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shorten seeding time #413

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Merged
merged 4 commits into from
Jul 3, 2023
Merged

shorten seeding time #413

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3867d5d
shorten seeding time
sbfnk Jul 3, 2023
1c3de1a
replace example with test
sbfnk Jul 3, 2023
897f4b1
add news item and bump version
sbfnk Jul 3, 2023
73c8187
Update NEWS.md
seabbs Jul 3, 2023
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replace example with test
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@sbfnk
sbfnk committed Jul 3, 2023
commit 1c3de1a820533980e3ed3345d206d7e411075861
5 changes: 0 additions & 5 deletions R/get.R
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Expand Up @@ -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))
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6 changes: 0 additions & 6 deletions man/get_seeding_time.Rd
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14 changes: 14 additions & 0 deletions tests/testthat/test-seeding-time.R
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@@ -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)
})