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Directly calculated growth #610

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Merged
merged 7 commits into from
Mar 22, 2024
Merged

Directly calculated growth #610

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72b3f1b
switch to directly calculated growth rate
seabbs Dec 30, 2020
0970731
remove superseded function
sbfnk Mar 12, 2024
79cc2fc
add news item
sbfnk Mar 12, 2024
717b8ff
avoid conversion
sbfnk Mar 12, 2024
a16e9bd
add skips
sbfnk Mar 12, 2024
7103a39
add test for exp(r)==R with fixed gt of 1 day
sbfnk Mar 18, 2024
6ffbc3c
fix typo and add reviewer
sbfnk Mar 22, 2024
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add test for exp(r)==R with fixed gt of 1 day
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@sbfnk
sbfnk committed Mar 18, 2024
commit 7103a39cd042eb3fbeba28fb94d309c21bc926a9
22 changes: 20 additions & 2 deletions tests/testthat/test-estimate_infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@ futile.logger::flog.threshold("FATAL")

reported_cases <- EpiNow2::example_confirmed[1:30]

default_estimate_infections <- function(..., add_stan = list(), delay = TRUE) {
default_estimate_infections <- function(..., add_stan = list(), gt = TRUE,
delay = TRUE) {
futile.logger::flog.threshold("FATAL")

def_stan <- list(
Expand All @@ -15,7 +16,9 @@ default_estimate_infections <- function(..., add_stan = list(), delay = TRUE) {
stan_args <- do.call(stan_opts, def_stan)

suppressWarnings(estimate_infections(...,
generation_time = generation_time_opts(example_generation_time),
generation_time = fifelse(
gt, generation_time_opts(example_generation_time), generation_time_opts()
),
delays = ifelse(delay, list(delay_opts(example_reporting_delay)), list(delay_opts()))[[1]],
stan = stan_args, verbose = FALSE
))
Expand All @@ -27,6 +30,7 @@ test_estimate_infections <- function(...) {
expect_true(nrow(out$samples) > 0)
expect_true(nrow(out$summarised) > 0)
expect_true(nrow(out$observations) > 0)
invisible(out)
}

# Test functionality ------------------------------------------------------
Expand Down Expand Up @@ -89,6 +93,20 @@ test_that("estimate_infections successfully returns estimates using a random wal
test_estimate_infections(reported_cases, gp = NULL, rt = rt_opts(rw = 7))
})

test_that("estimate_infections works without setting a generation time", {
skip_on_cran()
df <- test_estimate_infections(reported_cases, gt = FALSE, delay = FALSE)
## check exp(r) == R
growth_rate <- df$samples[variable == "growth_rate"][,
list(date, sample, growth_rate = value)
]
R <- df$samples[variable == "R"][,
list(date, sample, R = value)
]
combined <- merge(growth_rate, R, by = c("date", "sample"), all = FALSE)
expect_equal(exp(combined$growth_rate), combined$R)
})

test_that("estimate_infections fails as expected when given a very short timeout", {
skip_on_cran()
expect_error(output <- capture.output(suppressMessages(
Expand Down
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