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(v0.8.0.9027) adding susceptibility() and resistance()

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dr. M.S. (Matthijs) Berends
2019-11-10 12:16:56 +01:00
parent 228a4245cb
commit 59ededa8dc
85 changed files with 1526 additions and 932 deletions
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70
tests/testthat/test-count.R
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@ -22,67 +22,67 @@
context("count.R")
test_that("counts work", {
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
# AMX resistance in `example_isolates`
expect_equal(count_R(example_isolates$AMX), 683)
expect_equal(count_I(example_isolates$AMX), 3)
expect_equal(count_S(example_isolates$AMX), 543)
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
count_IR(example_isolates$AMX))
expect_equal(count_S(example_isolates$AMX) + count_I(example_isolates$AMX),
count_SI(example_isolates$AMX))
expect_equal(count_R(example_isolates$AMX), 683)
expect_equal(count_I(example_isolates$AMX), 3)
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
suppressWarnings(count_IR(example_isolates$AMX)))
expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
count_SI(example_isolates$AMX))
library(dplyr)
expect_equal(example_isolates %>% count_S(AMC), 1342)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE) +
example_isolates %>% count_IR(AMC, GEN, only_all_tested = TRUE))
example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
# count of cases
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro = count_SI(CIP),
genta = count_SI(GEN),
combination = count_SI(CIP, GEN)) %>%
summarise(cipro = count_susceptible(CIP),
genta = count_susceptible(GEN),
combination = count_susceptible(CIP, GEN)) %>%
pull(combination),
c(253, 465, 192, 558))
# count_df
expect_equal(
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
c(example_isolates$AMX %>% count_SI(),
example_isolates$AMX %>% count_R())
c(example_isolates$AMX %>% count_susceptible(),
example_isolates$AMX %>% count_resistant())
)
expect_equal(
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_IR())
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(example_isolates$AMX %>% count_S(),
c(suppressWarnings(example_isolates$AMX %>% count_S()),
example_isolates$AMX %>% count_I(),
example_isolates$AMX %>% count_R())
)
# warning for speed loss
expect_warning(count_R(as.character(example_isolates$AMC)))
expect_warning(count_I(as.character(example_isolates$AMC)))
expect_warning(count_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_warning(count_S(example_isolates$AMC,
as.character(example_isolates$GEN)))
expect_warning(count_resistant(as.character(example_isolates$AMC)))
expect_warning(count_resistant(example_isolates$AMC,
as.character(example_isolates$GEN)))
# check for errors
expect_error(count_IR("test", minimum = "test"))
expect_error(count_IR("test", as_percent = "test"))
expect_error(count_I("test", minimum = "test"))
expect_error(count_I("test", as_percent = "test"))
expect_error(count_S("test", minimum = "test"))
expect_error(count_S("test", as_percent = "test"))
expect_error(count_resistant("test", minimum = "test"))
expect_error(count_resistant("test", as_percent = "test"))
expect_error(count_susceptible("test", minimum = "test"))
expect_error(count_susceptible("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(example_isolates[, "date"]))