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(v1.5.0.9039) handle first isolates for missing antibiograms

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-03-08 02:38:32 +01:00
parent 461793dc34
commit a7c9b4c295
21 changed files with 79 additions and 62 deletions
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4
tests/testthat/test-first_isolate.R
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@ -196,6 +196,10 @@ test_that("first isolates work", {
expect_equal(sum(first_isolate(test_unknown)),
1045)
# empty rsi results
expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
1287)
# shortcuts
expect_identical(filter_first_isolate(example_isolates),
subset(example_isolates, first_isolate(example_isolates)))

8
tests/testthat/test-rsi.R
View File

@ -95,20 +95,20 @@ test_that("mic2rsi works", {
mo = "B_STRPT_PNMN",
ab = "AMP",
guideline = "EUCAST 2020")),
c("S", "S", "I", "I", "R"), info = pkg_env$strange)
c("S", "S", "I", "I", "R"))
# S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
expect_equal(as.character(
as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "CLSI 2019")),
c("S", "S", "I", "R", "R"), info = pkg_env$strange)
c("S", "S", "I", "R", "R"))
# cutoffs at MIC = 8
expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("S"), info = pkg_env$strange)
as.rsi("S"))
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R"), info = pkg_env$strange)
as.rsi("R"))
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%