mirror of https://github.com/msberends/AMR.git
39 lines
1.7 KiB
R
39 lines
1.7 KiB
R
context("rsi_analysis.R")
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test_that("rsi works", {
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# amox resistance in `septic_patients` should be around 53.86%
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amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
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expect_equal(amox_R, 0.5386, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = FALSE), 0.5386, tolerance = 0.0001)
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# and pita+genta susceptibility around 98.09%
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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 = FALSE), 0.9809, tolerance = 0.0001)
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})
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test_that("prediction of rsi works", {
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amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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col_ab = "amox",
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col_date = "date",
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info = FALSE)
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amox_R <- amox_R %>% pull("probR")
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# amox resistance will decrease according to `septic_patients`
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expect_true(amox_R[2] > amox_R[20])
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$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 = FALSE))
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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col_ab = "NOT EXISTING COLUMN",
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col_date = "date",
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info = FALSE))
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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col_ab = "amox",
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col_date = "NOT EXISTING COLUMN",
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info = FALSE))
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})
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