mirror of https://github.com/msberends/AMR.git
ATC and DDD update
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Package: AMR
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Version: 1.8.2.9036
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Version: 1.8.2.9037
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Date: 2022-10-29
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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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3
NEWS.md
3
NEWS.md
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# AMR 1.8.2.9036
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# AMR 1.8.2.9037
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@ -53,6 +53,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
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* Updated support for all WHONET 2022 microorganism codes
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* Antimicrobial interpretation 'SDD' (susceptible dose-dependent, coined by CLSI) will be interpreted as 'I' to comply with EUCAST's 'I' in `as.rsi()`
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* Fix for `mo_shortname()` in case of higher taxonomic ranks (order, class, phylum)
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* Updated DDDs and ATCs for the `antibiotics` data set - ATC codes J04AB06 (enviomycin) and D06AX14 (ozenoxacin) were added
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### Other
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* New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
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"ECO" 3198 "Econazole" "Antifungals/antimycotics" "D01AC03,G01AF05" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "econazol,econazole,econazolum,ecostatin,ecostatin cream,palavale,pevaryl,spectazole,spectazole cream" ""
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"ENX" 3229 "Enoxacin" "Quinolones" "J01MA04" "Quinolone antibacterials" "Fluoroquinolones" ",enox" "almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacin,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex" 0.8 "g" "16816-1,3590-7"
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"ENR" 71188 "Enrofloxacin" "Quinolones" "NA" "" "baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum" ""
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"ENV" 135565326 "Enviomycin" "Antimycobacterials" "NA" ",tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum" ""
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"ENV" 135565326 "Enviomycin" "Antimycobacterials" "J04AB06" ",tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum" ""
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"EPE" "Eperozolid" "Other antibacterials" "NA" "" "" ""
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"EPC" 71392 "Epicillin" "Beta-lactams/penicillins" "J01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "" "dexacillin,dihydroampicillin,epicilina,epicillin,epicilline,epicillinum" 2 "g" 2 "g" ""
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"EPP" 68916 "Epiroprim" "Other antibacterials" "NA" "" "epiroprim,epiroprima,epiroprime,epiroprimum" ""
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@ -220,7 +220,7 @@
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"KAN" 6032 "Kanamycin" "Aminoglycosides" "A07AA08,J01GB04,S01AA24" "Aminoglycoside antibacterials" "Other aminoglycosides" "hlk,k,kan,kana,km" "kanamicina,kanamycin,kanamycin a,kanamycin base,kanamycine,kanamycinum,kantrex,kenamycin a,klebcil,liposomal kanamycin" 3 "g" 1 "g" "23889-9,3698-8,3699-6,3700-2,47395-9"
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"KAH" "Kanamycin-high" "Aminoglycosides" "NA" ",k_h,kahl" "" ""
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"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "NA" "" "" ""
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"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "D01AC08,G01AF11,H02CA03,J02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ktc" "extina,fungarest,fungoral,ketocanazole,ketoconazol,ketoconazole,ketoconazolum,ketoderm,nizoral,xolegel" 0.2 "g" "10990-0,12393-5,25259-3,60091-6,60092-4"
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"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "D01AC08,G01AF11,H02CA03,J02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ktc" "extina,fungarest,fungoral,ketocanazole,ketoconazol,ketoconazole,ketoconazolum,ketoderm,nizoral,xolegel" 0.6 "g" "10990-0,12393-5,25259-3,60091-6,60092-4"
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"KIT" "Kitasamycin" "Macrolides/lincosamides" "NA" ",leucomycin" "" ""
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"LAS" 5360807 "Lasalocid" "Other antibacterials" "NA" "" "avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum" "87598-9"
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"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "J01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "mox,moxa,moxalactam" "disodium moxalactam,festamoxin,lamoxactam,latamoxef,latamoxefum,shiomarin" 4 "g" ""
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"OXA" 6196 "Oxacillin" "Beta-lactams/penicillins" "J01CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxal,oxs" "bactocill,ossacillina,oxacilina,oxacillin,oxacillin sodium,oxacilline,oxacillinum,oxazocillin,oxazocilline,prostaphlin,prostaphlyn,sodium oxacillin" 2 "g" 2 "g" "25265-0,3882-8"
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"OXO" 4628 "Oxolinic acid" "Quinolones" "J01MB05" "Quinolone antibacterials" "Other quinolones" "" "acide oxolinique,acido ossolico,acido oxolinico,acidum oxolinicum,aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,oxolinic acid,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid" 1 "g" ""
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"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "D06AA03,G01AA07,J01AA06,S01AA04" "Tetracyclines" "Tetracyclines" "" "adamycin,berkmycen,biostat,biostat pa,dabicycline,dalimycin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hydroxytetracyclinum,imperacin,lenocycline,macocyn,medamycin,mepatar,oksisyklin,ossitetraciclina,oxacycline,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxydon,oxymycin,oxymykoin,oxypam,oxysteclin,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracycline,oxytetracycline base,oxytetracyclinum,proteroxyna,riomitsin,ryomycin,solkaciclina,stecsolin,stevacin,tarocyn,tarosin,teravit,terrafungine,terramitsin,terramycin,terramycin im,tetran,unimycin,ursocyclin,ursocycline,vendarcin" 1 "g" 1 "g" "17396-3,25266-8,87595-5"
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"OZN" "Ozenoxacin" "NA" "" "" ""
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"OZN" "Ozenoxacin" "D06AX14" "" "" ""
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"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "NA" "" "aminopar,aminosalicylic,aminosalicylic acid,aminosalyl,aminox,apacil,deapasil,entepas,ferrosan,gabbropas,helipidyl,hellipidyl,neopasalate,osacyl,pamacyl,pamisyl,paramycin,parasal,parasalicil,parasalindon,pasalon,pasara,pascorbic,pasdium,paser granules,paskalium,pasmed,pasnodia,pasolac,propasa,rezipas,teebacin,wln: zr cq dvq" ""
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"PAN" 72015 "Panipenem" "Carbapenems" "NA" "" "panipenem,panipenemum,penipanem" ""
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"PAR" 165580 "Paromomycin" "Other antibacterials" "A07AA06" "" "aminosidin,aminosidine,aminosidine i,aminosidine sulfate,amminosidin,crestomycin,estomycin,gabbromicina,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,hydroxymycin sulfate,monomycin,monomycin a,neomycin e,paramomycin,paramomycin sulfate,paromomicina,paromomycin,paromomycin i,paromomycine,paromomycinum,paucimycin,paucimycinum,quintomycin c" 3 "g" ""
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"RZM" 10993211 "Razupenem" "Carbapenems" "NA" "" "razupenem" ""
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"RTP" 6918462 "Retapamulin" "Other antibacterials" "D06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" ",ret" "altabax,altargo,retapamulin" ""
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"RZF" "Rezafungin" "Antifungals" "NA" "" "" ""
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"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" ""
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"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" 0.45 ""
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"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "dekamycin iv,hetangmycin,ribastamin,ribostamicina,ribostamycin,ribostamycine,ribostamycinum,vistamycin,xylostatin" 1 "g" ""
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"RID1" 16659285 "Ridinilazole" "Other antibacterials" "NA" "" "ridinilazole" ""
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"RIB" 135398743 "Rifabutin" "Antimycobacterials" "J04AB04" "Drugs for treatment of tuberculosis" "Antibiotics" "rifb" "alfacid,ansamicin,ansamycin,ansatipin,ansatipine,mycobutin,rifabutin,rifabutina,rifabutine,rifabutinum" 0.15 "g" "24032-5"
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# update ATC codes from WHOCC website -------------------------------------
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# last time checked: 2021-08-16
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# last time checked: 2022-10-29
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library(rvest)
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updated_atc <- as.list(antibiotics$atc)
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get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
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@ -781,7 +782,7 @@ antibiotics$atc <- updated_atc
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# update DDDs from WHOCC website ------------------------------------------
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# last time checked: 2021-08-19
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# last time checked: 2022-10-29
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ddd_oral <- rep(NA_real_, nrow(antibiotics))
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ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
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ddd_iv <- rep(NA_real_, nrow(antibiotics))
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@ -823,7 +824,7 @@ antibiotics$iv_units <- ddd_iv_units
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# Wrap up -----------------------------------------------------------------
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# set as data.frame again
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antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
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antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE))
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class(antibiotics$ab) <- c("ab", "character")
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antibiotics <- dplyr::arrange(antibiotics, name)
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@ -141,6 +141,7 @@ breakpoints_new <- breakpoints %>%
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# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
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mutate(disk_dose = disk_dose %>%
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gsub("μ", "u", ., fixed = TRUE) %>%
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gsub("µ", "u", ., fixed = TRUE) %>% # this is another micro sign, although we cannot see it
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gsub("–", "-", ., fixed = TRUE)) %>%
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arrange(desc(guideline), ab, mo, method) %>%
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filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
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@ -188,6 +189,6 @@ rsi_translation %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[OR
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# Save to package ----
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rsi_translation <- breakpoints_new
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usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
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usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz", version = 2)
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rm(rsi_translation)
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devtools::load_all(".")
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"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
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"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
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"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
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"EUCAST 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
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"EUCAST 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
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"EUCAST 2022" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
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"EUCAST 2022" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
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"EUCAST 2022" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
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"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
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"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
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"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
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"EUCAST 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
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"EUCAST 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
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"EUCAST 2021" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
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"EUCAST 2021" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
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"EUCAST 2021" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
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"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
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"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
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"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
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"EUCAST 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
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"EUCAST 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
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"EUCAST 2020" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
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"EUCAST 2020" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
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"EUCAST 2020" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
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"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
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"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
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"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
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"EUCAST 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
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"EUCAST 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
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"EUCAST 2019" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
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"EUCAST 2019" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 18 18 FALSE
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"EUCAST 2019" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 16 16 FALSE
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"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
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"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
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"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
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"EUCAST 2018" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
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"EUCAST 2018" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
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"EUCAST 2018" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
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"EUCAST 2018" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 16 FALSE
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"EUCAST 2018" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 1 16 FALSE
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# test languages
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expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
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dutch <- suppressWarnings(mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE)) # should be transformable to English again
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dutch <- suppressWarnings(mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]")], language = "nl", keep_synonyms = TRUE)) # should be transformable to English again
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expect_identical(suppressWarnings(mo_name(dutch, language = NULL, keep_synonyms = TRUE)),
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microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
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microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]")]) # gigantic test - will run ALL names
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# manual property function
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expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
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\item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
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\item \code{abbr}\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
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\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
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\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs
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\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 171 drugs
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\item \code{oral_units}\cr Units of \code{oral_ddd}
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\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs
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\item \code{iv_units}\cr Units of \code{iv_ddd}
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