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Fix tests #540

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merged 4 commits into from
Feb 5, 2024
Merged

Fix tests #540

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9472743
don't use deprecated fixed option
sbfnk Feb 5, 2024
6cb63df
use more samples to ensure timeout is hit
sbfnk Feb 5, 2024
4d665f9
update snapshots
sbfnk Feb 5, 2024
55a644f
avoid using array-vector arithmetic in dist_skel
sbfnk Feb 5, 2024
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8 changes: 4 additions & 4 deletions R/dist.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1403,12 +1403,12 @@
## apply stragey depending on choice
if (strategy == "mean") {
x <- dist_spec(
mean = x$mean_mean,
sd = x$sd_mean,
mean = c(x$mean_mean),
sd = c(x$sd_mean),
mean_sd = 0,
sd_sd = 0,
distribution = x$dist,
max = x$max
max = c(x$max)
)
} else if (strategy == "sample") {
lower_bound <- ifelse(x$dist == "gamma", 0, -Inf)
Expand All @@ -1422,7 +1422,7 @@
mean_sd = 0,
sd_sd = 0,
distribution = x$dist,
max = x$max
max = c(x$max)

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)
}
return(x)
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2 changes: 1 addition & 1 deletion R/opts.R
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Expand Up @@ -63,8 +63,8 @@
if (!("mean" %in% names(dot_options))) {
dot_options$mean <- 1
}
dot_options$fixed <- fixed
dist <- do.call(dist_spec, dot_options)
if (fixed) dist <- fix_dist(dist)

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deprecated_options_given <- TRUE
} else if (!missing(disease) && !missing(source)) {
dist <- get_generation_time(disease, source, max, fixed)
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8 changes: 5 additions & 3 deletions tests/testthat/_snaps/calc_CrI.md
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Original file line number Diff line number Diff line change
@@ -1,12 +1,14 @@
# calc_CrI works as expected with default arguments

value CrI
<num> <char>
1: 1.45 lower_90
2: 9.55 upper_90

# calc_CrI works as expected when grouping

type value CrI
1: car 1.45 lower_90
2: car 9.55 upper_90
type value CrI
<char> <num> <char>
1: car 1.45 lower_90
2: car 9.55 upper_90

18 changes: 12 additions & 6 deletions tests/testthat/_snaps/calc_CrIs.md
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@@ -1,15 +1,21 @@
# calc_CrI works as expected with default arguments

. lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
1: . 1.45 3.25 4.6 6.4 7.75 9.55
Key: <.>
. lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
<char> <num> <num> <num> <num> <num> <num>
1: . 1.45 3.25 4.6 6.4 7.75 9.55

# calc_CrI works as expected when grouping

type lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
1: car 1.45 3.25 4.6 6.4 7.75 9.55
Key: <type>
type lower_90 lower_50 lower_20 upper_20 upper_50 upper_90
<char> <num> <num> <num> <num> <num> <num>
1: car 1.45 3.25 4.6 6.4 7.75 9.55

# calc_CrI works as expected when given a custom CrI list

. lower_95 lower_40 lower_10 upper_10 upper_40 upper_95
1: . 1.225 3.7 5.05 5.95 7.3 9.775
Key: <.>
. lower_95 lower_40 lower_10 upper_10 upper_40 upper_95
<char> <num> <num> <num> <num> <num> <num>
1: . 1.225 3.7 5.05 5.95 7.3 9.775

18 changes: 12 additions & 6 deletions tests/testthat/_snaps/calc_summary_measures.md
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Original file line number Diff line number Diff line change
@@ -1,21 +1,27 @@
# calc_summary_measures works as expected with default arguments

type median mean sd lower_90 lower_50 lower_20 upper_20 upper_50
1: car 5.5 5.5 3.02765 1.45 3.25 4.6 6.4 7.75
type median mean sd lower_90 lower_50 lower_20 upper_20 upper_50
<char> <num> <num> <num> <num> <num> <num> <num> <num>
1: car 5.5 5.5 3.02765 1.45 3.25 4.6 6.4 7.75
upper_90
<num>
1: 9.55

# calc_CrI works as expected when grouping

type median mean sd lower_90 lower_50 lower_20 upper_20 upper_50
1: car 5.5 5.5 3.02765 1.45 3.25 4.6 6.4 7.75
type median mean sd lower_90 lower_50 lower_20 upper_20 upper_50
<char> <num> <num> <num> <num> <num> <num> <num> <num>
1: car 5.5 5.5 3.02765 1.45 3.25 4.6 6.4 7.75
upper_90
<num>
1: 9.55

# calc_CrI works as expected when given a custom CrI list

type median mean sd lower_95 lower_40 lower_10 upper_10 upper_40
1: car 5.5 5.5 3.02765 1.225 3.7 5.05 5.95 7.3
type median mean sd lower_95 lower_40 lower_10 upper_10 upper_40
<char> <num> <num> <num> <num> <num> <num> <num> <num>
1: car 5.5 5.5 3.02765 1.225 3.7 5.05 5.95 7.3
upper_95
<num>
1: 9.775

10 changes: 6 additions & 4 deletions tests/testthat/_snaps/calc_summary_stats.md
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Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
# calc_summary_stats works as expected with default arguments

median mean sd
1: 5.5 5.5 3.02765
median mean sd
<num> <num> <num>
1: 5.5 5.5 3.02765

# calc_summary_stats works as expected when grouping

type median mean sd
1: car 5.5 5.5 3.02765
type median mean sd
<char> <num> <num> <num>
1: car 5.5 5.5 3.02765

17 changes: 8 additions & 9 deletions tests/testthat/test-dist_spec.R
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Expand Up @@ -29,10 +29,9 @@ test_that("dist_spec returns correct output for uncertain gamma distribution", {
})

test_that("dist_spec returns correct output for fixed distribution", {
result <- dist_spec(
result <- fix_dist(dist_spec(
mean = 5, mean_sd = 3, sd = 1, max = 19, distribution = "lognormal",
fixed = TRUE
)
))
expect_equal(dim(result$mean_mean), 0)
expect_equal(dim(result$sd_mean), 0)
expect_equal(result$fixed, array(1L))
Expand Down Expand Up @@ -74,12 +73,12 @@ test_that("+.dist_spec returns correct output for sum of two distributions", {
})

test_that("+.dist_spec returns correct output for sum of two fixed distributions", {
lognormal <- dist_spec(
mean = 5, sd = 1, max = 19, distribution = "lognormal", fixed = TRUE
)
gamma <- dist_spec(
mean = 3, sd = 2, max = 19, distribution = "gamma", fixed = TRUE
)
lognormal <- fix_dist(dist_spec(
mean = 5, sd = 1, max = 19, distribution = "lognormal"
))
gamma <- fix_dist(dist_spec(
mean = 3, sd = 2, max = 19, distribution = "gamma"
))
result <- lognormal + gamma
expect_equal(dim(result$mean_mean), 0)
expect_equal(dim(result$sd_mean), 0)
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-estimate_infections.R
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Expand Up @@ -86,12 +86,12 @@ test_that("estimate_infections fails as expected when given a very short timeout
expect_error(output <- capture.output(suppressMessages(
out <- default_estimate_infections(
reported_cases,
add_stan = list(future = TRUE, max_execution_time = 1)
add_stan = list(future = TRUE, max_execution_time = 1, samples = 2000)
))), "all chains failed")
expect_error(output <- capture.output(suppressMessages(
out <- default_estimate_infections(
reported_cases,
add_stan = list(future = FALSE, max_execution_time = 1)
add_stan = list(future = FALSE, max_execution_time = 1, samples = 2000)
))), "timed out")
})

Expand Down
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