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rsi family for resistance analysis

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-03 14:49:29 +02:00
parent 227121af3d
commit ae2433a020
15 changed files with 421 additions and 196 deletions
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61
tests/testthat/test-resistance.R → tests/testthat/test-rsi_IR.R
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@ -1,19 +1,23 @@
context("resistance.R")
context("rsi_IR.R")
test_that("resistance works", {
# check shortcuts
expect_equal(resistance(septic_patients$amox, include_I = TRUE),
IR(septic_patients$amox))
rsi_IR(septic_patients$amox))
expect_equal(resistance(septic_patients$amox, include_I = FALSE),
R(septic_patients$amox))
rsi_R(septic_patients$amox))
expect_equal(intermediate(septic_patients$amox),
rsi_I(septic_patients$amox))
expect_equal(susceptibility(septic_patients$amox, include_I = TRUE),
SI(septic_patients$amox))
rsi_SI(septic_patients$amox))
expect_equal(susceptibility(septic_patients$amox, include_I = FALSE),
S(septic_patients$amox))
rsi_S(septic_patients$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)
# amox resistance in `septic_patients`
expect_equal(rsi_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
expect_equal(rsi_I(septic_patients$amox), 0.0030, tolerance = 0.0001)
expect_equal(1 - rsi_R(septic_patients$amox) - rsi_I(septic_patients$amox),
rsi_S(septic_patients$amox))
# pita+genta susceptibility around 98.09%
expect_equal(susceptibility(septic_patients$pita,
@ -26,6 +30,18 @@ test_that("resistance works", {
0.9535,
tolerance = 0.0001)
# percentages
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(R = rsi_R(cipr, as_percent = TRUE),
I = rsi_I(cipr, as_percent = TRUE),
S = rsi_S(cipr, as_percent = TRUE),
n = rsi_n(cipr),
total = n()) %>%
pull(n) %>%
sum(),
1404)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
@ -34,7 +50,7 @@ test_that("resistance works", {
genta_p = susceptibility(gent, as_percent = TRUE),
genta_n = n_rsi(gent),
combination_p = susceptibility(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
combination_n = rsi_n(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
@ -45,22 +61,29 @@ test_that("resistance works", {
# check for errors
expect_error(IR(septic_patients %>% select(amox, amcl)))
expect_error(IR("test", minimum = "test"))
expect_error(IR("test", as_percent = "test"))
expect_error(S("test", minimum = "test"))
expect_error(S("test", as_percent = "test"))
expect_error(S(septic_patients %>% select(amox, amcl)))
expect_error(S("R", septic_patients %>% select(amox, amcl)))
expect_error(rsi_IR(septic_patients %>% select(amox, amcl)))
expect_error(rsi_IR("test", minimum = "test"))
expect_error(rsi_IR("test", as_percent = "test"))
expect_error(rsi_I(septic_patients %>% select(amox, amcl)))
expect_error(rsi_I("test", minimum = "test"))
expect_error(rsi_I("test", as_percent = "test"))
expect_error(rsi_S("test", minimum = "test"))
expect_error(rsi_S("test", as_percent = "test"))
expect_error(rsi_S(septic_patients %>% select(amox, amcl)))
expect_error(rsi_S("R", septic_patients %>% select(amox, amcl)))
# check too low amount of isolates
expect_identical(IR(septic_patients$amox, minimum = nrow(septic_patients) + 1),
expect_identical(rsi_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
NA)
expect_identical(S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
expect_identical(rsi_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
NA)
expect_identical(rsi_S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
NA)
# warning for speed loss
expect_warning(S(septic_patients$amcl, as.character(septic_patients$gent)))
expect_warning(rsi_R(as.character(septic_patients$gent)))
expect_warning(rsi_I(as.character(septic_patients$gent)))
expect_warning(rsi_S(septic_patients$amcl, as.character(septic_patients$gent)))
})