mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 08:06:13 +01:00
178 lines
7.8 KiB
R
Executable File
178 lines
7.8 KiB
R
Executable File
context("portion.R")
|
|
|
|
test_that("portions works", {
|
|
# amox resistance in `septic_patients`
|
|
expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001)
|
|
expect_equal(portion_I(septic_patients$amox), 0.0025597, tolerance = 0.0001)
|
|
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
|
|
portion_S(septic_patients$amox))
|
|
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
|
|
portion_IR(septic_patients$amox))
|
|
expect_equal(portion_S(septic_patients$amox) + portion_I(septic_patients$amox),
|
|
portion_SI(septic_patients$amox))
|
|
|
|
expect_equal(septic_patients %>% portion_S(amcl),
|
|
0.7062363,
|
|
tolerance = 0.001)
|
|
expect_equal(septic_patients %>% portion_S(amcl, gent),
|
|
0.9210074,
|
|
tolerance = 0.001)
|
|
|
|
# amcl+genta susceptibility around 92.1%
|
|
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
|
|
septic_patients$gent,
|
|
interpretation = "S")),
|
|
0.9210074,
|
|
tolerance = 0.000001)
|
|
|
|
# percentages
|
|
expect_equal(septic_patients %>%
|
|
group_by(hospital_id) %>%
|
|
summarise(R = portion_R(cipr, as_percent = TRUE),
|
|
I = portion_I(cipr, as_percent = TRUE),
|
|
S = portion_S(cipr, as_percent = TRUE),
|
|
n = n_rsi(cipr),
|
|
total = n()) %>%
|
|
pull(n) %>%
|
|
sum(),
|
|
1409)
|
|
|
|
# count of cases
|
|
expect_equal(septic_patients %>%
|
|
group_by(hospital_id) %>%
|
|
summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
|
|
cipro_n = n_rsi(cipr),
|
|
genta_p = portion_S(gent, as_percent = TRUE),
|
|
genta_n = n_rsi(gent),
|
|
combination_p = portion_S(cipr, gent, as_percent = TRUE),
|
|
combination_n = n_rsi(cipr, gent)) %>%
|
|
pull(combination_n),
|
|
c(202, 488, 201, 499))
|
|
|
|
expect_warning(portion_R(as.character(septic_patients$amcl)))
|
|
expect_warning(portion_S(as.character(septic_patients$amcl)))
|
|
expect_warning(portion_S(as.character(septic_patients$amcl,
|
|
septic_patients$gent)))
|
|
expect_warning(n_rsi(as.character(septic_patients$amcl,
|
|
septic_patients$gent)))
|
|
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
|
|
septic_patients$gent))),
|
|
1828)
|
|
|
|
# check for errors
|
|
expect_error(portion_IR("test", minimum = "test"))
|
|
expect_error(portion_IR("test", as_percent = "test"))
|
|
expect_error(portion_I("test", minimum = "test"))
|
|
expect_error(portion_I("test", as_percent = "test"))
|
|
expect_error(portion_S("test", minimum = "test"))
|
|
expect_error(portion_S("test", as_percent = "test"))
|
|
|
|
# check too low amount of isolates
|
|
expect_identical(suppressWarnings(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
|
|
NA)
|
|
expect_identical(suppressWarnings(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
|
|
NA)
|
|
expect_identical(suppressWarnings(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
|
|
NA)
|
|
|
|
# warning for speed loss
|
|
expect_warning(portion_R(as.character(septic_patients$gent)))
|
|
expect_warning(portion_I(as.character(septic_patients$gent)))
|
|
expect_warning(portion_S(septic_patients$amcl, as.character(septic_patients$gent)))
|
|
|
|
})
|
|
|
|
test_that("old rsi works", {
|
|
# amox resistance in `septic_patients` should be around 58.53%
|
|
expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001)
|
|
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001)
|
|
|
|
# pita+genta susceptibility around 98.09%
|
|
expect_equal(suppressWarnings(rsi(septic_patients$pita,
|
|
septic_patients$gent,
|
|
interpretation = "S",
|
|
info = TRUE)),
|
|
0.9498886,
|
|
tolerance = 0.0001)
|
|
|
|
# count of cases
|
|
expect_equal(septic_patients %>%
|
|
group_by(hospital_id) %>%
|
|
summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S",
|
|
as_percent = TRUE, warning = FALSE)),
|
|
cipro_n = n_rsi(cipr),
|
|
genta_S = suppressWarnings(rsi(gent, interpretation = "S",
|
|
as_percent = TRUE, warning = FALSE)),
|
|
genta_n = n_rsi(gent),
|
|
combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
|
|
as_percent = TRUE, warning = FALSE)),
|
|
combination_n = n_rsi(cipr, gent)) %>%
|
|
pull(combination_n),
|
|
c(202, 488, 201, 499))
|
|
|
|
# portion_df
|
|
expect_equal(
|
|
septic_patients %>% select(amox) %>% portion_df() %>% pull(Value),
|
|
c(septic_patients$amox %>% portion_S(),
|
|
septic_patients$amox %>% portion_I(),
|
|
septic_patients$amox %>% portion_R())
|
|
)
|
|
expect_equal(
|
|
septic_patients %>% select(amox) %>% portion_df(combine_IR = TRUE) %>% pull(Value),
|
|
c(septic_patients$amox %>% portion_S(),
|
|
septic_patients$amox %>% portion_IR())
|
|
)
|
|
|
|
|
|
})
|
|
|
|
test_that("prediction of rsi works", {
|
|
amox_R <- septic_patients %>%
|
|
filter(mo == "B_ESCHR_COL") %>%
|
|
rsi_predict(col_ab = "amox",
|
|
col_date = "date",
|
|
minimum = 10,
|
|
info = TRUE) %>%
|
|
pull("value")
|
|
# amox resistance will increase according to data set `septic_patients`
|
|
expect_true(amox_R[3] < amox_R[20])
|
|
|
|
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
model = "binomial",
|
|
col_ab = "amox",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
model = "loglin",
|
|
col_ab = "amox",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
model = "lin",
|
|
col_ab = "amox",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
|
|
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
model = "INVALID MODEL",
|
|
col_ab = "amox",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
col_ab = "NOT EXISTING COLUMN",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
col_ab = "amox",
|
|
col_date = "NOT EXISTING COLUMN",
|
|
info = TRUE))
|
|
# almost all E. coli are mero S in the Netherlands :)
|
|
expect_error(resistance_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"),
|
|
col_ab = "mero",
|
|
col_date = "date",
|
|
info = TRUE))
|
|
|
|
expect_error(portion_df(c("A", "B", "C")))
|
|
expect_error(portion_df(septic_patients[,"date"]))
|
|
})
|