P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 19:41:51 +02:00
Code Releases Activity

Fix unit tests for custom reference_data (#239)

Browse Source 
- Do not override my_bp$mo / my_bp$ab in tests: assigning plain character
  strips the <mo>/<ab> class, which check_reference_data() rejects. Use the
  mo/ab values already present in the source row instead.
- Use NA_character_ instead of NA for my_bp$host so the host column keeps
  its character class.
- Pass breakpoint_type = "animal" explicitly in the host-fallback test since
  the custom reference_data only contains animal-type breakpoints.

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U
This commit is contained in:
Claude
2026-04-25 11:37:32 +00:00
parent c43339d6ed
commit 7277534d40
1 changed files with 16 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
tests/testthat/test-sir.R
View File

@@ -532,30 +532,32 @@ test_that("test-sir.R", {
# issue #239 — custom reference_data support
test_that("custom reference_data: non-EUCAST/CLSI guideline produces R", {
# use any MIC/human row as structural template, then override mo/ab/guideline/breakpoints
# Take the first MIC/human row (B_ACHRMB_XYLS / MEM) as a template.
# Only override guideline and breakpoints; keep mo/ab as <mo>/<ab> class objects.
my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
clinical_breakpoints$type == "human", ][1, ]
my_bp$guideline <- "MyLab 2025"
my_bp$mo <- "B_ESCHR_COLI"
my_bp$ab <- "AMC"
my_bp$breakpoint_S <- 8
my_bp$breakpoint_R <- 32
# guideline omitted: all rows in reference_data are used
mo_val <- as.character(my_bp$mo) # "B_ACHRMB_XYLS"
ab_val <- as.character(my_bp$ab) # "MEM"
# guideline omitted: all rows in reference_data are used; R via open interval (>)
expect_equal(as.character(suppressMessages(
as.sir(as.mic(64), mo = "E. coli", ab = "AMC", reference_data = my_bp)
as.sir(as.mic(64), mo = mo_val, ab = ab_val, reference_data = my_bp)
)), "R")
expect_equal(as.character(suppressMessages(
as.sir(as.mic(16), mo = "E. coli", ab = "AMC", reference_data = my_bp)
as.sir(as.mic(16), mo = mo_val, ab = ab_val, reference_data = my_bp)
)), "I")
# at R breakpoint value must be I (open interval: > not >=)
expect_equal(as.character(suppressMessages(
as.sir(as.mic(32), mo = "E. coli", ab = "AMC", reference_data = my_bp)
as.sir(as.mic(32), mo = mo_val, ab = ab_val, reference_data = my_bp)
)), "I")
# guideline explicitly set: same result when it matches the data
expect_equal(as.character(suppressMessages(
as.sir(as.mic(64), mo = "E. coli", ab = "AMC",
as.sir(as.mic(64), mo = mo_val, ab = ab_val,
guideline = "MyLab 2025", reference_data = my_bp)
)), "R")
})
@@ -564,16 +566,18 @@ test_that("custom reference_data: host = NA acts as host-agnostic fallback", {
my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
clinical_breakpoints$type == "human", ][1, ]
my_bp$guideline <- "MyLab 2025"
my_bp$mo <- "B_ESCHR_COLI"
my_bp$ab <- "AMC"
my_bp$type <- "animal"
my_bp$host <- NA
my_bp$host <- NA_character_ # must stay character class, not logical NA
my_bp$breakpoint_S <- 8
my_bp$breakpoint_R <- 32
mo_val <- as.character(my_bp$mo)
ab_val <- as.character(my_bp$ab)
# NA host should match when no species-specific row exists; guideline omitted
result <- suppressMessages(
as.sir(as.mic(64), mo = "E. coli", ab = "AMC", host = "dogs", reference_data = my_bp)
as.sir(as.mic(64), mo = mo_val, ab = ab_val,
host = "dogs", breakpoint_type = "animal", reference_data = my_bp)
)
expect_equal(as.character(result), "R")
})