AMR/tests/testthat/test-rsi_analysis.R

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context("rsi_analysis.R")
test_that("rsi works", {
# amox resistance in `septic_patients` should be around 53.86%
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expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = FALSE),
0.5386,
tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
expect_equal(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE),
0.9809,
tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = c("pita", "gent"),
interpretation = "S",
info = FALSE),
0.9809,
tolerance = 0.0001)
# mero+pita+genta susceptibility around 98.58%
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expect_equal(rsi_df(septic_patients,
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ab = c("mero", "pita", "gent"),
interpretation = "IS",
info = FALSE),
0.9858,
tolerance = 0.0001)
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# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_S = 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_n = n_rsi(gent),
combination_S = rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(138, 474, 170, 464, 183))
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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",
info = FALSE) %>%
pull("probR")
# amox resistance will decrease using dataset `septic_patients`
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expect_true(amox_R[2] > 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",
info = FALSE))
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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",
info = FALSE))
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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",
info = FALSE))
})