From b09c702b838dc8bda5e69d86d98f66dda7541193 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Mon, 3 Jul 2023 14:56:45 -0500
Subject: [PATCH] shorten seeding time (#413)

* shorten seeding time

* replace example with test

* add news item and bump version

* Update NEWS.md

---------

Co-authored-by: Sam Abbott <s.e.abbott12@gmail.com>
---
 DESCRIPTION                        |  2 +-
 NEWS.md                            |  1 +
 R/get.R                            |  5 +++--
 tests/testthat/test-seeding-time.R | 14 ++++++++++++++
 4 files changed, 19 insertions(+), 3 deletions(-)
 create mode 100644 tests/testthat/test-seeding-time.R

diff --git a/DESCRIPTION b/DESCRIPTION
index de3af42a1..cf9dcddf0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Type: Package
 Package: EpiNow2
 Title: Estimate Real-Time Case Counts and Time-Varying
     Epidemiological Parameters
-Version: 1.3.6.7000
+Version: 1.3.6.8000
 Authors@R: 
     c(person(given = "Sam",
              family = "Abbott",
diff --git a/NEWS.md b/NEWS.md
index b428f3b2e..1b685f2ea 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -20,6 +20,7 @@ This release is in development. For a stable release install 1.3.5 from CRAN.
 * [pak](https://pak.r-lib.org/) is now suggested for installing the developmental version of the package. By @jamesmbaazam in #407 and reviewed by @seabbs. This has been successfully tested on MacOS Ventura, Ubuntu 20.04, and Windows 10. Users are advised to use `remotes::install_github("epiforecasts/EpiNow2")` if `pak` fails and if both fail, raise an issue.
 * `dist_fit()`'s `samples` argument now takes a default value of 1000 instead of NULL. If a supplied `samples` is less than 1000, it is changed to 1000 and a warning is thrown to indicate the change. By @jamesmbazam in #389 and reviewed by @seabbs.
 * The internal distribution interface has been streamlined to reduce code duplication. By @sbfnk in #363 and reviewed by @seabbs.
+* A small bug has been fixed where the seeding time was one day too long. By @sbfnk in #413 and reviewed by @seabbs.
 
 # EpiNow2 1.3.5
 
diff --git a/R/get.R b/R/get.R
index bf233076c..a13d08af3 100644
--- a/R/get.R
+++ b/R/get.R
@@ -318,10 +318,11 @@ get_seeding_time <- function(delays, generation_time) {
   } else {
     seeding_time <- as.integer(seeding_time)
   }
-  ## make sure we have at least gt_max seeding time
+  ## make sure we have at least (length of total gt pmf - 1) seeding time
   seeding_time <- max(
     seeding_time,
-    sum(generation_time$max) + sum(generation_time$np_pmf_max)
+    sum(generation_time$max) + sum(generation_time$np_pmf_max) -
+      length(generation_time$max) - length(generation_time$np_pmf_max)
   )
   return(seeding_time)
 }
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)
+})