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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 19:26:13 +01:00

ATC and DDD update

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dr. M.S. (Matthijs) Berends 2022-10-29 19:01:23 +02:00
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27 changed files with 23 additions and 20 deletions

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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.2.9036
Version: 1.8.2.9037
Date: 2022-10-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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@ -1,4 +1,4 @@
# AMR 1.8.2.9036
# AMR 1.8.2.9037
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -53,6 +53,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Updated support for all WHONET 2022 microorganism codes
* Antimicrobial interpretation 'SDD' (susceptible dose-dependent, coined by CLSI) will be interpreted as 'I' to comply with EUCAST's 'I' in `as.rsi()`
* Fix for `mo_shortname()` in case of higher taxonomic ranks (order, class, phylum)
* Updated DDDs and ATCs for the `antibiotics` data set - ATC codes J04AB06 (enviomycin) and D06AX14 (ozenoxacin) were added
### Other
* 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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79ed9c5d9ddd2c270a5bbb579a920992
93d91939c6b687fa5edc600378483369

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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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@ -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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@ -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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547b6b086e20bcfb918b3db6f55f84a5
13bb2f3cde83ef51e3c9e18b2e696b4f

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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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@ -86,9 +86,9 @@ for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
# test languages
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- suppressWarnings(mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE)) # should be transformable to English again
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
expect_identical(suppressWarnings(mo_name(dutch, language = NULL, keep_synonyms = TRUE)),
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi|[(]class[)]")]) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))

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@ -17,7 +17,7 @@
\item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
\item \code{abbr}\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 171 drugs
\item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs
\item \code{iv_units}\cr Units of \code{iv_ddd}