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(v0.7.0.9005) ab algorithm update
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@ -59,12 +59,12 @@ genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhal
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genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints
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genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram positives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram negatives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints
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genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints
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genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints
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genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints
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genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints
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genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints
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@ -135,7 +135,7 @@ genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative
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genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
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gramstain is Gram positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
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@ -5,8 +5,8 @@
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# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
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# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
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# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
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# LiPuma JJ, 2015 (PMID 16217180).
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# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
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# LiPuma JJ, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
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eucast_rules_file <- dplyr::arrange(
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.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
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sep = "\t",
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@ -289,6 +289,9 @@ antibiotics <- filter(antibiotics, ab != "MOX")
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antibiotics <- filter(antibiotics, ab != "RFP")
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antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
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antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
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# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
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antibiotics <- filter(antibiotics, ab != "PME")
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antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
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# ESBL E-test codes:
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antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
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antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
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@ -318,13 +318,13 @@ MOs <- MOs %>%
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stringsAsFactors = FALSE),
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data.frame(mo = "B_GRAMN",
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col_id = NA_integer_,
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fullname = "(unknown Gram negatives)",
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fullname = "(unknown Gram-negatives)",
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kingdom = "Bacteria",
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phylum = "(unknown phylum)",
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class = "(unknown class)",
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order = "(unknown order)",
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family = "(unknown family)",
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genus = "(unknown Gram negatives)",
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genus = "(unknown Gram-negatives)",
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species = "(unknown species)",
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subspecies = "(unknown subspecies)",
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rank = "species",
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@ -334,13 +334,13 @@ MOs <- MOs %>%
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stringsAsFactors = FALSE),
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data.frame(mo = "B_GRAMP",
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col_id = NA_integer_,
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fullname = "(unknown Gram positives)",
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fullname = "(unknown Gram-positives)",
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kingdom = "Bacteria",
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phylum = "(unknown phylum)",
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class = "(unknown class)",
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order = "(unknown order)",
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family = "(unknown family)",
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genus = "(unknown Gram positives)",
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genus = "(unknown Gram-positives)",
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species = "(unknown species)",
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subspecies = "(unknown subspecies)",
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rank = "species",
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@ -457,7 +457,7 @@ MOs <- MOs %>%
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mutate(prevalence = case_when(
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class == "Gammaproteobacteria"
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| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
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| mo == "UNKNOWN"
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| mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP")
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~ 1,
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phylum %in% c("Proteobacteria",
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"Firmicutes",
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@ -494,8 +494,8 @@ saveRDS(MOs, "microorganisms.rds")
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saveRDS(MOs.old, "microorganisms.old.rds")
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# on the server:
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usethis::use_data(microorganisms, overwrite = TRUE)
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usethis::use_data(microorganisms.old, overwrite = TRUE)
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usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
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usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
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rm(microorganisms)
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rm(microorganisms.old)
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# and update the year in R/data.R
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@ -2,8 +2,8 @@ lang pattern replacement fixed ignore.case
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de Coagulase-negative Staphylococcus Koagulase-negative Staphylococcus FALSE FALSE
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de Coagulase-positive Staphylococcus Koagulase-positive Staphylococcus FALSE FALSE
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de Beta-haemolytic Streptococcus Beta-hämolytischer Streptococcus FALSE FALSE
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de unknown Gram negatives unbekannte Gramnegativen FALSE FALSE
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de unknown Gram positives unbekannte Grampositiven FALSE FALSE
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de unknown Gram-negatives unbekannte Gramnegativen FALSE FALSE
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de unknown Gram-positives unbekannte Grampositiven FALSE FALSE
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de unknown name unbekannte Name FALSE FALSE
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de unknown kingdom unbekanntes Reich FALSE FALSE
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de unknown phylum unbekannter Stamm FALSE FALSE
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@ -16,8 +16,8 @@ de unknown subspecies unbekannte Unterart FALSE FALSE
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de unknown rank unbekannter Rang FALSE FALSE
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de (CoNS) (KNS) TRUE FALSE
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de (CoPS) (KPS) TRUE FALSE
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de Gram negative Gramnegativ FALSE FALSE
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de Gram positive Grampositiv FALSE FALSE
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de Gram-negative Gramnegativ FALSE FALSE
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de Gram-positive Grampositiv FALSE FALSE
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de Bacteria Bakterien FALSE FALSE
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de Fungi Hefen/Pilze FALSE FALSE
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de Protozoa Protozoen FALSE FALSE
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@ -29,8 +29,8 @@ de ([([ ]*?)Group \\1Gruppe FALSE FALSE
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nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
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nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
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nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE
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nl unknown Gram negatives onbekende Gram-negatieven FALSE FALSE
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nl unknown Gram positives onbekende Gram-positieven FALSE FALSE
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nl unknown Gram-negatives onbekende Gram-negatieven FALSE FALSE
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nl unknown Gram-positives onbekende Gram-positieven FALSE FALSE
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nl unknown name onbekende naam FALSE FALSE
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nl unknown kingdom onbekend koninkrijk FALSE FALSE
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nl unknown phylum onbekend fylum FALSE FALSE
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@ -43,8 +43,8 @@ nl unknown subspecies onbekende ondersoort FALSE FALSE
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nl unknown rank onbekende rang FALSE FALSE
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nl (CoNS) (CNS) TRUE FALSE
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nl (CoPS) (CPS) TRUE FALSE
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nl Gram negative Gram-negatief FALSE FALSE
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nl Gram positive Gram-positief FALSE FALSE
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nl Gram-negative Gram-negatief FALSE FALSE
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nl Gram-positive Gram-positief FALSE FALSE
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nl Bacteria Bacteriën FALSE FALSE
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nl Fungi Schimmels/gisten FALSE FALSE
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nl Protozoa protozoën FALSE FALSE
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@ -55,8 +55,8 @@ nl ([([ ]*?)Group \\1Groep FALSE FALSE
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es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
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es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
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es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
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es unknown Gram negatives Gram negativos desconocidos FALSE FALSE
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es unknown Gram positives Gram positivos desconocidos FALSE FALSE
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es unknown Gram-negatives Gram negativos desconocidos FALSE FALSE
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es unknown Gram-positives Gram positivos desconocidos FALSE FALSE
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es unknown name nombre desconocido FALSE FALSE
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es unknown kingdom reino desconocido FALSE FALSE
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es unknown phylum filo desconocido FALSE FALSE
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@ -69,8 +69,8 @@ es unknown subspecies subespecie desconocida FALSE FALSE
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es unknown rank rango desconocido FALSE FALSE
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es (CoNS) (SCN) TRUE FALSE
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es (CoPS) (SCP) TRUE FALSE
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es Gram negative Gram negativo FALSE FALSE
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es Gram positive Gram positivo FALSE FALSE
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es Gram-negative Gram negativo FALSE FALSE
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es Gram-positive Gram positivo FALSE FALSE
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es Bacteria Bacterias FALSE FALSE
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es Fungi Hongos FALSE FALSE
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es Protozoa Protozoarios FALSE FALSE
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@ -82,8 +82,8 @@ es ([([ ]*?)Group \\1Grupo FALSE FALSE
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it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
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it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
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it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE
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it unknown Gram negatives Gram negativi sconosciuti FALSE FALSE
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it unknown Gram positives Gram positivi sconosciuti FALSE FALSE
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it unknown Gram-negatives Gram negativi sconosciuti FALSE FALSE
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it unknown Gram-positives Gram positivi sconosciuti FALSE FALSE
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it unknown name nome sconosciuto FALSE FALSE
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it unknown kingdom regno sconosciuto FALSE FALSE
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it unknown phylum phylum sconosciuto FALSE FALSE
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@ -94,8 +94,8 @@ it unknown genus genere sconosciuto FALSE FALSE
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it unknown species specie sconosciute FALSE FALSE
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it unknown subspecies sottospecie sconosciute FALSE FALSE
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it unknown rank grado sconosciuto FALSE FALSE
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it Gram negative Gram negativo FALSE FALSE
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it Gram positive Gram positivo FALSE FALSE
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it Gram-negative Gram negativo FALSE FALSE
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it Gram-positive Gram positivo FALSE FALSE
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it Bacteria Batteri FALSE FALSE
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it Fungi Fungo FALSE FALSE
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it Protozoa Protozoi FALSE FALSE
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@ -107,8 +107,8 @@ it ([([ ]*?)Group \\1Gruppo FALSE FALSE
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fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE
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fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
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fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE
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fr unknown Gram negatives Gram négatifs inconnus FALSE FALSE
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fr unknown Gram positives Gram positifs inconnus FALSE FALSE
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fr unknown Gram-negatives Gram négatifs inconnus FALSE FALSE
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fr unknown Gram-positives Gram positifs inconnus FALSE FALSE
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fr unknown name nom inconnu FALSE FALSE
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fr unknown kingdom règme inconnu FALSE FALSE
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fr unknown phylum embranchement inconnu FALSE FALSE
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@ -119,8 +119,8 @@ fr unknown genus genre inconnu FALSE FALSE
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fr unknown species espèce inconnue FALSE FALSE
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fr unknown subspecies sous-espèce inconnue FALSE FALSE
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fr unknown rank rang inconnu FALSE FALSE
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fr Gram negative Gram négatif FALSE FALSE
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fr Gram positive Gram positif FALSE FALSE
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fr Gram-negative Gram négatif FALSE FALSE
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fr Gram-positive Gram positif FALSE FALSE
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fr Bacteria Bactéries FALSE FALSE
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fr Fungi Champignons FALSE FALSE
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fr Protozoa Protozoaires FALSE FALSE
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@ -131,8 +131,8 @@ fr ([([ ]*?)Group \\1Groupe FALSE FALSE
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pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE
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pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE
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pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
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pt unknown Gram negatives Gram negativos desconhecidos FALSE FALSE
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pt unknown Gram positives Gram positivos desconhecidos FALSE FALSE
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pt unknown Gram-negatives Gram negativos desconhecidos FALSE FALSE
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pt unknown Gram-positives Gram positivos desconhecidos FALSE FALSE
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pt unknown name nome desconhecido FALSE FALSE
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pt unknown kingdom reino desconhecido FALSE FALSE
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pt unknown phylum filo desconhecido FALSE FALSE
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@ -143,8 +143,8 @@ pt unknown genus gênero desconhecido FALSE FALSE
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pt unknown species espécies desconhecida FALSE FALSE
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pt unknown subspecies subespécies desconhecida FALSE FALSE
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pt unknown rank classificação desconhecido FALSE FALSE
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pt Gram negative Gram negativo FALSE FALSE
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pt Gram positive Gram positivo FALSE FALSE
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pt Gram-negative Gram negativo FALSE FALSE
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pt Gram-positive Gram positivo FALSE FALSE
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pt Bacteria Bactérias FALSE FALSE
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pt Fungi Fungos FALSE FALSE
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pt Protozoa Protozoários FALSE FALSE
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