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ATC and DDD update

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dr. M.S. (Matthijs) Berends
2022-10-29 19:01:23 +02:00
parent fa620f8ebd
commit 3d9faf89cf
27 changed files with 23 additions and 20 deletions
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data-raw/antibiotics.txt
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@ -164,7 +164,7 @@
"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" ""
"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"
"ENR" 71188 "Enrofloxacin" "Quinolones" "NA" "" "baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum" ""
"ENV" 135565326 "Enviomycin" "Antimycobacterials" "NA" ",tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum" ""
"ENV" 135565326 "Enviomycin" "Antimycobacterials" "J04AB06" ",tuberactinomycin" "enviomicina,enviomycin,enviomycina,enviomycinum" ""
"EPE" "Eperozolid" "Other antibacterials" "NA" "" "" ""
"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" ""
"EPP" 68916 "Epiroprim" "Other antibacterials" "NA" "" "epiroprim,epiroprima,epiroprime,epiroprimum" ""
@ -220,7 +220,7 @@
"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"
"KAH" "Kanamycin-high" "Aminoglycosides" "NA" ",k_h,kahl" "" ""
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "NA" "" "" ""
"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"
"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"
"KIT" "Kitasamycin" "Macrolides/lincosamides" "NA" ",leucomycin" "" ""
"LAS" 5360807 "Lasalocid" "Other antibacterials" "NA" "" "avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum" "87598-9"
"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" ""
@ -294,7 +294,7 @@
"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"
"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" ""
"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"
"OZN" "Ozenoxacin" "NA" "" "" ""
"OZN" "Ozenoxacin" "D06AX14" "" "" ""
"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" ""
"PAN" 72015 "Panipenem" "Carbapenems" "NA" "" "panipenem,panipenemum,penipanem" ""
"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" ""
@ -340,7 +340,7 @@
"RZM" 10993211 "Razupenem" "Carbapenems" "NA" "" "razupenem" ""
"RTP" 6918462 "Retapamulin" "Other antibacterials" "D06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" ",ret" "altabax,altargo,retapamulin" ""
"RZF" "Rezafungin" "Antifungals" "NA" "" "" ""
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" ""
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali,ribociclib" 0.45 ""
"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "" "dekamycin iv,hetangmycin,ribastamin,ribostamicina,ribostamycin,ribostamycine,ribostamycinum,vistamycin,xylostatin" 1 "g" ""
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "NA" "" "ridinilazole" ""
"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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data-raw/reproduction_of_antibiotics.R
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@ -731,8 +731,9 @@ antibiotics <- antibiotics %>%
# update ATC codes from WHOCC website -------------------------------------
# last time checked: 2021-08-16
# last time checked: 2022-10-29
library(rvest)
updated_atc <- as.list(antibiotics$atc)
get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
@ -781,7 +782,7 @@ antibiotics$atc <- updated_atc
# update DDDs from WHOCC website ------------------------------------------
# last time checked: 2021-08-19
# last time checked: 2022-10-29
ddd_oral <- rep(NA_real_, nrow(antibiotics))
ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
ddd_iv <- rep(NA_real_, nrow(antibiotics))
@ -823,7 +824,7 @@ antibiotics$iv_units <- ddd_iv_units
# Wrap up -----------------------------------------------------------------
# set as data.frame again
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE))
class(antibiotics$ab) <- c("ab", "character")
antibiotics <- dplyr::arrange(antibiotics, name)

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data-raw/reproduction_of_rsi_translation.R
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@ -141,6 +141,7 @@ breakpoints_new <- breakpoints %>%
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
mutate(disk_dose = disk_dose %>%
gsub("μ", "u", ., fixed = TRUE) %>%
gsub("µ", "u", ., fixed = TRUE) %>% # this is another micro sign, although we cannot see it
gsub("–", "-", ., fixed = TRUE)) %>%
arrange(desc(guideline), ab, mo, method) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
@ -188,6 +189,6 @@ rsi_translation %>% filter(guideline == "EUCAST 2022", ab == "AMC", mo == "B_[OR
# Save to package ----
rsi_translation <- breakpoints_new
usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz", version = 2)
rm(rsi_translation)
devtools::load_all(".")

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data-raw/rsi_translation.txt
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@ -91,7 +91,7 @@
"EUCAST 2022" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2022" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
"EUCAST 2022" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
"EUCAST 2022" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
"EUCAST 2022" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
"EUCAST 2022" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
"EUCAST 2022" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
@ -1218,7 +1218,7 @@
"EUCAST 2021" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2021" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
"EUCAST 2021" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
"EUCAST 2021" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
"EUCAST 2021" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
"EUCAST 2021" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
"EUCAST 2021" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
@ -2143,7 +2143,7 @@
"EUCAST 2020" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2020" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
"EUCAST 2020" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
"EUCAST 2020" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
"EUCAST 2020" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
"EUCAST 2020" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 18 FALSE
"EUCAST 2020" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 0.001 16 FALSE
@ -2973,7 +2973,7 @@
"EUCAST 2019" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2019" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
"EUCAST 2019" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
"EUCAST 2019" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
"EUCAST 2019" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
"EUCAST 2019" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 18 18 FALSE
"EUCAST 2019" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 16 16 FALSE
@ -3742,7 +3742,7 @@
"EUCAST 2018" "MIC" "F_CANDD_TRPC" "Candida tropicalis" 2 "ANI" "Anidulafungin" "Candida" 0.064 0.064 FALSE
"EUCAST 2018" "DISK" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" "30ug" 26 21 FALSE
"EUCAST 2018" "MIC" "B_[ORD]_ENTRBCTR" "Enterobacterales" 5 "ATM" "Aztreonam" "Enterobacteriaceae" 1 4 FALSE
"EUCAST 2018" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30µg" 29 26 FALSE
"EUCAST 2018" "DISK" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 29 26 FALSE
"EUCAST 2018" "MIC" "B_AERMN" "Aeromonas" 3 "ATM" "Aztreonam" "Aeromonas" "30ug" 1 4 FALSE
"EUCAST 2018" "DISK" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" "30ug" 50 16 FALSE
"EUCAST 2018" "MIC" "B_PSDMN" "Pseudomonas" 3 "ATM" "Aztreonam" "Pseudo" 1 16 FALSE

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