mirror of https://github.com/msberends/AMR.git
122 lines
5.2 KiB
R
Executable File
122 lines
5.2 KiB
R
Executable File
context("resistance.R")
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test_that("resistance works", {
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# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(resistance(septic_patients$amox, include_I = TRUE), 0.6633, tolerance = 0.0001)
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expect_equal(susceptibility(septic_patients$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$pita,
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septic_patients$gent),
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0.9535,
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tolerance = 0.0001)
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
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septic_patients$gent,
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interpretation = "S")),
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0.9535,
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tolerance = 0.0001)
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# count of cases
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expect_equal(septic_patients %>%
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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)) %>%
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pull(combination_n),
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c(202, 482, 201, 499))
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expect_warning(resistance(as.character(septic_patients$amcl)))
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expect_warning(susceptibility(as.character(septic_patients$amcl)))
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expect_warning(susceptibility(as.character(septic_patients$amcl,
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septic_patients$gent)))
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})
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test_that("old rsi works", {
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# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(rsi(septic_patients$amox), 0.6633, tolerance = 0.0001)
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expect_equal(rsi(septic_patients$amox, interpretation = "S"), 1 - 0.6633, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = TRUE),
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0.6633,
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tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(rsi(septic_patients$pita,
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septic_patients$gent,
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interpretation = "S",
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info = TRUE),
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0.9535,
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tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = c("pita", "gent"),
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interpretation = "S",
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info = TRUE),
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0.9535,
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tolerance = 0.0001)
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# more than 2 not allowed
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expect_error(rsi_df(septic_patients,
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ab = c("mero", "pita", "gent"),
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interpretation = "IS",
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info = TRUE))
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# count of cases
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(cipro_S = rsi(cipr, interpretation = "S",
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as_percent = TRUE, warning = FALSE),
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cipro_n = n_rsi(cipr),
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genta_S = rsi(gent, interpretation = "S",
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as_percent = TRUE, warning = FALSE),
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genta_n = n_rsi(gent),
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combination_S = rsi(cipr, gent, interpretation = "S",
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as_percent = TRUE, warning = FALSE),
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combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
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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 %>%
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filter(bactid == "ESCCOL") %>%
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rsi_predict(col_ab = "amox",
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col_date = "date",
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info = TRUE) %>%
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pull("probR")
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# amox resistance will increase according to data set `septic_patients`
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expect_true(amox_R[3] < amox_R[20])
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "binomial",
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col_ab = "amox",
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col_date = "date",
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info = TRUE))
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "loglin",
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col_ab = "amox",
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col_date = "date",
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info = TRUE))
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "lin",
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col_ab = "amox",
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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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model = "INVALID MODEL",
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col_ab = "amox",
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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",
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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",
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col_date = "NOT EXISTING COLUMN",
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info = TRUE))
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})
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