--- a
+++ b/R/ref_priors.R
@@ -0,0 +1,50 @@
+
+## ON THE PURPOSE OF THESE FUNCTIONS
+
+## These functions are no longer used in outbreaker2, but were part of the
+## original implementation, and are still used in testing procedures to ensure
+## that Rcpp versions give identical results.
+
+
+
+
+
+
+## We use an exponential prior for the mutation rate; the prior rate, which does
+## not change in the MCMC, is enclosed in the returned function.
+
+.prior_mu <- function(param, rate) {
+    stats::dexp(param$mu, rate, log = TRUE)
+}
+
+
+
+
+
+
+## We use a beta prior for the reporting probability (which contrains it to lie
+## between 0 and 1); the 2 shape parameters, which do not change in the MCMC,
+## are enclosed in the returned function.
+
+.prior_pi <- function(param, shape1, shape2) {
+    stats::dbeta(param$pi, shape1, shape2, log = TRUE)
+}
+
+
+## We use a beta prior for the contact reporting coverage (which contrains it to lie
+## between 0 and 1); the 2 shape parameters, which do not change in the MCMC,
+## are enclosed in the returned function.
+
+.prior_eps <- function(param, shape1, shape2) {
+    stats::dbeta(param$eps, shape1, shape2, log = TRUE)
+}
+
+
+
+## We use a beta prior for the non-infectious contact rate (which contrains it
+## to lie between 0 and 1); the 2 shape parameters, which do not change in the
+## MCMC, are enclosed in the returned function.
+
+.prior_lambda <- function(param, shape1, shape2) {
+    stats::dbeta(param$lambda, shape1, shape2, log = TRUE)
+}