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Only set seeds in testing when needed. #590

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Merged
merged 5 commits into from
Mar 1, 2024
Merged

Only set seeds in testing when needed. #590

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d74d24b
remove unneeded seeds
sbfnk Mar 1, 2024
3d0f864
update snapshots
sbfnk Mar 1, 2024
31e10e2
add news item
sbfnk Mar 1, 2024
069980d
add missing dependency
sbfnk Mar 1, 2024
855befd
add reviewer
sbfnk Mar 1, 2024
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update snapshots
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@sbfnk @seabbs
sbfnk authored and seabbs committed Mar 1, 2024
commit 3d0f86466dbfb10e1f9b3ec76373ca901bc7fa82
56 changes: 28 additions & 28 deletions tests/testthat/_snaps/simulate-infections.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,20 +16,20 @@
12: infections 2023-01-12 117.41367
13: infections 2023-01-13 93.93093
14: infections 2023-01-14 75.14475
15: reported_cases 2023-01-01 128.00000
16: reported_cases 2023-01-02 151.00000
17: reported_cases 2023-01-03 145.00000
18: reported_cases 2023-01-04 188.00000
19: reported_cases 2023-01-05 252.00000
20: reported_cases 2023-01-06 276.00000
21: reported_cases 2023-01-07 371.00000
22: reported_cases 2023-01-08 273.00000
23: reported_cases 2023-01-09 234.00000
24: reported_cases 2023-01-10 192.00000
25: reported_cases 2023-01-11 157.00000
26: reported_cases 2023-01-12 120.00000
27: reported_cases 2023-01-13 78.00000
28: reported_cases 2023-01-14 63.00000
15: reported_cases 2023-01-01 125.00000
16: reported_cases 2023-01-02 135.00000
17: reported_cases 2023-01-03 195.00000
18: reported_cases 2023-01-04 224.00000
19: reported_cases 2023-01-05 253.00000
20: reported_cases 2023-01-06 328.00000
21: reported_cases 2023-01-07 364.00000
22: reported_cases 2023-01-08 278.00000
23: reported_cases 2023-01-09 206.00000
24: reported_cases 2023-01-10 169.00000
25: reported_cases 2023-01-11 144.00000
26: reported_cases 2023-01-12 109.00000
27: reported_cases 2023-01-13 80.00000
28: reported_cases 2023-01-14 95.00000
variable date value

# simulate_infections works as expected with additional parameters
Expand All @@ -50,19 +50,19 @@
12: infections 2023-01-12 190.8991
13: infections 2023-01-13 180.8132
14: infections 2023-01-14 171.1484
15: reported_cases 2023-01-01 425.0000
16: reported_cases 2023-01-02 335.0000
17: reported_cases 2023-01-03 376.0000
18: reported_cases 2023-01-04 250.0000
19: reported_cases 2023-01-05 301.0000
20: reported_cases 2023-01-06 275.0000
21: reported_cases 2023-01-07 844.0000
22: reported_cases 2023-01-08 235.0000
23: reported_cases 2023-01-09 205.0000
24: reported_cases 2023-01-10 251.0000
25: reported_cases 2023-01-11 239.0000
26: reported_cases 2023-01-12 80.0000
27: reported_cases 2023-01-13 128.0000
28: reported_cases 2023-01-14 276.0000
15: reported_cases 2023-01-01 155.0000
16: reported_cases 2023-01-02 563.0000
17: reported_cases 2023-01-03 146.0000
18: reported_cases 2023-01-04 644.0000
19: reported_cases 2023-01-05 282.0000
20: reported_cases 2023-01-06 473.0000
21: reported_cases 2023-01-07 193.0000
22: reported_cases 2023-01-08 262.0000
23: reported_cases 2023-01-09 19.0000
24: reported_cases 2023-01-10 277.0000
25: reported_cases 2023-01-11 177.0000
26: reported_cases 2023-01-12 273.0000
27: reported_cases 2023-01-13 97.0000
28: reported_cases 2023-01-14 265.0000
variable date value

4 changes: 4 additions & 0 deletions tests/testthat/test-simulate-infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,19 +16,23 @@ test_simulate_infections <- function(obs = obs_opts(family = "poisson"), ...) {
}

test_that("simulate_infections works as expected with standard parameters", {
set.seed(123)
sim <- test_simulate_infections()
expect_equal(nrow(sim), 2 * nrow(R))
expect_snapshot_output(sim)
set.seed(Sys.time())
})

test_that("simulate_infections works as expected with additional parameters", {
set.seed(123)
sim <- test_simulate_infections(
generation_time = generation_time_opts(fix_dist(example_generation_time)),
delays = delay_opts(fix_dist(example_reporting_delay)),
obs = obs_opts(family = "negbin", phi = list(mean = 0.5, sd = 0))
)
expect_equal(nrow(sim), 2 * nrow(R))
expect_snapshot_output(sim)
set.seed(Sys.time())
})

test_that("simulate_infections fails with uncertain parameters", {
Expand Down