P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 08:32:04 +02:00
Code Releases Activity

(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-12 16:24:38 +01:00
parent e1b7252ff6
commit a7ef22a21e
27 changed files with 15755 additions and 15399 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
tests/testthat/test-data.R
View File

@ -45,15 +45,15 @@ test_that("data works", {
expect_true(all(clinical_breakpoints$ab %in% AMR::antimicrobials$ab))
expect_true(all(intrinsic_resistant$mo %in% microorganisms$mo))
expect_true(all(intrinsic_resistant$ab %in% AMR::antimicrobials$ab))
expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_false(anyNA(microorganisms.codes$code))
expect_false(anyNA(microorganisms.codes$mo))
expect_true(all(dosage$ab %in% AMR::antimicrobials$ab))
expect_true(all(dosage$name %in% AMR::antimicrobials$name))
# check valid disks/MICs
expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE]))))
expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE]))))
expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE]))))
expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE]))))
expect_false(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE])))
expect_true(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE])))
expect_false(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE])))
expect_true(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE])))
# antibiotic names must always be coercible to their original AB code
expect_identical(as.ab(AMR::antimicrobials$name), AMR::antimicrobials$ab)