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RcppExports.cpp
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// Generated by using Rcpp::compileAttributes() -> do not edit by hand
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif
// BASiCS_DenoisedRates
arma::mat BASiCS_DenoisedRates(NumericMatrix CountsBio, NumericMatrix Mu, NumericMatrix TransInvDelta, NumericMatrix PhiNu, int N, int q0, int n);
RcppExport SEXP _BASiCS_BASiCS_DenoisedRates(SEXP CountsBioSEXP, SEXP MuSEXP, SEXP TransInvDeltaSEXP, SEXP PhiNuSEXP, SEXP NSEXP, SEXP q0SEXP, SEXP nSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< NumericMatrix >::type CountsBio(CountsBioSEXP);
Rcpp::traits::input_parameter< NumericMatrix >::type Mu(MuSEXP);
Rcpp::traits::input_parameter< NumericMatrix >::type TransInvDelta(TransInvDeltaSEXP);
Rcpp::traits::input_parameter< NumericMatrix >::type PhiNu(PhiNuSEXP);
Rcpp::traits::input_parameter< int >::type N(NSEXP);
Rcpp::traits::input_parameter< int >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int >::type n(nSEXP);
rcpp_result_gen = Rcpp::wrap(BASiCS_DenoisedRates(CountsBio, Mu, TransInvDelta, PhiNu, N, q0, n));
return rcpp_result_gen;
END_RCPP
}
// BASiCS_MCMCcpp
Rcpp::List BASiCS_MCMCcpp(int N, int Thin, int Burn, arma::mat Counts, arma::mat BatchDesign, arma::vec muSpikes, arma::vec mu0, arma::vec delta0, arma::vec phi0, arma::vec s0, arma::vec nu0, arma::vec theta0, arma::vec mu_mu, double s2mu, double adelta, double bdelta, double s2delta, double prior_delta, arma::vec aphi, double as, double bs, double atheta, double btheta, double ar, arma::vec LSmu0, arma::vec LSdelta0, double LSphi0, arma::vec LSnu0, arma::vec LStheta0, arma::vec sumByCellBio, arma::vec sumByGeneAll, arma::vec sumByGeneBio, int StoreAdapt, int EndAdapt, int PrintProgress, double const& mintol_mu, double const& mintol_delta, double const& mintol_nu, double const& mintol_theta, double const& geneExponent, double const& cellExponent, int threads);
RcppExport SEXP _BASiCS_BASiCS_MCMCcpp(SEXP NSEXP, SEXP ThinSEXP, SEXP BurnSEXP, SEXP CountsSEXP, SEXP BatchDesignSEXP, SEXP muSpikesSEXP, SEXP mu0SEXP, SEXP delta0SEXP, SEXP phi0SEXP, SEXP s0SEXP, SEXP nu0SEXP, SEXP theta0SEXP, SEXP mu_muSEXP, SEXP s2muSEXP, SEXP adeltaSEXP, SEXP bdeltaSEXP, SEXP s2deltaSEXP, SEXP prior_deltaSEXP, SEXP aphiSEXP, SEXP asSEXP, SEXP bsSEXP, SEXP athetaSEXP, SEXP bthetaSEXP, SEXP arSEXP, SEXP LSmu0SEXP, SEXP LSdelta0SEXP, SEXP LSphi0SEXP, SEXP LSnu0SEXP, SEXP LStheta0SEXP, SEXP sumByCellBioSEXP, SEXP sumByGeneAllSEXP, SEXP sumByGeneBioSEXP, SEXP StoreAdaptSEXP, SEXP EndAdaptSEXP, SEXP PrintProgressSEXP, SEXP mintol_muSEXP, SEXP mintol_deltaSEXP, SEXP mintol_nuSEXP, SEXP mintol_thetaSEXP, SEXP geneExponentSEXP, SEXP cellExponentSEXP, SEXP threadsSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< int >::type N(NSEXP);
Rcpp::traits::input_parameter< int >::type Thin(ThinSEXP);
Rcpp::traits::input_parameter< int >::type Burn(BurnSEXP);
Rcpp::traits::input_parameter< arma::mat >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::mat >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec >::type muSpikes(muSpikesSEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type phi0(phi0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type s0(s0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type theta0(theta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double >::type s2mu(s2muSEXP);
Rcpp::traits::input_parameter< double >::type adelta(adeltaSEXP);
Rcpp::traits::input_parameter< double >::type bdelta(bdeltaSEXP);
Rcpp::traits::input_parameter< double >::type s2delta(s2deltaSEXP);
Rcpp::traits::input_parameter< double >::type prior_delta(prior_deltaSEXP);
Rcpp::traits::input_parameter< arma::vec >::type aphi(aphiSEXP);
Rcpp::traits::input_parameter< double >::type as(asSEXP);
Rcpp::traits::input_parameter< double >::type bs(bsSEXP);
Rcpp::traits::input_parameter< double >::type atheta(athetaSEXP);
Rcpp::traits::input_parameter< double >::type btheta(bthetaSEXP);
Rcpp::traits::input_parameter< double >::type ar(arSEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSmu0(LSmu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSdelta0(LSdelta0SEXP);
Rcpp::traits::input_parameter< double >::type LSphi0(LSphi0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSnu0(LSnu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LStheta0(LStheta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByCellBio(sumByCellBioSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneAll(sumByGeneAllSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneBio(sumByGeneBioSEXP);
Rcpp::traits::input_parameter< int >::type StoreAdapt(StoreAdaptSEXP);
Rcpp::traits::input_parameter< int >::type EndAdapt(EndAdaptSEXP);
Rcpp::traits::input_parameter< int >::type PrintProgress(PrintProgressSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_mu(mintol_muSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_delta(mintol_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_nu(mintol_nuSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_theta(mintol_thetaSEXP);
Rcpp::traits::input_parameter< double const& >::type geneExponent(geneExponentSEXP);
Rcpp::traits::input_parameter< double const& >::type cellExponent(cellExponentSEXP);
Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
rcpp_result_gen = Rcpp::wrap(BASiCS_MCMCcpp(N, Thin, Burn, Counts, BatchDesign, muSpikes, mu0, delta0, phi0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, aphi, as, bs, atheta, btheta, ar, LSmu0, LSdelta0, LSphi0, LSnu0, LStheta0, sumByCellBio, sumByGeneAll, sumByGeneBio, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, threads));
return rcpp_result_gen;
END_RCPP
}
// BASiCS_MCMCcppNoSpikes
Rcpp::List BASiCS_MCMCcppNoSpikes(int N, int Thin, int Burn, arma::mat Counts, arma::mat BatchDesign, arma::vec mu0, arma::vec delta0, arma::vec s0, arma::vec nu0, arma::vec theta0, arma::vec mu_mu, double s2mu, double adelta, double bdelta, double s2delta, double prior_delta, double as, double bs, double atheta, double btheta, double SizeTimesConstrain, arma::vec Index, int RefGene, arma::vec RefGenes, arma::vec ConstrainGene, arma::vec NotConstrainGene, int StochasticRef, double ar, arma::vec LSmu0, arma::vec LSdelta0, arma::vec LSnu0, arma::vec LStheta0, arma::vec sumByCellAll, arma::vec sumByGeneAll, int StoreAdapt, int EndAdapt, int PrintProgress, double const& mintol_mu, double const& mintol_delta, double const& mintol_nu, double const& mintol_theta, double const& geneExponent, double const& cellExponent, bool fixNu, int threads);
RcppExport SEXP _BASiCS_BASiCS_MCMCcppNoSpikes(SEXP NSEXP, SEXP ThinSEXP, SEXP BurnSEXP, SEXP CountsSEXP, SEXP BatchDesignSEXP, SEXP mu0SEXP, SEXP delta0SEXP, SEXP s0SEXP, SEXP nu0SEXP, SEXP theta0SEXP, SEXP mu_muSEXP, SEXP s2muSEXP, SEXP adeltaSEXP, SEXP bdeltaSEXP, SEXP s2deltaSEXP, SEXP prior_deltaSEXP, SEXP asSEXP, SEXP bsSEXP, SEXP athetaSEXP, SEXP bthetaSEXP, SEXP SizeTimesConstrainSEXP, SEXP IndexSEXP, SEXP RefGeneSEXP, SEXP RefGenesSEXP, SEXP ConstrainGeneSEXP, SEXP NotConstrainGeneSEXP, SEXP StochasticRefSEXP, SEXP arSEXP, SEXP LSmu0SEXP, SEXP LSdelta0SEXP, SEXP LSnu0SEXP, SEXP LStheta0SEXP, SEXP sumByCellAllSEXP, SEXP sumByGeneAllSEXP, SEXP StoreAdaptSEXP, SEXP EndAdaptSEXP, SEXP PrintProgressSEXP, SEXP mintol_muSEXP, SEXP mintol_deltaSEXP, SEXP mintol_nuSEXP, SEXP mintol_thetaSEXP, SEXP geneExponentSEXP, SEXP cellExponentSEXP, SEXP fixNuSEXP, SEXP threadsSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< int >::type N(NSEXP);
Rcpp::traits::input_parameter< int >::type Thin(ThinSEXP);
Rcpp::traits::input_parameter< int >::type Burn(BurnSEXP);
Rcpp::traits::input_parameter< arma::mat >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::mat >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type s0(s0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type theta0(theta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double >::type s2mu(s2muSEXP);
Rcpp::traits::input_parameter< double >::type adelta(adeltaSEXP);
Rcpp::traits::input_parameter< double >::type bdelta(bdeltaSEXP);
Rcpp::traits::input_parameter< double >::type s2delta(s2deltaSEXP);
Rcpp::traits::input_parameter< double >::type prior_delta(prior_deltaSEXP);
Rcpp::traits::input_parameter< double >::type as(asSEXP);
Rcpp::traits::input_parameter< double >::type bs(bsSEXP);
Rcpp::traits::input_parameter< double >::type atheta(athetaSEXP);
Rcpp::traits::input_parameter< double >::type btheta(bthetaSEXP);
Rcpp::traits::input_parameter< double >::type SizeTimesConstrain(SizeTimesConstrainSEXP);
Rcpp::traits::input_parameter< arma::vec >::type Index(IndexSEXP);
Rcpp::traits::input_parameter< int >::type RefGene(RefGeneSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RefGenes(RefGenesSEXP);
Rcpp::traits::input_parameter< arma::vec >::type ConstrainGene(ConstrainGeneSEXP);
Rcpp::traits::input_parameter< arma::vec >::type NotConstrainGene(NotConstrainGeneSEXP);
Rcpp::traits::input_parameter< int >::type StochasticRef(StochasticRefSEXP);
Rcpp::traits::input_parameter< double >::type ar(arSEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSmu0(LSmu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSdelta0(LSdelta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSnu0(LSnu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LStheta0(LStheta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByCellAll(sumByCellAllSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneAll(sumByGeneAllSEXP);
Rcpp::traits::input_parameter< int >::type StoreAdapt(StoreAdaptSEXP);
Rcpp::traits::input_parameter< int >::type EndAdapt(EndAdaptSEXP);
Rcpp::traits::input_parameter< int >::type PrintProgress(PrintProgressSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_mu(mintol_muSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_delta(mintol_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_nu(mintol_nuSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_theta(mintol_thetaSEXP);
Rcpp::traits::input_parameter< double const& >::type geneExponent(geneExponentSEXP);
Rcpp::traits::input_parameter< double const& >::type cellExponent(cellExponentSEXP);
Rcpp::traits::input_parameter< bool >::type fixNu(fixNuSEXP);
Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
rcpp_result_gen = Rcpp::wrap(BASiCS_MCMCcppNoSpikes(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, adelta, bdelta, s2delta, prior_delta, as, bs, atheta, btheta, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads));
return rcpp_result_gen;
END_RCPP
}
// BASiCS_MCMCcppReg
Rcpp::List BASiCS_MCMCcppReg(int N, int Thin, int Burn, arma::mat Counts, arma::mat BatchDesign, arma::vec muSpikes, arma::vec mu0, arma::vec delta0, arma::vec phi0, arma::vec s0, arma::vec nu0, arma::vec theta0, arma::vec mu_mu, double s2mu, arma::vec aphi, double as, double bs, double atheta, double btheta, int k, arma::vec m0, arma::mat V0, double sigma2_a0, double sigma2_b0, arma::vec beta0, double sigma20, double eta0, arma::vec lambda0, double const& variance, double ar, arma::vec LSmu0, arma::vec LSdelta0, double LSphi0, arma::vec LSnu0, arma::vec LStheta0, arma::vec sumByCellBio, arma::vec sumByGeneAll, arma::vec sumByGeneBio, int StoreAdapt, int EndAdapt, int PrintProgress, bool FixLocations, bool RBFMinMax, arma::vec RBFLocations, double const& mintol_mu, double const& mintol_delta, double const& mintol_nu, double const& mintol_theta, double const& geneExponent, double const& cellExponent, int threads);
RcppExport SEXP _BASiCS_BASiCS_MCMCcppReg(SEXP NSEXP, SEXP ThinSEXP, SEXP BurnSEXP, SEXP CountsSEXP, SEXP BatchDesignSEXP, SEXP muSpikesSEXP, SEXP mu0SEXP, SEXP delta0SEXP, SEXP phi0SEXP, SEXP s0SEXP, SEXP nu0SEXP, SEXP theta0SEXP, SEXP mu_muSEXP, SEXP s2muSEXP, SEXP aphiSEXP, SEXP asSEXP, SEXP bsSEXP, SEXP athetaSEXP, SEXP bthetaSEXP, SEXP kSEXP, SEXP m0SEXP, SEXP V0SEXP, SEXP sigma2_a0SEXP, SEXP sigma2_b0SEXP, SEXP beta0SEXP, SEXP sigma20SEXP, SEXP eta0SEXP, SEXP lambda0SEXP, SEXP varianceSEXP, SEXP arSEXP, SEXP LSmu0SEXP, SEXP LSdelta0SEXP, SEXP LSphi0SEXP, SEXP LSnu0SEXP, SEXP LStheta0SEXP, SEXP sumByCellBioSEXP, SEXP sumByGeneAllSEXP, SEXP sumByGeneBioSEXP, SEXP StoreAdaptSEXP, SEXP EndAdaptSEXP, SEXP PrintProgressSEXP, SEXP FixLocationsSEXP, SEXP RBFMinMaxSEXP, SEXP RBFLocationsSEXP, SEXP mintol_muSEXP, SEXP mintol_deltaSEXP, SEXP mintol_nuSEXP, SEXP mintol_thetaSEXP, SEXP geneExponentSEXP, SEXP cellExponentSEXP, SEXP threadsSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< int >::type N(NSEXP);
Rcpp::traits::input_parameter< int >::type Thin(ThinSEXP);
Rcpp::traits::input_parameter< int >::type Burn(BurnSEXP);
Rcpp::traits::input_parameter< arma::mat >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::mat >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec >::type muSpikes(muSpikesSEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type phi0(phi0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type s0(s0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type theta0(theta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double >::type s2mu(s2muSEXP);
Rcpp::traits::input_parameter< arma::vec >::type aphi(aphiSEXP);
Rcpp::traits::input_parameter< double >::type as(asSEXP);
Rcpp::traits::input_parameter< double >::type bs(bsSEXP);
Rcpp::traits::input_parameter< double >::type atheta(athetaSEXP);
Rcpp::traits::input_parameter< double >::type btheta(bthetaSEXP);
Rcpp::traits::input_parameter< int >::type k(kSEXP);
Rcpp::traits::input_parameter< arma::vec >::type m0(m0SEXP);
Rcpp::traits::input_parameter< arma::mat >::type V0(V0SEXP);
Rcpp::traits::input_parameter< double >::type sigma2_a0(sigma2_a0SEXP);
Rcpp::traits::input_parameter< double >::type sigma2_b0(sigma2_b0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type beta0(beta0SEXP);
Rcpp::traits::input_parameter< double >::type sigma20(sigma20SEXP);
Rcpp::traits::input_parameter< double >::type eta0(eta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type lambda0(lambda0SEXP);
Rcpp::traits::input_parameter< double const& >::type variance(varianceSEXP);
Rcpp::traits::input_parameter< double >::type ar(arSEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSmu0(LSmu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSdelta0(LSdelta0SEXP);
Rcpp::traits::input_parameter< double >::type LSphi0(LSphi0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSnu0(LSnu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LStheta0(LStheta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByCellBio(sumByCellBioSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneAll(sumByGeneAllSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneBio(sumByGeneBioSEXP);
Rcpp::traits::input_parameter< int >::type StoreAdapt(StoreAdaptSEXP);
Rcpp::traits::input_parameter< int >::type EndAdapt(EndAdaptSEXP);
Rcpp::traits::input_parameter< int >::type PrintProgress(PrintProgressSEXP);
Rcpp::traits::input_parameter< bool >::type FixLocations(FixLocationsSEXP);
Rcpp::traits::input_parameter< bool >::type RBFMinMax(RBFMinMaxSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RBFLocations(RBFLocationsSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_mu(mintol_muSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_delta(mintol_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_nu(mintol_nuSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_theta(mintol_thetaSEXP);
Rcpp::traits::input_parameter< double const& >::type geneExponent(geneExponentSEXP);
Rcpp::traits::input_parameter< double const& >::type cellExponent(cellExponentSEXP);
Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
rcpp_result_gen = Rcpp::wrap(BASiCS_MCMCcppReg(N, Thin, Burn, Counts, BatchDesign, muSpikes, mu0, delta0, phi0, s0, nu0, theta0, mu_mu, s2mu, aphi, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, ar, LSmu0, LSdelta0, LSphi0, LSnu0, LStheta0, sumByCellBio, sumByGeneAll, sumByGeneBio, StoreAdapt, EndAdapt, PrintProgress, FixLocations, RBFMinMax, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, threads));
return rcpp_result_gen;
END_RCPP
}
// BASiCS_MCMCcppRegNoSpikes
Rcpp::List BASiCS_MCMCcppRegNoSpikes(int N, int Thin, int Burn, arma::mat Counts, arma::mat BatchDesign, arma::vec mu0, arma::vec delta0, arma::vec s0, arma::vec nu0, arma::vec theta0, arma::vec mu_mu, double s2mu, double as, double bs, double atheta, double btheta, int k, arma::vec m0, arma::mat V0, double sigma2_a0, double sigma2_b0, arma::vec beta0, double sigma20, double eta0, arma::vec lambda0, double const& variance, double SizeTimesConstrain, arma::vec Index, int RefGene, arma::vec RefGenes, arma::vec ConstrainGene, arma::vec NotConstrainGene, int StochasticRef, double ar, arma::vec LSmu0, arma::vec LSdelta0, arma::vec LSnu0, arma::vec LStheta0, arma::vec sumByCellAll, arma::vec sumByGeneAll, int StoreAdapt, int EndAdapt, int PrintProgress, bool RBFMinMax, bool FixLocations, arma::vec RBFLocations, double const& mintol_mu, double const& mintol_delta, double const& mintol_nu, double const& mintol_theta, double const& geneExponent, double const& cellExponent, bool fixNu, int threads);
RcppExport SEXP _BASiCS_BASiCS_MCMCcppRegNoSpikes(SEXP NSEXP, SEXP ThinSEXP, SEXP BurnSEXP, SEXP CountsSEXP, SEXP BatchDesignSEXP, SEXP mu0SEXP, SEXP delta0SEXP, SEXP s0SEXP, SEXP nu0SEXP, SEXP theta0SEXP, SEXP mu_muSEXP, SEXP s2muSEXP, SEXP asSEXP, SEXP bsSEXP, SEXP athetaSEXP, SEXP bthetaSEXP, SEXP kSEXP, SEXP m0SEXP, SEXP V0SEXP, SEXP sigma2_a0SEXP, SEXP sigma2_b0SEXP, SEXP beta0SEXP, SEXP sigma20SEXP, SEXP eta0SEXP, SEXP lambda0SEXP, SEXP varianceSEXP, SEXP SizeTimesConstrainSEXP, SEXP IndexSEXP, SEXP RefGeneSEXP, SEXP RefGenesSEXP, SEXP ConstrainGeneSEXP, SEXP NotConstrainGeneSEXP, SEXP StochasticRefSEXP, SEXP arSEXP, SEXP LSmu0SEXP, SEXP LSdelta0SEXP, SEXP LSnu0SEXP, SEXP LStheta0SEXP, SEXP sumByCellAllSEXP, SEXP sumByGeneAllSEXP, SEXP StoreAdaptSEXP, SEXP EndAdaptSEXP, SEXP PrintProgressSEXP, SEXP RBFMinMaxSEXP, SEXP FixLocationsSEXP, SEXP RBFLocationsSEXP, SEXP mintol_muSEXP, SEXP mintol_deltaSEXP, SEXP mintol_nuSEXP, SEXP mintol_thetaSEXP, SEXP geneExponentSEXP, SEXP cellExponentSEXP, SEXP fixNuSEXP, SEXP threadsSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< int >::type N(NSEXP);
Rcpp::traits::input_parameter< int >::type Thin(ThinSEXP);
Rcpp::traits::input_parameter< int >::type Burn(BurnSEXP);
Rcpp::traits::input_parameter< arma::mat >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::mat >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type s0(s0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type theta0(theta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double >::type s2mu(s2muSEXP);
Rcpp::traits::input_parameter< double >::type as(asSEXP);
Rcpp::traits::input_parameter< double >::type bs(bsSEXP);
Rcpp::traits::input_parameter< double >::type atheta(athetaSEXP);
Rcpp::traits::input_parameter< double >::type btheta(bthetaSEXP);
Rcpp::traits::input_parameter< int >::type k(kSEXP);
Rcpp::traits::input_parameter< arma::vec >::type m0(m0SEXP);
Rcpp::traits::input_parameter< arma::mat >::type V0(V0SEXP);
Rcpp::traits::input_parameter< double >::type sigma2_a0(sigma2_a0SEXP);
Rcpp::traits::input_parameter< double >::type sigma2_b0(sigma2_b0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type beta0(beta0SEXP);
Rcpp::traits::input_parameter< double >::type sigma20(sigma20SEXP);
Rcpp::traits::input_parameter< double >::type eta0(eta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type lambda0(lambda0SEXP);
Rcpp::traits::input_parameter< double const& >::type variance(varianceSEXP);
Rcpp::traits::input_parameter< double >::type SizeTimesConstrain(SizeTimesConstrainSEXP);
Rcpp::traits::input_parameter< arma::vec >::type Index(IndexSEXP);
Rcpp::traits::input_parameter< int >::type RefGene(RefGeneSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RefGenes(RefGenesSEXP);
Rcpp::traits::input_parameter< arma::vec >::type ConstrainGene(ConstrainGeneSEXP);
Rcpp::traits::input_parameter< arma::vec >::type NotConstrainGene(NotConstrainGeneSEXP);
Rcpp::traits::input_parameter< int >::type StochasticRef(StochasticRefSEXP);
Rcpp::traits::input_parameter< double >::type ar(arSEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSmu0(LSmu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSdelta0(LSdelta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LSnu0(LSnu0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type LStheta0(LStheta0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByCellAll(sumByCellAllSEXP);
Rcpp::traits::input_parameter< arma::vec >::type sumByGeneAll(sumByGeneAllSEXP);
Rcpp::traits::input_parameter< int >::type StoreAdapt(StoreAdaptSEXP);
Rcpp::traits::input_parameter< int >::type EndAdapt(EndAdaptSEXP);
Rcpp::traits::input_parameter< int >::type PrintProgress(PrintProgressSEXP);
Rcpp::traits::input_parameter< bool >::type RBFMinMax(RBFMinMaxSEXP);
Rcpp::traits::input_parameter< bool >::type FixLocations(FixLocationsSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RBFLocations(RBFLocationsSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_mu(mintol_muSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_delta(mintol_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_nu(mintol_nuSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol_theta(mintol_thetaSEXP);
Rcpp::traits::input_parameter< double const& >::type geneExponent(geneExponentSEXP);
Rcpp::traits::input_parameter< double const& >::type cellExponent(cellExponentSEXP);
Rcpp::traits::input_parameter< bool >::type fixNu(fixNuSEXP);
Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
rcpp_result_gen = Rcpp::wrap(BASiCS_MCMCcppRegNoSpikes(N, Thin, Burn, Counts, BatchDesign, mu0, delta0, s0, nu0, theta0, mu_mu, s2mu, as, bs, atheta, btheta, k, m0, V0, sigma2_a0, sigma2_b0, beta0, sigma20, eta0, lambda0, variance, SizeTimesConstrain, Index, RefGene, RefGenes, ConstrainGene, NotConstrainGene, StochasticRef, ar, LSmu0, LSdelta0, LSnu0, LStheta0, sumByCellAll, sumByGeneAll, StoreAdapt, EndAdapt, PrintProgress, RBFMinMax, FixLocations, RBFLocations, mintol_mu, mintol_delta, mintol_nu, mintol_theta, geneExponent, cellExponent, fixNu, threads));
return rcpp_result_gen;
END_RCPP
}
// muUpdate
arma::mat muUpdate(arma::vec const& mu0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& invdelta, arma::vec const& phinu, arma::vec const& sum_bycell_bio, arma::vec const& mu_mu, double const& s2_mu, int const& q0, int const& n, arma::vec& mu1, arma::vec& u, arma::vec& ind, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_muUpdate(SEXP mu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP invdeltaSEXP, SEXP phinuSEXP, SEXP sum_bycell_bioSEXP, SEXP mu_muSEXP, SEXP s2_muSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP mu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type phinu(phinuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bycell_bio(sum_bycell_bioSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double const& >::type s2_mu(s2_muSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type mu1(mu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(muUpdate(mu0, prop_var, Counts, invdelta, phinu, sum_bycell_bio, mu_mu, s2_mu, q0, n, mu1, u, ind, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// deltaUpdate
arma::mat deltaUpdate(arma::vec const& delta0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& mu, arma::vec const& phinu, double const& a_delta, double const& b_delta, double const& s2delta, double const& prior_delta, int const& q0, int const& n, arma::vec& delta1, arma::vec& u, arma::vec& ind, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_deltaUpdate(SEXP delta0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP muSEXP, SEXP phinuSEXP, SEXP a_deltaSEXP, SEXP b_deltaSEXP, SEXP s2deltaSEXP, SEXP prior_deltaSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP delta1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type phinu(phinuSEXP);
Rcpp::traits::input_parameter< double const& >::type a_delta(a_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type b_delta(b_deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type s2delta(s2deltaSEXP);
Rcpp::traits::input_parameter< double const& >::type prior_delta(prior_deltaSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type delta1(delta1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(deltaUpdate(delta0, prop_var, Counts, mu, phinu, a_delta, b_delta, s2delta, prior_delta, q0, n, delta1, u, ind, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// phiUpdate
Rcpp::List phiUpdate(arma::vec const& phi0, double const& prop_var, arma::mat const& Counts, arma::vec const& mu, arma::vec const& invdelta, arma::vec const& nu, arma::vec const& aphi, arma::vec const& sum_bygene_bio, int const& q0, int const& n, arma::vec& phi1, double const& exponent);
RcppExport SEXP _BASiCS_phiUpdate(SEXP phi0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP muSEXP, SEXP invdeltaSEXP, SEXP nuSEXP, SEXP aphiSEXP, SEXP sum_bygene_bioSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP phi1SEXP, SEXP exponentSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type phi0(phi0SEXP);
Rcpp::traits::input_parameter< double const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type aphi(aphiSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bygene_bio(sum_bygene_bioSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type phi1(phi1SEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
rcpp_result_gen = Rcpp::wrap(phiUpdate(phi0, prop_var, Counts, mu, invdelta, nu, aphi, sum_bygene_bio, q0, n, phi1, exponent));
return rcpp_result_gen;
END_RCPP
}
// sUpdateBatch
arma::vec sUpdateBatch(arma::vec const& s0, arma::vec const& nu, arma::vec const& thetaBatch, double const& as, double const& bs, arma::mat const& BatchDesign, int const& n, arma::vec& s1, double const& exponent);
RcppExport SEXP _BASiCS_sUpdateBatch(SEXP s0SEXP, SEXP nuSEXP, SEXP thetaBatchSEXP, SEXP asSEXP, SEXP bsSEXP, SEXP BatchDesignSEXP, SEXP nSEXP, SEXP s1SEXP, SEXP exponentSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type s0(s0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type thetaBatch(thetaBatchSEXP);
Rcpp::traits::input_parameter< double const& >::type as(asSEXP);
Rcpp::traits::input_parameter< double const& >::type bs(bsSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type s1(s1SEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
rcpp_result_gen = Rcpp::wrap(sUpdateBatch(s0, nu, thetaBatch, as, bs, BatchDesign, n, s1, exponent));
return rcpp_result_gen;
END_RCPP
}
// nuUpdateBatch
arma::mat nuUpdateBatch(arma::vec const& nu0, arma::vec const& prop_var, arma::mat const& Counts, double const& SumSpikeInput, arma::mat const& BatchDesign, arma::vec const& mu, arma::vec const& invdelta, arma::vec const& phi, arma::vec const& s, arma::vec const& thetaBatch, arma::vec const& sum_bygene_all, int const& q0, int const& n, arma::vec& nu1, arma::vec& u, arma::vec& ind, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_nuUpdateBatch(SEXP nu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP SumSpikeInputSEXP, SEXP BatchDesignSEXP, SEXP muSEXP, SEXP invdeltaSEXP, SEXP phiSEXP, SEXP sSEXP, SEXP thetaBatchSEXP, SEXP sum_bygene_allSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP nu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< double const& >::type SumSpikeInput(SumSpikeInputSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type phi(phiSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type s(sSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type thetaBatch(thetaBatchSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bygene_all(sum_bygene_allSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type nu1(nu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(nuUpdateBatch(nu0, prop_var, Counts, SumSpikeInput, BatchDesign, mu, invdelta, phi, s, thetaBatch, sum_bygene_all, q0, n, nu1, u, ind, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// thetaUpdateBatch
arma::mat thetaUpdateBatch(arma::vec const& theta0, arma::vec const& prop_var, arma::mat const& BatchDesign, arma::vec const& BatchSizes, arma::vec const& s, arma::vec const& nu, double const& a_theta, double const& b_theta, int const& n, int const& nBatch, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_thetaUpdateBatch(SEXP theta0SEXP, SEXP prop_varSEXP, SEXP BatchDesignSEXP, SEXP BatchSizesSEXP, SEXP sSEXP, SEXP nuSEXP, SEXP a_thetaSEXP, SEXP b_thetaSEXP, SEXP nSEXP, SEXP nBatchSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type theta0(theta0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type BatchSizes(BatchSizesSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type s(sSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< double const& >::type a_theta(a_thetaSEXP);
Rcpp::traits::input_parameter< double const& >::type b_theta(b_thetaSEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< int const& >::type nBatch(nBatchSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(thetaUpdateBatch(theta0, prop_var, BatchDesign, BatchSizes, s, nu, a_theta, b_theta, n, nBatch, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// muUpdateNoSpikes
arma::mat muUpdateNoSpikes(arma::vec const& mu0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& invdelta, arma::vec const& nu, arma::vec const& sum_bycell_all, arma::vec const& mu_mu, double const& s2_mu, int const& q0, int const& n, arma::vec& mu1, arma::vec& u, arma::vec& ind, double const& SizeTimesConstrain, int const& RefGene, arma::uvec const& ConstrainGene, arma::uvec const& NotConstrainGene, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_muUpdateNoSpikes(SEXP mu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP invdeltaSEXP, SEXP nuSEXP, SEXP sum_bycell_allSEXP, SEXP mu_muSEXP, SEXP s2_muSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP mu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP SizeTimesConstrainSEXP, SEXP RefGeneSEXP, SEXP ConstrainGeneSEXP, SEXP NotConstrainGeneSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bycell_all(sum_bycell_allSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double const& >::type s2_mu(s2_muSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type mu1(mu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type SizeTimesConstrain(SizeTimesConstrainSEXP);
Rcpp::traits::input_parameter< int const& >::type RefGene(RefGeneSEXP);
Rcpp::traits::input_parameter< arma::uvec const& >::type ConstrainGene(ConstrainGeneSEXP);
Rcpp::traits::input_parameter< arma::uvec const& >::type NotConstrainGene(NotConstrainGeneSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(muUpdateNoSpikes(mu0, prop_var, Counts, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// nuUpdateBatchNoSpikes
arma::mat nuUpdateBatchNoSpikes(arma::vec const& nu0, arma::vec const& prop_var, arma::mat const& Counts, arma::mat const& BatchDesign, arma::vec const& mu, arma::vec const& invdelta, arma::vec const& s, arma::vec const& thetaBatch, arma::vec const& sum_bygene_all, int const& q0, int const& n, arma::vec& nu1, arma::vec& u, arma::vec& ind, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_nuUpdateBatchNoSpikes(SEXP nu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP BatchDesignSEXP, SEXP muSEXP, SEXP invdeltaSEXP, SEXP sSEXP, SEXP thetaBatchSEXP, SEXP sum_bygene_allSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP nu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type nu0(nu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type BatchDesign(BatchDesignSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type s(sSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type thetaBatch(thetaBatchSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bygene_all(sum_bygene_allSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type nu1(nu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(nuUpdateBatchNoSpikes(nu0, prop_var, Counts, BatchDesign, mu, invdelta, s, thetaBatch, sum_bygene_all, q0, n, nu1, u, ind, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// designMatrix
arma::mat designMatrix(int const& k, /* Number of Gaussian radial basis functions to use for regression */ arma::vec RBFLocations, arma::vec const& mu, double const& variance);
RcppExport SEXP _BASiCS_designMatrix(SEXP kSEXP, SEXP RBFLocationsSEXP, SEXP muSEXP, SEXP varianceSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< int const& >::type k(kSEXP);
Rcpp::traits::input_parameter< /* Number of Gaussian radial basis functions to use for regression */ arma::vec >::type RBFLocations(RBFLocationsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< double const& >::type variance(varianceSEXP);
rcpp_result_gen = Rcpp::wrap(designMatrix(k, RBFLocations, mu, variance));
return rcpp_result_gen;
END_RCPP
}
// estimateRBFLocations
arma::vec estimateRBFLocations(arma::vec const& log_mu, int const& k, bool RBFMinMax);
RcppExport SEXP _BASiCS_estimateRBFLocations(SEXP log_muSEXP, SEXP kSEXP, SEXP RBFMinMaxSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type log_mu(log_muSEXP);
Rcpp::traits::input_parameter< int const& >::type k(kSEXP);
Rcpp::traits::input_parameter< bool >::type RBFMinMax(RBFMinMaxSEXP);
rcpp_result_gen = Rcpp::wrap(estimateRBFLocations(log_mu, k, RBFMinMax));
return rcpp_result_gen;
END_RCPP
}
// muUpdateReg
arma::mat muUpdateReg(arma::vec const& mu0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& delta, arma::vec const& phinu, arma::vec const& sum_bycell_bio, arma::vec const& mu_mu, double const& s2_mu, int const& q0, int const& n, arma::vec& mu1, arma::vec& u, arma::vec& ind, int const& k, arma::vec const& lambda, arma::vec const& beta, arma::mat const& X, double const& sigma2, double variance, bool FixLocations, bool RBFMinMax, arma::vec RBFLocations, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_muUpdateReg(SEXP mu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP deltaSEXP, SEXP phinuSEXP, SEXP sum_bycell_bioSEXP, SEXP mu_muSEXP, SEXP s2_muSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP mu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP kSEXP, SEXP lambdaSEXP, SEXP betaSEXP, SEXP XSEXP, SEXP sigma2SEXP, SEXP varianceSEXP, SEXP FixLocationsSEXP, SEXP RBFMinMaxSEXP, SEXP RBFLocationsSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type delta(deltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type phinu(phinuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bycell_bio(sum_bycell_bioSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double const& >::type s2_mu(s2_muSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type mu1(mu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< int const& >::type k(kSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type lambda(lambdaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type X(XSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< double >::type variance(varianceSEXP);
Rcpp::traits::input_parameter< bool >::type FixLocations(FixLocationsSEXP);
Rcpp::traits::input_parameter< bool >::type RBFMinMax(RBFMinMaxSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RBFLocations(RBFLocationsSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(muUpdateReg(mu0, prop_var, Counts, delta, phinu, sum_bycell_bio, mu_mu, s2_mu, q0, n, mu1, u, ind, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// deltaUpdateReg
arma::mat deltaUpdateReg(arma::vec const& delta0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& mu, arma::vec const& phinu, int const& q0, int const& n, arma::vec& delta1, arma::vec& u, arma::vec& ind, arma::vec const& lambda, arma::mat const& X, double const& sigma2, arma::vec const& beta, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_deltaUpdateReg(SEXP delta0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP muSEXP, SEXP phinuSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP delta1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP lambdaSEXP, SEXP XSEXP, SEXP sigma2SEXP, SEXP betaSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type phinu(phinuSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type delta1(delta1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type lambda(lambdaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type X(XSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(deltaUpdateReg(delta0, prop_var, Counts, mu, phinu, q0, n, delta1, u, ind, lambda, X, sigma2, beta, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// betaUpdateReg
arma::vec betaUpdateReg(double const& sigma2, arma::mat const& VAux, arma::vec const& mAux);
RcppExport SEXP _BASiCS_betaUpdateReg(SEXP sigma2SEXP, SEXP VAuxSEXP, SEXP mAuxSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type VAux(VAuxSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mAux(mAuxSEXP);
rcpp_result_gen = Rcpp::wrap(betaUpdateReg(sigma2, VAux, mAux));
return rcpp_result_gen;
END_RCPP
}
// sigma2UpdateReg
double sigma2UpdateReg(arma::vec const& delta, arma::vec const& beta, arma::vec const& lambda, arma::mat const& V1, double const& mInvVm0, arma::vec const& m, double const& sigma2_a0, double const& sigma2_b0, int const& q0, double const& exponent);
RcppExport SEXP _BASiCS_sigma2UpdateReg(SEXP deltaSEXP, SEXP betaSEXP, SEXP lambdaSEXP, SEXP V1SEXP, SEXP mInvVm0SEXP, SEXP mSEXP, SEXP sigma2_a0SEXP, SEXP sigma2_b0SEXP, SEXP q0SEXP, SEXP exponentSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type delta(deltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type lambda(lambdaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type V1(V1SEXP);
Rcpp::traits::input_parameter< double const& >::type mInvVm0(mInvVm0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type m(mSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2_a0(sigma2_a0SEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2_b0(sigma2_b0SEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
rcpp_result_gen = Rcpp::wrap(sigma2UpdateReg(delta, beta, lambda, V1, mInvVm0, m, sigma2_a0, sigma2_b0, q0, exponent));
return rcpp_result_gen;
END_RCPP
}
// lambdaUpdateReg
arma::vec lambdaUpdateReg(arma::vec const& delta, arma::mat const& X, arma::vec const& beta, double const& sigma2, double const& eta, int const& q0, arma::vec lambda1, double const& exponent);
RcppExport SEXP _BASiCS_lambdaUpdateReg(SEXP deltaSEXP, SEXP XSEXP, SEXP betaSEXP, SEXP sigma2SEXP, SEXP etaSEXP, SEXP q0SEXP, SEXP lambda1SEXP, SEXP exponentSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type delta(deltaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type X(XSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< double const& >::type eta(etaSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< arma::vec >::type lambda1(lambda1SEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
rcpp_result_gen = Rcpp::wrap(lambdaUpdateReg(delta, X, beta, sigma2, eta, q0, lambda1, exponent));
return rcpp_result_gen;
END_RCPP
}
// muUpdateRegNoSpikes
arma::mat muUpdateRegNoSpikes(arma::vec const& mu0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& delta, arma::vec const& invdelta, arma::vec const& nu, arma::vec const& sum_bycell_all, arma::vec const& mu_mu, double const& s2_mu, int const& q0, int const& n, arma::vec& mu1, arma::vec& u, arma::vec& ind, double const& SizeTimesConstrain, /* No-spikes arguments from here */ int const& RefGene, arma::uvec const& ConstrainGene, arma::uvec const& NotConstrainGene, int const& k, /* Regression arguments from here */ arma::vec const& lambda, arma::vec const& beta, arma::mat const& X, double const& sigma2, double variance, bool FixLocations, bool RBFMinMax, arma::vec RBFLocations, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_muUpdateRegNoSpikes(SEXP mu0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP deltaSEXP, SEXP invdeltaSEXP, SEXP nuSEXP, SEXP sum_bycell_allSEXP, SEXP mu_muSEXP, SEXP s2_muSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP mu1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP SizeTimesConstrainSEXP, SEXP RefGeneSEXP, SEXP ConstrainGeneSEXP, SEXP NotConstrainGeneSEXP, SEXP kSEXP, SEXP lambdaSEXP, SEXP betaSEXP, SEXP XSEXP, SEXP sigma2SEXP, SEXP varianceSEXP, SEXP FixLocationsSEXP, SEXP RBFMinMaxSEXP, SEXP RBFLocationsSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type mu0(mu0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type delta(deltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type invdelta(invdeltaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type sum_bycell_all(sum_bycell_allSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu_mu(mu_muSEXP);
Rcpp::traits::input_parameter< double const& >::type s2_mu(s2_muSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type mu1(mu1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< double const& >::type SizeTimesConstrain(SizeTimesConstrainSEXP);
Rcpp::traits::input_parameter< /* No-spikes arguments from here */ int const& >::type RefGene(RefGeneSEXP);
Rcpp::traits::input_parameter< arma::uvec const& >::type ConstrainGene(ConstrainGeneSEXP);
Rcpp::traits::input_parameter< arma::uvec const& >::type NotConstrainGene(NotConstrainGeneSEXP);
Rcpp::traits::input_parameter< int const& >::type k(kSEXP);
Rcpp::traits::input_parameter< /* Regression arguments from here */ arma::vec const& >::type lambda(lambdaSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type X(XSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< double >::type variance(varianceSEXP);
Rcpp::traits::input_parameter< bool >::type FixLocations(FixLocationsSEXP);
Rcpp::traits::input_parameter< bool >::type RBFMinMax(RBFMinMaxSEXP);
Rcpp::traits::input_parameter< arma::vec >::type RBFLocations(RBFLocationsSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(muUpdateRegNoSpikes(mu0, prop_var, Counts, delta, invdelta, nu, sum_bycell_all, mu_mu, s2_mu, q0, n, mu1, u, ind, SizeTimesConstrain, RefGene, ConstrainGene, NotConstrainGene, k, lambda, beta, X, sigma2, variance, FixLocations, RBFMinMax, RBFLocations, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// deltaUpdateRegNoSpikes
arma::mat deltaUpdateRegNoSpikes(arma::vec const& delta0, arma::vec const& prop_var, arma::mat const& Counts, arma::vec const& mu, arma::vec const& nu, int const& q0, int const& n, arma::vec& delta1, arma::vec& u, arma::vec& ind, arma::vec const& lambda, arma::mat const& X, double const& sigma2, arma::vec const& beta, double const& exponent, double const& mintol);
RcppExport SEXP _BASiCS_deltaUpdateRegNoSpikes(SEXP delta0SEXP, SEXP prop_varSEXP, SEXP CountsSEXP, SEXP muSEXP, SEXP nuSEXP, SEXP q0SEXP, SEXP nSEXP, SEXP delta1SEXP, SEXP uSEXP, SEXP indSEXP, SEXP lambdaSEXP, SEXP XSEXP, SEXP sigma2SEXP, SEXP betaSEXP, SEXP exponentSEXP, SEXP mintolSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec const& >::type delta0(delta0SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type prop_var(prop_varSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type Counts(CountsSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type mu(muSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type nu(nuSEXP);
Rcpp::traits::input_parameter< int const& >::type q0(q0SEXP);
Rcpp::traits::input_parameter< int const& >::type n(nSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type delta1(delta1SEXP);
Rcpp::traits::input_parameter< arma::vec& >::type u(uSEXP);
Rcpp::traits::input_parameter< arma::vec& >::type ind(indSEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type lambda(lambdaSEXP);
Rcpp::traits::input_parameter< arma::mat const& >::type X(XSEXP);
Rcpp::traits::input_parameter< double const& >::type sigma2(sigma2SEXP);
Rcpp::traits::input_parameter< arma::vec const& >::type beta(betaSEXP);
Rcpp::traits::input_parameter< double const& >::type exponent(exponentSEXP);
Rcpp::traits::input_parameter< double const& >::type mintol(mintolSEXP);
rcpp_result_gen = Rcpp::wrap(deltaUpdateRegNoSpikes(delta0, prop_var, Counts, mu, nu, q0, n, delta1, u, ind, lambda, X, sigma2, beta, exponent, mintol));
return rcpp_result_gen;
END_RCPP
}
// rDirichlet
arma::vec rDirichlet(arma::vec alpha);
RcppExport SEXP _BASiCS_rDirichlet(SEXP alphaSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< arma::vec >::type alpha(alphaSEXP);
rcpp_result_gen = Rcpp::wrap(rDirichlet(alpha));
return rcpp_result_gen;
END_RCPP
}
static const R_CallMethodDef CallEntries[] = {
{"_BASiCS_BASiCS_DenoisedRates", (DL_FUNC) &_BASiCS_BASiCS_DenoisedRates, 7},
{"_BASiCS_BASiCS_MCMCcpp", (DL_FUNC) &_BASiCS_BASiCS_MCMCcpp, 42},
{"_BASiCS_BASiCS_MCMCcppNoSpikes", (DL_FUNC) &_BASiCS_BASiCS_MCMCcppNoSpikes, 45},
{"_BASiCS_BASiCS_MCMCcppReg", (DL_FUNC) &_BASiCS_BASiCS_MCMCcppReg, 51},
{"_BASiCS_BASiCS_MCMCcppRegNoSpikes", (DL_FUNC) &_BASiCS_BASiCS_MCMCcppRegNoSpikes, 54},
{"_BASiCS_muUpdate", (DL_FUNC) &_BASiCS_muUpdate, 15},
{"_BASiCS_deltaUpdate", (DL_FUNC) &_BASiCS_deltaUpdate, 16},
{"_BASiCS_phiUpdate", (DL_FUNC) &_BASiCS_phiUpdate, 12},
{"_BASiCS_sUpdateBatch", (DL_FUNC) &_BASiCS_sUpdateBatch, 9},
{"_BASiCS_nuUpdateBatch", (DL_FUNC) &_BASiCS_nuUpdateBatch, 18},
{"_BASiCS_thetaUpdateBatch", (DL_FUNC) &_BASiCS_thetaUpdateBatch, 12},
{"_BASiCS_muUpdateNoSpikes", (DL_FUNC) &_BASiCS_muUpdateNoSpikes, 19},
{"_BASiCS_nuUpdateBatchNoSpikes", (DL_FUNC) &_BASiCS_nuUpdateBatchNoSpikes, 16},
{"_BASiCS_designMatrix", (DL_FUNC) &_BASiCS_designMatrix, 4},
{"_BASiCS_estimateRBFLocations", (DL_FUNC) &_BASiCS_estimateRBFLocations, 3},
{"_BASiCS_muUpdateReg", (DL_FUNC) &_BASiCS_muUpdateReg, 24},
{"_BASiCS_deltaUpdateReg", (DL_FUNC) &_BASiCS_deltaUpdateReg, 16},
{"_BASiCS_betaUpdateReg", (DL_FUNC) &_BASiCS_betaUpdateReg, 3},
{"_BASiCS_sigma2UpdateReg", (DL_FUNC) &_BASiCS_sigma2UpdateReg, 10},
{"_BASiCS_lambdaUpdateReg", (DL_FUNC) &_BASiCS_lambdaUpdateReg, 8},
{"_BASiCS_muUpdateRegNoSpikes", (DL_FUNC) &_BASiCS_muUpdateRegNoSpikes, 29},
{"_BASiCS_deltaUpdateRegNoSpikes", (DL_FUNC) &_BASiCS_deltaUpdateRegNoSpikes, 16},
{"_BASiCS_rDirichlet", (DL_FUNC) &_BASiCS_rDirichlet, 1},
{NULL, NULL, 0}
};
RcppExport void R_init_BASiCS(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}