AMR/tests/testthat/test-resistance.R

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context("resistance.R")
test_that("resistance works", {
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# 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)
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# pita+genta susceptibility around 98.09%
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expect_equal(susceptibility(septic_patients$pita,
septic_patients$gent),
0.9535,
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tolerance = 0.0001)
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S")),
0.9535,
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tolerance = 0.0001)
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# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
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summarise(cipro_p = susceptibility(cipr, as_percent = TRUE),
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cipro_n = n_rsi(cipr),
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genta_p = susceptibility(gent, as_percent = TRUE),
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genta_n = n_rsi(gent),
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combination_p = susceptibility(cipr, gent, as_percent = TRUE),
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combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
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expect_warning(resistance(as.character(septic_patients$amcl)))
expect_warning(susceptibility(as.character(septic_patients$amcl)))
expect_warning(susceptibility(as.character(septic_patients$amcl,
septic_patients$gent)))
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})
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test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 66.33%
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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)
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expect_equal(rsi_df(septic_patients,
ab = "amox",
info = TRUE),
0.6633,
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tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9535,
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tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = c("pita", "gent"),
interpretation = "S",
info = TRUE),
0.9535,
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tolerance = 0.0001)
# more than 2 not allowed
expect_error(rsi_df(septic_patients,
ab = c("mero", "pita", "gent"),
interpretation = "IS",
info = TRUE))
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
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summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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cipro_n = n_rsi(cipr),
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genta_S = suppressWarnings(rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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genta_n = n_rsi(gent),
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combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
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})
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test_that("prediction of rsi works", {
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amox_R <- septic_patients %>%
filter(bactid == "ESCCOL") %>%
rsi_predict(col_ab = "amox",
col_date = "date",
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minimum = 10,
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info = TRUE) %>%
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pull("value")
# amox resistance will increase according to data set `septic_patients`
expect_true(amox_R[3] < amox_R[20])
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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"),
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model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
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info = TRUE))
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expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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col_ab = "NOT EXISTING COLUMN",
col_date = "date",
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info = TRUE))
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expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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col_ab = "amox",
col_date = "NOT EXISTING COLUMN",
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info = TRUE))
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})