P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 00:32:34 +02:00
Code Releases Activity

Update clinical breakpoints and fix some as.mo() bugs (#117)

Browse Source 
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
inst/tinytest/test-mo_property.R
View File

@ -166,15 +166,13 @@ expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
# old codes must throw a warning in mo_* family
# expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
# outcome of mo_fullname must always return the fullname from the data set
x <- data.frame(
mo = microorganisms$mo,
# fullname from the original data:
f1 = microorganisms$fullname,
# newly created fullname based on MO code:
f2 = mo_fullname(microorganisms$mo, language = "en"),
f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
stringsAsFactors = FALSE
)
expect_equal(nrow(subset(x, f1 != f2)), 0)