AMR/tests/testthat/test-rsi_analysis.R

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2018-03-27 17:43:42 +02:00
context("rsi_analysis.R")
test_that("rsi works", {
# amox resistance in `septic_patients` should be around 53.86%
amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
expect_equal(amox_R, 0.5386, tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = "amox",
info = FALSE), 0.5386, tolerance = 0.0001)
# and pita+genta susceptibility around 98.09%
expect_equal(rsi_df(septic_patients,
ab = c("pita", "gent"),
interpretation = "S",
info = FALSE), 0.9809, tolerance = 0.0001)
})
test_that("prediction of rsi works", {
amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
col_ab = "amox",
col_date = "date",
info = FALSE)
amox_R <- amox_R %>% pull("probR")
# amox resistance will decrease according to `septic_patients`
expect_true(amox_R[2] > amox_R[20])
expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
model = "INVALID MODEL",
col_ab = "amox",
col_date = "date",
info = FALSE))
expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = FALSE))
expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
col_ab = "amox",
col_date = "NOT EXISTING COLUMN",
info = FALSE))
})