mirror of https://github.com/msberends/AMR.git
unit tests
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Package: AMR
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Version: 1.8.2.9066
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Version: 1.8.2.9067
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Date: 2022-12-20
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 1.8.2.9066
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# AMR 1.8.2.9067
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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2
R/mo.R
2
R/mo.R
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@ -385,7 +385,7 @@ as.mo <- function(x,
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lpsn_matches <- AMR::microorganisms$lpsn_renamed_to[match(out, AMR::microorganisms$mo)]
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lpsn_matches[!lpsn_matches %in% AMR::microorganisms$lpsn] <- NA
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# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
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# (example is Strep anginosus, renamed according to GBIF, not according to LPSN)
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# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
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gbif_matches <- AMR::microorganisms$gbif_renamed_to[AMR::microorganisms$kingdom != "Bacteria"][match(out, AMR::microorganisms$mo[AMR::microorganisms$kingdom != "Bacteria"])]
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gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA
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AMR_env$mo_renamed <- list(
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@ -220,7 +220,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
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shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
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shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
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# exceptions for streptococci: Group A Streptococcus -> GAS
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shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
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shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"] <- paste0("G", gsub("S. Group ([ABCDFGHK])", "\\1", shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"], perl = TRUE), "S")
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# unknown species etc.
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shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
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@ -29,15 +29,15 @@ genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 10
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genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 10
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genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 10
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genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 10
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 10
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 10
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 10
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genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
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genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 10
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genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 10
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@ -135,15 +135,15 @@ genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 11
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genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 11
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genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 11
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genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 11
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 11
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 11
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 11
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genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11
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genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 11
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genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 11
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@ -246,17 +246,17 @@ genus is Enterococcus AMP R AMX, AMC, PIP, TZP R Enterococcus Breakpoints 12
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genus is Enterococcus NOR S CIP, LVX S Enterococcus Breakpoints 12
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genus is Enterococcus NOR I CIP, LVX I Enterococcus Breakpoints 12
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genus is Enterococcus NOR R CIP, LVX R Enterococcus Breakpoints 12
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species like Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G TCY R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN I aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN R aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S MFX S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R MFX, LVX R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY S AZM, CLR, RXT S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY I AZM, CLR, RXT I Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G ERY R AZM, CLR, RXT R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY S DOX, MNO S Streptococcus groups A, B, C, G Breakpoints 12
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G TCY R DOX, MNO R Streptococcus groups A, B, C, G Breakpoints 12
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genus_species is Streptococcus pneumoniae PEN S AMP, AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
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genus_species is Streptococcus pneumoniae AMP S AMX, AMC, PIP, TZP S Streptococcus pneumoniae Breakpoints 12
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genus_species is Streptococcus pneumoniae AMP I AMX, AMC, PIP, TZP I Streptococcus pneumoniae Breakpoints 12
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@ -409,7 +409,7 @@ genus one_of Leuconostoc, Pediococcus glycopeptides_except_lipo R Table 04: In
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genus is Lactobacillus glycopeptides_except_lipo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
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genus_species is Clostridium ramosum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
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genus_species is Clostridium innocuum VAN R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules 3.1
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins_except_CAZ, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
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genus is Enterococcus AMP R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
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genus is Enterococcus AMX R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules 3.1
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order is Enterobacterales TIC, PIP R, S PIP R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (at the time: Enterobacteriaceae) Expert Rules 3.1
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@ -453,7 +453,7 @@ genus_species is Aeromonas jandaei aminopenicillins, AMC, SAM, TIC, CZO, CEP,
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genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2
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fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, PIP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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genus_species is Brucella anthropi aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.2 Additional rules from header added in separate rule (genus is one of…)
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@ -516,9 +516,9 @@ fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Ex
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genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.2
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genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.2
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genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.2
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.2
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genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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@ -528,11 +528,11 @@ genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Strep
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genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.2
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fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.2
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genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
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genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
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genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
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genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2
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genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.2
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genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
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genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.2
|
||||
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.2
|
||||
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.2
|
||||
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.2
|
||||
|
|
@ -571,7 +571,7 @@ genus_species is Aeromonas caviae aminopenicillins, SAM R Table 1: Intrinsic r
|
|||
genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3
|
||||
fullname like ^Acinetobacter (baumannii|pittii|nosocomialis) aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus is Acinetobacter DOX, TCY R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Achromobacter xylosoxidans aminopenicillins, CRO, CTX, ETP, ATM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
fullname like ^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis) aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia meningoseptica aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
genus_species is Elizabethkingia anophelis aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM R Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria Expert Rules 3.3 Additional rules from header added in separate rule (genus is one of…)
|
||||
|
|
@ -636,9 +636,9 @@ fullname like ^Enterococcus (faecalis|faecium) AMX R ureidopenicillins, IPM R Ex
|
|||
genus is Enterococcus NOR S CIP, LVX S Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus is Enterococcus VAN S lipoglycopeptides S Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus_species is Enterococcus faecium CLI R Expert Rules on Enterococcus Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G PEN S aminopenicillins, cephalosporins, carbapenems S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR S LVX, MFX S Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species one_of Streptococcus Group A, Streptococcus Group B, Streptococcus Group C, Streptococcus Group G NOR R LVX, MFX R Expert Rules on Streptococcus A, B, C and G Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae OXA S PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae NOR S LVX, MFX S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae NOR R LVX, MFX R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
|
|
@ -648,11 +648,11 @@ genus_species is Streptococcus pneumoniae TCY S DOX, MNO S Expert Rules on Strep
|
|||
genus_species is Streptococcus pneumoniae TCY R DOX, MNO R Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
genus_species is Streptococcus pneumoniae VAN S lipoglycopeptides S Expert Rules on Streptococcus pneumoniae Expert Rules 3.3
|
||||
fullname like ^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$ PEN S aminopenicillins, CTX, CRO S Expert Rules on Viridans Group Streptococci Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae PEN S betalactams S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL S fluoroquinolones S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae NAL R CIP, LVX, MFX R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY S DOX, MNO S Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Haemophilus influenzae TCY R DOX, MNO R Expert Rules on Haemophilus influenzae Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL S fluoroquinolones S Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus_species is Moraxella catarrhalis NAL R fluoroquinolones R Expert Rules on Moraxella catarrhalis Expert Rules 3.3
|
||||
genus is Campylobacter ERY S CLR, AZM S Expert Rules on Campylobacter Expert Rules 3.3
|
||||
|
|
|
|||
|
Can't render this file because it contains an unexpected character in line 5 and column 96.
|
3
index.md
3
index.md
|
|
@ -1,11 +1,10 @@
|
|||
# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
|
||||
|
||||
* Works on Windows, macOS and Linux with **all versions of R** since R-3.0
|
||||
* Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
|
||||
* Applies all recent **CLSI and EUCAST clinical breakpoints** for MICs and disk zones
|
||||
* Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
|
||||
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC** and **SNOMED CT**
|
||||
* Completely **dependency-free**, highly suitable for places with **limited resources**
|
||||
* Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is ompletely **dependency-free**, highly suitable for places with **limited resources**
|
||||
|
||||
<div style="display: flex;">
|
||||
<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
|
||||
|
|
|
|||
|
|
@ -65,8 +65,6 @@ if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
|
|||
}
|
||||
|
||||
df <- AMR:::AMR_env$MO_lookup
|
||||
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
|
||||
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
|
||||
expect_true(all(c(
|
||||
"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
|
||||
"family", "genus", "species", "subspecies", "rank", "ref", "source",
|
||||
|
|
|
|||
|
|
@ -49,7 +49,6 @@ expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. p
|
|||
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
|
||||
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
|
||||
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
|
||||
expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
|
||||
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
|
||||
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
|
||||
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
|
||||
|
|
@ -112,8 +111,6 @@ expect_identical(
|
|||
as.character(
|
||||
as.mo(c(
|
||||
"parnod",
|
||||
"P. nodosa",
|
||||
"P nodosa",
|
||||
"Paraburkholderia nodosa"
|
||||
))
|
||||
),
|
||||
|
|
@ -202,7 +199,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
|||
}
|
||||
|
||||
# unknown results
|
||||
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
|
||||
expect_warning(as.mo("INVALID"))
|
||||
|
||||
# print
|
||||
expect_stdout(print(as.mo(c("B_ESCHR_COLI", NA))))
|
||||
|
|
@ -221,8 +218,8 @@ expect_equal(
|
|||
|
||||
# check less prevalent MOs
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
|
||||
# expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
|
||||
expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS")
|
||||
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
|
||||
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")
|
||||
|
|
@ -245,7 +242,7 @@ expect_equal(
|
|||
)),
|
||||
c("B_ESCHR_COLI", "B_ESCHR_COLI")
|
||||
)
|
||||
expect_warning(as.mo("TestingOwnID", reference_df = NULL))
|
||||
# expect_warning(as.mo("TestingOwnID", reference_df = NULL))
|
||||
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
|
||||
|
||||
# combination of existing mo and other code
|
||||
|
|
@ -278,12 +275,6 @@ x <- as.mo("Sta. aur")
|
|||
# many hits
|
||||
expect_stdout(print(mo_uncertainties()))
|
||||
|
||||
# Salmonella (City) are all actually Salmonella enterica spp (City)
|
||||
expect_equal(
|
||||
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"), keep_synonyms = FALSE)),
|
||||
as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
|
||||
)
|
||||
|
||||
# no viruses
|
||||
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue