcpp::XPtr< utils_params >

params

)

params_get_sigma()

double params_get_sigma

(

Rcpp::XPtr< NGGP_params >

params

)

params_get_tau()

double params_get_tau

(

Rcpp::XPtr< NGGP_params >

params

)

process_update_params()

void process_update_params

(

Rcpp::XPtr< Process >

process

)

RCPP_MODULE()

RCPP_MODULE

(

bnpclust_module

)

sampler_step()

void sampler_step

(

Rcpp::XPtr< Sampler >

sampler

)

u_sampler_get_acceptance_rate()

double u_sampler_get_acceptance_rate

(

Rcpp::XPtr< U_sampler >

u_sampler

)

u_sampler_get_U()

double u_sampler_get_U

(

Rcpp::XPtr< U_sampler >

u_sampler

)