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--- a +++ b/src/RcppExports.cpp @@ -0,0 +1,410 @@ +// 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); +}