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[dfe06d]: / src / RcppExports.cpp

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// Generated by using Rcpp::compileAttributes() -> do not edit by hand

// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393



#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



// cpp_are_possible_ancestors

std::vector<int> cpp_are_possible_ancestors(Rcpp::IntegerVector t_inf, size_t i);

RcppExport SEXP _outbreaker2_cpp_are_possible_ancestors(SEXP t_infSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type t_inf(t_infSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_are_possible_ancestors(t_inf, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_sample1

size_t cpp_sample1(std::vector<int> x);

RcppExport SEXP _outbreaker2_cpp_sample1(SEXP xSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< std::vector<int> >::type x(xSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_sample1(x));

    return rcpp_result_gen;

END_RCPP

}

// cpp_pick_possible_ancestor

size_t cpp_pick_possible_ancestor(Rcpp::IntegerVector t_inf, size_t i);

RcppExport SEXP _outbreaker2_cpp_pick_possible_ancestor(SEXP t_infSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type t_inf(t_infSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_pick_possible_ancestor(t_inf, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_find_descendents

Rcpp::IntegerVector cpp_find_descendents(Rcpp::IntegerVector alpha, size_t i);

RcppExport SEXP _outbreaker2_cpp_find_descendents(SEXP alphaSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type alpha(alphaSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_find_descendents(alpha, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_find_local_cases

Rcpp::IntegerVector cpp_find_local_cases(Rcpp::IntegerVector alpha, size_t i);

RcppExport SEXP _outbreaker2_cpp_find_local_cases(SEXP alphaSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::IntegerVector >::type alpha(alphaSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_find_local_cases(alpha, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_swap_cases

Rcpp::List cpp_swap_cases(Rcpp::List param, size_t i);

RcppExport SEXP _outbreaker2_cpp_swap_cases(SEXP paramSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_swap_cases(param, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_get_n_mutations

size_t cpp_get_n_mutations(Rcpp::List data, size_t i, size_t j);

RcppExport SEXP _outbreaker2_cpp_get_n_mutations(SEXP dataSEXP, SEXP iSEXP, SEXP jSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    Rcpp::traits::input_parameter< size_t >::type j(jSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_get_n_mutations(data, i, j));

    return rcpp_result_gen;

END_RCPP

}

// cpp_lookup_sequenced_ancestor

Rcpp::List cpp_lookup_sequenced_ancestor(Rcpp::List data, Rcpp::List param, size_t i);

RcppExport SEXP _outbreaker2_cpp_lookup_sequenced_ancestor(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< size_t >::type i(iSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_lookup_sequenced_ancestor(data, param, i));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_genetic

double cpp_ll_genetic(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_ll_genetic(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_genetic(data, param, i, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_timing_infections

double cpp_ll_timing_infections(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_ll_timing_infections(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_timing_infections(data, param, i, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_timing_sampling

double cpp_ll_timing_sampling(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_ll_timing_sampling(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_timing_sampling(data, param, i, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_reporting

double cpp_ll_reporting(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_ll_reporting(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_reporting(data, param, i, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_contact

double cpp_ll_contact(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_ll_contact(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_contact(data, param, i, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_timing

double cpp_ll_timing(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_functions);

RcppExport SEXP _outbreaker2_cpp_ll_timing(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_functions(custom_functionsSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_timing(data, param, i, custom_functions));

    return rcpp_result_gen;

END_RCPP

}

// cpp_ll_all

double cpp_ll_all(Rcpp::List data, Rcpp::List param, SEXP i, Rcpp::RObject custom_functions);

RcppExport SEXP _outbreaker2_cpp_ll_all(SEXP dataSEXP, SEXP paramSEXP, SEXP iSEXP, SEXP custom_functionsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< SEXP >::type i(iSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_functions(custom_functionsSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_ll_all(data, param, i, custom_functions));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_mu

Rcpp::List cpp_move_mu(Rcpp::List param, Rcpp::List data, Rcpp::List config, Rcpp::RObject custom_ll, Rcpp::RObject custom_prior);

RcppExport SEXP _outbreaker2_cpp_move_mu(SEXP paramSEXP, SEXP dataSEXP, SEXP configSEXP, SEXP custom_llSEXP, SEXP custom_priorSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_ll(custom_llSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_prior(custom_priorSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_mu(param, data, config, custom_ll, custom_prior));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_pi

Rcpp::List cpp_move_pi(Rcpp::List param, Rcpp::List data, Rcpp::List config, Rcpp::RObject custom_ll, Rcpp::RObject custom_prior);

RcppExport SEXP _outbreaker2_cpp_move_pi(SEXP paramSEXP, SEXP dataSEXP, SEXP configSEXP, SEXP custom_llSEXP, SEXP custom_priorSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_ll(custom_llSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_prior(custom_priorSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_pi(param, data, config, custom_ll, custom_prior));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_eps

Rcpp::List cpp_move_eps(Rcpp::List param, Rcpp::List data, Rcpp::List config, Rcpp::RObject custom_ll, Rcpp::RObject custom_prior);

RcppExport SEXP _outbreaker2_cpp_move_eps(SEXP paramSEXP, SEXP dataSEXP, SEXP configSEXP, SEXP custom_llSEXP, SEXP custom_priorSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_ll(custom_llSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_prior(custom_priorSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_eps(param, data, config, custom_ll, custom_prior));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_lambda

Rcpp::List cpp_move_lambda(Rcpp::List param, Rcpp::List data, Rcpp::List config, Rcpp::RObject custom_ll, Rcpp::RObject custom_prior);

RcppExport SEXP _outbreaker2_cpp_move_lambda(SEXP paramSEXP, SEXP dataSEXP, SEXP configSEXP, SEXP custom_llSEXP, SEXP custom_priorSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_ll(custom_llSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_prior(custom_priorSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_lambda(param, data, config, custom_ll, custom_prior));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_t_inf

Rcpp::List cpp_move_t_inf(Rcpp::List param, Rcpp::List data, Rcpp::RObject list_custom_ll);

RcppExport SEXP _outbreaker2_cpp_move_t_inf(SEXP paramSEXP, SEXP dataSEXP, SEXP list_custom_llSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type list_custom_ll(list_custom_llSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_t_inf(param, data, list_custom_ll));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_alpha

Rcpp::List cpp_move_alpha(Rcpp::List param, Rcpp::List data, Rcpp::RObject list_custom_ll);

RcppExport SEXP _outbreaker2_cpp_move_alpha(SEXP paramSEXP, SEXP dataSEXP, SEXP list_custom_llSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type list_custom_ll(list_custom_llSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_alpha(param, data, list_custom_ll));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_swap_cases

Rcpp::List cpp_move_swap_cases(Rcpp::List param, Rcpp::List data, Rcpp::RObject list_custom_ll);

RcppExport SEXP _outbreaker2_cpp_move_swap_cases(SEXP paramSEXP, SEXP dataSEXP, SEXP list_custom_llSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type list_custom_ll(list_custom_llSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_swap_cases(param, data, list_custom_ll));

    return rcpp_result_gen;

END_RCPP

}

// cpp_move_kappa

Rcpp::List cpp_move_kappa(Rcpp::List param, Rcpp::List data, Rcpp::List config, Rcpp::RObject list_custom_ll);

RcppExport SEXP _outbreaker2_cpp_move_kappa(SEXP paramSEXP, SEXP dataSEXP, SEXP configSEXP, SEXP list_custom_llSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::RNGScope rcpp_rngScope_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type data(dataSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type list_custom_ll(list_custom_llSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_move_kappa(param, data, config, list_custom_ll));

    return rcpp_result_gen;

END_RCPP

}

// cpp_prior_mu

double cpp_prior_mu(Rcpp::List param, Rcpp::List config, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_prior_mu(SEXP paramSEXP, SEXP configSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_prior_mu(param, config, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_prior_pi

double cpp_prior_pi(Rcpp::List param, Rcpp::List config, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_prior_pi(SEXP paramSEXP, SEXP configSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_prior_pi(param, config, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_prior_eps

double cpp_prior_eps(Rcpp::List param, Rcpp::List config, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_prior_eps(SEXP paramSEXP, SEXP configSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_prior_eps(param, config, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_prior_lambda

double cpp_prior_lambda(Rcpp::List param, Rcpp::List config, Rcpp::RObject custom_function);

RcppExport SEXP _outbreaker2_cpp_prior_lambda(SEXP paramSEXP, SEXP configSEXP, SEXP custom_functionSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_function(custom_functionSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_prior_lambda(param, config, custom_function));

    return rcpp_result_gen;

END_RCPP

}

// cpp_prior_all

double cpp_prior_all(Rcpp::List param, Rcpp::List config, Rcpp::RObject custom_functions);

RcppExport SEXP _outbreaker2_cpp_prior_all(SEXP paramSEXP, SEXP configSEXP, SEXP custom_functionsSEXP) {

BEGIN_RCPP

    Rcpp::RObject rcpp_result_gen;

    Rcpp::traits::input_parameter< Rcpp::List >::type param(paramSEXP);

    Rcpp::traits::input_parameter< Rcpp::List >::type config(configSEXP);

    Rcpp::traits::input_parameter< Rcpp::RObject >::type custom_functions(custom_functionsSEXP);

    rcpp_result_gen = Rcpp::wrap(cpp_prior_all(param, config, custom_functions));

    return rcpp_result_gen;

END_RCPP

}



static const R_CallMethodDef CallEntries[] = {

    {"_outbreaker2_cpp_are_possible_ancestors", (DL_FUNC) &_outbreaker2_cpp_are_possible_ancestors, 2},

    {"_outbreaker2_cpp_sample1", (DL_FUNC) &_outbreaker2_cpp_sample1, 1},

    {"_outbreaker2_cpp_pick_possible_ancestor", (DL_FUNC) &_outbreaker2_cpp_pick_possible_ancestor, 2},

    {"_outbreaker2_cpp_find_descendents", (DL_FUNC) &_outbreaker2_cpp_find_descendents, 2},

    {"_outbreaker2_cpp_find_local_cases", (DL_FUNC) &_outbreaker2_cpp_find_local_cases, 2},

    {"_outbreaker2_cpp_swap_cases", (DL_FUNC) &_outbreaker2_cpp_swap_cases, 2},

    {"_outbreaker2_cpp_get_n_mutations", (DL_FUNC) &_outbreaker2_cpp_get_n_mutations, 3},

    {"_outbreaker2_cpp_lookup_sequenced_ancestor", (DL_FUNC) &_outbreaker2_cpp_lookup_sequenced_ancestor, 3},

    {"_outbreaker2_cpp_ll_genetic", (DL_FUNC) &_outbreaker2_cpp_ll_genetic, 4},

    {"_outbreaker2_cpp_ll_timing_infections", (DL_FUNC) &_outbreaker2_cpp_ll_timing_infections, 4},

    {"_outbreaker2_cpp_ll_timing_sampling", (DL_FUNC) &_outbreaker2_cpp_ll_timing_sampling, 4},

    {"_outbreaker2_cpp_ll_reporting", (DL_FUNC) &_outbreaker2_cpp_ll_reporting, 4},

    {"_outbreaker2_cpp_ll_contact", (DL_FUNC) &_outbreaker2_cpp_ll_contact, 4},

    {"_outbreaker2_cpp_ll_timing", (DL_FUNC) &_outbreaker2_cpp_ll_timing, 4},

    {"_outbreaker2_cpp_ll_all", (DL_FUNC) &_outbreaker2_cpp_ll_all, 4},

    {"_outbreaker2_cpp_move_mu", (DL_FUNC) &_outbreaker2_cpp_move_mu, 5},

    {"_outbreaker2_cpp_move_pi", (DL_FUNC) &_outbreaker2_cpp_move_pi, 5},

    {"_outbreaker2_cpp_move_eps", (DL_FUNC) &_outbreaker2_cpp_move_eps, 5},

    {"_outbreaker2_cpp_move_lambda", (DL_FUNC) &_outbreaker2_cpp_move_lambda, 5},

    {"_outbreaker2_cpp_move_t_inf", (DL_FUNC) &_outbreaker2_cpp_move_t_inf, 3},

    {"_outbreaker2_cpp_move_alpha", (DL_FUNC) &_outbreaker2_cpp_move_alpha, 3},

    {"_outbreaker2_cpp_move_swap_cases", (DL_FUNC) &_outbreaker2_cpp_move_swap_cases, 3},

    {"_outbreaker2_cpp_move_kappa", (DL_FUNC) &_outbreaker2_cpp_move_kappa, 4},

    {"_outbreaker2_cpp_prior_mu", (DL_FUNC) &_outbreaker2_cpp_prior_mu, 3},

    {"_outbreaker2_cpp_prior_pi", (DL_FUNC) &_outbreaker2_cpp_prior_pi, 3},

    {"_outbreaker2_cpp_prior_eps", (DL_FUNC) &_outbreaker2_cpp_prior_eps, 3},

    {"_outbreaker2_cpp_prior_lambda", (DL_FUNC) &_outbreaker2_cpp_prior_lambda, 3},

    {"_outbreaker2_cpp_prior_all", (DL_FUNC) &_outbreaker2_cpp_prior_all, 3},

    {NULL, NULL, 0}

};



RcppExport void R_init_outbreaker2(DllInfo *dll) {

    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);

    R_useDynamicSymbols(dll, FALSE);

}