mirror of https://github.com/msberends/AMR.git
53 lines
2.1 KiB
R
53 lines
2.1 KiB
R
context("first_isolates.R")
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test_that("keyantibiotics work", {
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expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
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expect_true(key_antibiotics_equal("SSS", "SSS"))
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expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
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expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
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})
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test_that("guess_bactid works", {
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expect_equal(guess_bactid("E. coli"), "ESCCOL")
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expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
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})
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test_that("first isolates work", {
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# septic_patients contains 1960 out of 2000 first isolates
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#septic_ptns <- septic_patients
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expect_equal(sum(first_isolate(tbl = septic_patients,
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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info = FALSE)), 1960)
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# septic_patients contains 1962 out of 2000 first *weighted* isolates
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#septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
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expect_equal(
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suppressWarnings(sum(
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_keyantibiotics = "keyab",
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type = "keyantibiotics",
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info = TRUE))),
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1962)
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# set 1500 random observations to be of specimen type 'Urine'
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random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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expect_lt(sum(
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first_isolate(tbl = mutate(septic_patients,
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specimen = if_else(row_number() %in% random_rows,
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"Urine",
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"Unknown")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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info = TRUE)),
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1501)
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})
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