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(v3.0.1.9031) fix MDRO for non-RStudio terminal

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dr. M.S. (Matthijs) Berends
2026-03-08 11:30:18 +01:00
parent e2102c081a
commit b6f8584994
6 changed files with 80 additions and 59 deletions
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27
tests/testthat/test-mdro.R
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@@ -313,14 +313,14 @@ test_that("test-mdro.R", {
# Inference message goes to message() / stderr, not stdout
# -> must use expect_message(), NOT expect_output()
expect_message(
suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, verbose = TRUE)),
suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = TRUE)),
"Inferring resistance"
)
# With TZP=R, PIP is inferred R -> 4MRGN criteria met -> level 3 (> 1)
result_no_pip <- suppressMessages(suppressWarnings(
mdro(pseud_no_pip, guideline = "mrgn", info = FALSE)
))
expect_true(as.integer(result_no_pip) > 1L)
inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE))
not_inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, infer_from_combinations = FALSE))
expect_equal(as.character(inferred), "4MRGN")
expect_equal(as.character(not_inferred), "Negative")
# Susceptibility in combo does NOT propagate: proxy = NA, not S
# -> 4MRGN criteria no longer met -> lower level than when TZP=R
pseud_tzp_s <- pseud_no_pip
@@ -328,18 +328,23 @@ test_that("test-mdro.R", {
result_tzp_s <- suppressMessages(suppressWarnings(
mdro(pseud_tzp_s, guideline = "mrgn", info = FALSE)
))
expect_true(as.integer(result_tzp_s) < as.integer(result_no_pip))
expect_true(as.integer(result_tzp_s) < as.integer(inferred))
# Multiple combos for the same base drug: AMX can come from AMC (amoxicillin/clavulanic acid)
# Multiple combos for the same base drug: AMX can come from AMC (amoxi/clavulanic acid) and AXS (amoxi/sulbactam)
ente_no_amx <- data.frame(
mo = as.mo("Enterococcus faecium"),
AMC = as.sir("R"), # amoxicillin/clavulanic acid; no AMX column
AMC = as.sir("R"), # amoxicillin/clavulanic acid
AXS = as.sir("R"), # amoxicillin/sulbactam
VAN = as.sir("R"),
TEC = as.sir("R"),
LNZ = as.sir("R"),
DAP = as.sir("R"),
stringsAsFactors = FALSE
)
# Should run without error and return an ordered factor; AMX inferred R from AMC
expect_inherits(suppressMessages(suppressWarnings(mdro(ente_no_amx, guideline = "EUCAST", info = FALSE))), c("factor", "ordered"))
# Should have multiple columns in the verbose explanation
out <- mdro(ente_no_amx, guideline = "EUCAST 3.3", info = FALSE, verbose = TRUE)
expect_identical(
out$all_nonsusceptible_columns,
"AMC, AMX (inferred from AMC/AXS), AXS, DAP, LNZ, TEC, VAN"
)
})