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add confidence intervals (fixed #70), remove combine_IR

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-20 16:08:01 +02:00
parent 85e2fbe4a3
commit aa2c0639d0
19 changed files with 248 additions and 144 deletions
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2
inst/tinytest/test-bug_drug_combinations.R
View File

@ -31,7 +31,7 @@ b <- suppressWarnings(bug_drug_combinations(example_isolates))
expect_inherits(b, "bug_drug_combinations")
expect_stdout(suppressMessages(print(b)))
expect_true(is.data.frame(format(b)))
expect_true(is.data.frame(format(b, combine_IR = TRUE, add_ab_group = FALSE)))
expect_true(is.data.frame(format(b, add_ab_group = FALSE)))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_true(example_isolates %>%
group_by(ward) %>%

7
inst/tinytest/test-count.R
View File

@ -94,13 +94,6 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
example_isolates$AMX %>% count_resistant()
)
)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(
suppressWarnings(example_isolates$AMX %>% count_S()),
suppressWarnings(example_isolates$AMX %>% count_IR())
)
)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(

11
inst/tinytest/test-proportion.R
View File

@ -32,6 +32,8 @@ expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolate
# AMX resistance in `example_isolates`
expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
expect_equal(rsi_confidence_interval(example_isolates$AMX)[1], 0.5688204, tolerance = 0.0001)
expect_equal(rsi_confidence_interval(example_isolates$AMX)[2], 0.6218738, tolerance = 0.0001)
expect_equal(
1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
proportion_S(example_isolates$AMX)
@ -99,13 +101,6 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
example_isolates$AMX %>% proportion_R()
)
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_IR = TRUE) %>% pull(value),
c(
example_isolates$AMX %>% proportion_S(),
example_isolates$AMX %>% proportion_IR()
)
)
expect_equal(
example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
c(
@ -114,6 +109,8 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
example_isolates$AMX %>% proportion_R()
)
)
expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, rsi_confidence_interval)))
}
expect_warning(proportion_R(as.character(example_isolates$AMC)))