--- a
+++ b/src/likelihoods.h
@@ -0,0 +1,88 @@
+#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