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new functions R, RI, SI, S

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-07-29 22:14:51 +02:00
parent 8421e3f005
commit 826694323b
10 changed files with 256 additions and 183 deletions
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7
tests/testthat/test-bactid.R
View File

@ -60,5 +60,12 @@ test_that("as.bactid works", {
expect_identical(as.bactid("ESCCOL"),
guess_bactid("ESCCOL"))
# test pull
expect_equal(nrow(septic_patients %>% mutate(bactid = as.bactid(bactid))),
2000)
# test data.frame
expect_equal(nrow(data.frame(test = as.bactid("ESCCOL"))),
1)
})

34
tests/testthat/test-resistance.R
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@ -1,6 +1,16 @@
context("resistance.R")
test_that("resistance works", {
# check shortcuts
expect_equal(resistance(septic_patients$amox, include_I = TRUE),
IR(septic_patients$amox))
expect_equal(resistance(septic_patients$amox, include_I = FALSE),
R(septic_patients$amox))
expect_equal(susceptibility(septic_patients$amox, include_I = TRUE),
SI(septic_patients$amox))
expect_equal(susceptibility(septic_patients$amox, include_I = FALSE),
S(septic_patients$amox))
# amox resistance in `septic_patients` should be around 66.33%
expect_equal(resistance(septic_patients$amox, include_I = TRUE), 0.6633, tolerance = 0.0001)
expect_equal(susceptibility(septic_patients$amox, include_I = FALSE), 1 - 0.6633, tolerance = 0.0001)
@ -37,18 +47,18 @@ test_that("resistance works", {
test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 66.33%
expect_equal(rsi(septic_patients$amox), 0.6633, tolerance = 0.0001)
expect_equal(rsi(septic_patients$amox, interpretation = "S"), 1 - 0.6633, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.6633, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.6633, tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = "amox",
info = TRUE),
0.6633,
tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
expect_equal(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE),
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9535,
tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
@ -66,14 +76,14 @@ test_that("old rsi works", {
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_S = rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE),
summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
cipro_n = n_rsi(cipr),
genta_S = rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE),
genta_S = suppressWarnings(rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
genta_n = n_rsi(gent),
combination_S = rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE),
combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))