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(v2.1.1.9196) fix eucast, unit tests

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dr. M.S. (Matthijs) Berends
2025-03-13 15:38:39 +01:00
parent 9aab129ea6
commit 861331b1df
25 changed files with 114 additions and 97 deletions
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10
data-raw/eucast_rules.tsv
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@ -304,11 +304,11 @@ genus_species is Streptococcus pneumoniae ERY I AZM, CLR, RXT I Streptococcus pn
genus_species is Streptococcus pneumoniae ERY R AZM, CLR, RXT R Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S S DOX, MNO S Streptococcus pneumoniae Breakpoints 12
genus_species is Streptococcus pneumoniae TCY-S R DOX, MNO R Streptococcus pneumoniae Breakpoints 12
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Streptococcus milleri, Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S S AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis PEN-S R AMC, AMP, AMX, CPD, CPT, CRO, CTX, CXM, DOR, ETP, FEP, IMR, IPM, MEM, MEV, OXA, PEN, PIP, SAM, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP S AMX, AMC, SAM, PIP, TZP S Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP I AMX, AMC, SAM, PIP, TZP I Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species one_of Milleri Group Streptococcus (MGS), Streptococcus acidominimus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus anginosus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus constellatus, Streptococcus criceti, Streptococcus cristatus, Streptococcus downei, Streptococcus equinus, Streptococcus ferus, Streptococcus gordonii, Streptococcus intermedius, Streptococcus macacae, Streptococcus mitis, Streptococcus mutans, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus oralis, Streptococcus parasanguinis, Streptococcus ratti, Streptococcus salivarius, Streptococcus salivarius, Streptococcus thermophilus, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus suis, Streptococcus uberis, Streptococcus vestibularis AMP R AMX, AMC, SAM, PIP, TZP R Viridans group streptococci Breakpoints 12 paste("Streptococcus", mo_species(microorganisms.groups$mo[which(microorganisms.groups$mo_group == "B_STRPT_VIRI")]), collapse = ", ")
genus_species is Haemophilus influenzae PEN-S S AMC, AMP, AMX, CFM, CPD, CPT, CRO, CTB, CTX, CXM, CZT, DOR, ETP, FEP, IMR, IPM, MEM, MEV, PEN, SAM, TZP S Haemophilus influenzae Breakpoints 12 x <- c(unique(clinical_breakpoints$ab[which(clinical_breakpoints$guideline == "EUCAST 2022" & clinical_breakpoints$mo == as.mo("H. influenzae"))]), "IMR", "MEV"); sort(x[x %in% betalactams()])
genus_species is Haemophilus influenzae PEN-S, BTL-S R, R AMP, AMX, PIP R Haemophilus influenzae Breakpoints 12
genus_species is Haemophilus influenzae AMC S SAM S Haemophilus influenzae Breakpoints 12

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