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

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* 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
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8
inst/tinytest/test-data.R
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@ -47,10 +47,10 @@ expect_false(any(is.na(microorganisms.codes$mo)))
expect_true(all(dosage$ab %in% antibiotics$ab))
expect_true(all(dosage$name %in% antibiotics$name))
# check valid disks/MICs
expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC"), "breakpoint_S", drop = TRUE]))))
expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC"), "breakpoint_R", drop = TRUE]))))
expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK"), "breakpoint_S", drop = TRUE]))))
expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK"), "breakpoint_R", drop = TRUE]))))
expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$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$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE]))))
# antibiotic names must always be coercible to their original AB code
expect_identical(as.ab(antibiotics$name), antibiotics$ab)