#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