Warn about default generation time options (#623)

* add warning about generation time default

* add test

* set default in test

R/opts.R

@@ -97,6 +97,14 @@ generation_time_opts <- function(dist = Fixed(1), ...,
       "information, see the relevant documentation pages using ",
       "`?generation_time_opts`")
   }
+  if (missing(dist)) {
+    warning(
+      "No generation time distribution given. Assuming a fixed generation ",
+      "time of 1 day, i.e. the reproduction number is the same as the daily ",
+      "growth rate. If this was intended then this warning can be silenced by ",
+      "setting `dist` explicitly to `Fixed(1)`."
+    )
+  }
   check_stan_delay(dist)
   attr(dist, "tolerance") <- tolerance
   attr(dist, "class") <- c("generation_time_opts", class(dist))

tests/testthat/test-delays.R

@@ -1,4 +1,4 @@
-test_stan_delays <- function(generation_time = generation_time_opts(),
+test_stan_delays <- function(generation_time = generation_time_opts(Fixed(1)),
                              delays = delay_opts(),
                              truncation = trunc_opts(),
                              params = c()) {

tests/testthat/test-opts.R

@@ -1,3 +1,7 @@
+test_that("default generation time options produce a warning", {
+  expect_warning(generation_time_opts(), "1 day")
+})
+
 test_that("deprecated arguments are caught", {
   expect_deprecated(stan_opts(init_fit = "cumulative"))
-})
+})