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Models:
Marco Lenoir
MarcoTheBlack/
outbreaker2
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[dfe06d]: / src / likelihoods.h

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#ifndef OUTBREAKER2_LIKELIHOODS_H

#define OUTBREAKER2_LIKELIHOODS_H



#include <Rcpp.h>



// Core likelihood functions



// [[Rcpp::export(rng = false)]]

double cpp_ll_genetic(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

		      Rcpp::RObject custom_function = R_NilValue);



double cpp_ll_genetic(Rcpp::List data, Rcpp::List param, size_t i,

		      Rcpp::RObject custom_function = R_NilValue);













// [[Rcpp::export(rng = false)]]

double cpp_ll_timing_infections(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

				Rcpp::RObject custom_function = R_NilValue);



double cpp_ll_timing_infections(Rcpp::List data, Rcpp::List param, size_t i,

				Rcpp::RObject custom_function = R_NilValue);













// [[Rcpp::export(rng = false)]]

double cpp_ll_timing_sampling(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

			      Rcpp::RObject custom_function = R_NilValue);



double cpp_ll_timing_sampling(Rcpp::List data, Rcpp::List param, size_t i,

			      Rcpp::RObject custom_function = R_NilValue);













// [[Rcpp::export(rng = false)]]

double cpp_ll_reporting(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

			Rcpp::RObject custom_function = R_NilValue);



double cpp_ll_reporting(Rcpp::List data, Rcpp::List param, size_t i,

			Rcpp::RObject custom_function = R_NilValue);













// [[Rcpp::export(rng = false)]]

double cpp_ll_contact(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

		      Rcpp::RObject custom_function = R_NilValue);



double cpp_ll_contact(Rcpp::List data, Rcpp::List param, size_t i,

		      Rcpp::RObject custom_function = R_NilValue);









// Aggregated functions, i.e. summing some of the above



// [[Rcpp::export(rng = false)]]

double cpp_ll_timing(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

		     Rcpp::RObject custom_functions = R_NilValue);



double cpp_ll_timing(Rcpp::List data, Rcpp::List param, size_t i,

		     Rcpp::RObject custom_functions = R_NilValue);













// [[Rcpp::export(rng = false)]]

double cpp_ll_all(Rcpp::List data, Rcpp::List param, SEXP i = R_NilValue,

		  Rcpp::RObject custom_functions = R_NilValue);



double cpp_ll_all(Rcpp::List data, Rcpp::List param, size_t i,

		  Rcpp::RObject custom_functions = R_NilValue);





#endif