From 1c3de1a820533980e3ed3345d206d7e411075861 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Mon, 3 Jul 2023 16:42:59 +0100
Subject: [PATCH] replace example with test

---
 R/get.R                            |  5 -----
 man/get_seeding_time.Rd            |  6 ------
 tests/testthat/test-seeding-time.R | 14 ++++++++++++++
 3 files changed, 14 insertions(+), 11 deletions(-)
 create mode 100644 tests/testthat/test-seeding-time.R

diff --git a/R/get.R b/R/get.R
index e376b55e6..a13d08af3 100644
--- a/R/get.R
+++ b/R/get.R
@@ -310,11 +310,6 @@ get_regions_with_most_reports <- function(reported_cases,
 ##' @param generation_time Generation time as specified using `dist_spec`
 ##' @return An integer seeding time
 ##' @author Sebastian Funk
-##' @examples
-##' gt1 <- dist_spec(mean = 5, sd = 1, max = 15)
-##' gt2 <- dist_spec(mean = 10, sd = 2, max = 10)
-##' delays <- dist_spec(mean = 5, sd = 1, max = 15)
-##' get_seeding_time(delays, gt1 + gt2)
 get_seeding_time <- function(delays, generation_time) {
   # Estimate the mean delay -----------------------------------------------
   seeding_time <- sum(mean(delays))
diff --git a/man/get_seeding_time.Rd b/man/get_seeding_time.Rd
index 53a9dca4f..77c7f51b6 100644
--- a/man/get_seeding_time.Rd
+++ b/man/get_seeding_time.Rd
@@ -18,12 +18,6 @@ An integer seeding time
 The seeding time is set to the mean of the specified delays, constrained
 to be at least the maximum generation time
 }
-\examples{
-gt1 <- dist_spec(mean = 5, sd = 1, max = 15)
-gt2 <- dist_spec(mean = 10, sd = 2, max = 10)
-delays <- dist_spec(mean = 5, sd = 1, max = 15)
-get_seeding_time(delays, gt1 + gt2)
-}
 \author{
 Sebastian Funk
 }
diff --git a/tests/testthat/test-seeding-time.R b/tests/testthat/test-seeding-time.R
new file mode 100644
index 000000000..5fe43a1d7
--- /dev/null
+++ b/tests/testthat/test-seeding-time.R
@@ -0,0 +1,14 @@
+test_that("Seeding times are correctly calculated", {
+  gt1 <- dist_spec(mean = 5, sd = 1, max = 10)
+  gt2 <- dist_spec(mean = 10, sd = 2, max = 15)
+  delay1 <- dist_spec(mean = 5, sd = 1, max = 10)
+  delay2 <- dist_spec(mean = 7, sd = 3, max = 15)
+  expect_equal(get_seeding_time(delay1, gt1 + gt2), 23L) ## 10 + 15 - 1 - 1
+  expect_equal(get_seeding_time(delay1 + delay2, gt1), 12L) ## 5 + 7
+})
+
+test_that("Short seeding times are rounded up to 1", {
+  delay <- dist_spec(mean = 0.5, sd = 1, max = 2)
+  gt <- dist_spec(mean = 1)
+  expect_equal(get_seeding_time(delay, gt), 1L)
+})