AMR/tests/testthat/test-portion.R

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R
Executable File

context("portion.R")
test_that("portions works", {
# amox resistance in `septic_patients`
expect_equal(portion_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.0030, 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$amox))
expect_equal(septic_patients %>% portion_S(amcl),
0.673,
tolerance = 0.001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.921,
tolerance = 0.001)
# amcl+genta susceptibility around 92.1%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
septic_patients$gent,
interpretation = "S")),
0.9208777,
tolerance = 0.000001)
# percentages
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(R = portion_R(cipr, as_percent = TRUE),
I = portion_I(cipr, as_percent = TRUE),
S = portion_S(cipr, as_percent = TRUE),
n = n_rsi(cipr),
total = n()) %>%
pull(n) %>%
sum(),
1404)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
cipro_n = n_rsi(cipr),
genta_p = portion_S(gent, as_percent = TRUE),
genta_n = n_rsi(gent),
combination_p = portion_S(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
expect_warning(portion_R(as.character(septic_patients$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$gent))),
1570)
# check for errors
expect_error(portion_IR("test", minimum = "test"))
expect_error(portion_IR("test", as_percent = "test"))
expect_error(portion_I("test", minimum = "test"))
expect_error(portion_I("test", as_percent = "test"))
expect_error(portion_S("test", minimum = "test"))
expect_error(portion_S("test", as_percent = "test"))
# check too low amount of isolates
expect_identical(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
NA)
expect_identical(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
NA)
expect_identical(portion_S(septic_patients$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 66.33%
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)
# pita+genta susceptibility around 98.09%
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9535,
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, 482, 201, 499))
# portion_df
expect_equal(
septic_patients %>% select(amox) %>% portion_df() %>% pull(Percentage),
c(septic_patients$amox %>% portion_S(),
septic_patients$amox %>% portion_I(),
septic_patients$amox %>% portion_R())
)
})
test_that("prediction of rsi works", {
amox_R <- septic_patients %>%
filter(bactid == "ESCCOL") %>%
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, bactid == "ESCCOL"),
model = "binomial",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "loglin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "lin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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, bactid == "ESCCOL"),
col_ab = "mero",
col_date = "date",
info = TRUE))
})