diff --git a/DESCRIPTION b/DESCRIPTION index 789e63d7..d91b368d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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) diff --git a/NEWS.md b/NEWS.md index e5224925..84c7653b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -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 diff --git a/R/sysdata.rda b/R/sysdata.rda index c8cfc242..fb754388 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index f516343c..ed812e3f 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -79ed9c5d9ddd2c270a5bbb579a920992 +93d91939c6b687fa5edc600378483369 diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index 557bb68c..7b305eb2 100644 Binary files a/data-raw/antibiotics.dta and b/data-raw/antibiotics.dta differ diff --git a/data-raw/antibiotics.feather b/data-raw/antibiotics.feather index ac03bdc4..9948df06 100644 Binary files a/data-raw/antibiotics.feather and b/data-raw/antibiotics.feather differ diff --git a/data-raw/antibiotics.parquet b/data-raw/antibiotics.parquet index 8e034355..a653447e 100644 Binary files a/data-raw/antibiotics.parquet and b/data-raw/antibiotics.parquet differ diff --git a/data-raw/antibiotics.rds b/data-raw/antibiotics.rds index 09864e6a..94076aee 100644 Binary files a/data-raw/antibiotics.rds and b/data-raw/antibiotics.rds differ diff --git a/data-raw/antibiotics.sas b/data-raw/antibiotics.sas index 3e5bfd7e..754daf95 100644 Binary files a/data-raw/antibiotics.sas and b/data-raw/antibiotics.sas differ diff --git a/data-raw/antibiotics.sav b/data-raw/antibiotics.sav index 645d0ae5..e65b356c 100644 Binary files a/data-raw/antibiotics.sav and b/data-raw/antibiotics.sav differ diff --git a/data-raw/antibiotics.txt b/data-raw/antibiotics.txt index eeb4c805..dd0aca5c 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -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" diff --git a/data-raw/antibiotics.xlsx b/data-raw/antibiotics.xlsx index 79f205c4..16adacfc 100644 Binary files a/data-raw/antibiotics.xlsx and b/data-raw/antibiotics.xlsx differ diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 8da235cf..29432298 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -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) diff --git a/data-raw/reproduction_of_rsi_translation.R b/data-raw/reproduction_of_rsi_translation.R index 39dbcd6f..e75f5bdc 100644 --- a/data-raw/reproduction_of_rsi_translation.R +++ b/data-raw/reproduction_of_rsi_translation.R @@ -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(".") diff --git a/data-raw/rsi.md5 b/data-raw/rsi.md5 index 7baeb8ed..0747d3c2 100644 --- a/data-raw/rsi.md5 +++ b/data-raw/rsi.md5 @@ -1 +1 @@ -547b6b086e20bcfb918b3db6f55f84a5 +13bb2f3cde83ef51e3c9e18b2e696b4f diff --git a/data-raw/rsi_translation.dta b/data-raw/rsi_translation.dta index f523bb9d..9481f365 100644 Binary files a/data-raw/rsi_translation.dta and b/data-raw/rsi_translation.dta differ diff --git a/data-raw/rsi_translation.feather b/data-raw/rsi_translation.feather index f6a3467e..ab583083 100644 Binary files a/data-raw/rsi_translation.feather and b/data-raw/rsi_translation.feather differ diff --git a/data-raw/rsi_translation.parquet b/data-raw/rsi_translation.parquet index 2065ca00..722f67ba 100644 Binary files a/data-raw/rsi_translation.parquet and b/data-raw/rsi_translation.parquet differ diff --git a/data-raw/rsi_translation.rds b/data-raw/rsi_translation.rds index 14399825..bc4b77ca 100644 Binary files a/data-raw/rsi_translation.rds and b/data-raw/rsi_translation.rds differ diff --git a/data-raw/rsi_translation.sas b/data-raw/rsi_translation.sas index 5db9e3b2..dc83a6f4 100644 Binary files a/data-raw/rsi_translation.sas and b/data-raw/rsi_translation.sas differ diff --git a/data-raw/rsi_translation.sav b/data-raw/rsi_translation.sav index b2af91d1..9a6abd45 100644 Binary files a/data-raw/rsi_translation.sav and b/data-raw/rsi_translation.sav differ diff --git a/data-raw/rsi_translation.txt b/data-raw/rsi_translation.txt index 57d68f6b..4ef39963 100644 --- a/data-raw/rsi_translation.txt +++ b/data-raw/rsi_translation.txt @@ -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 diff --git a/data-raw/rsi_translation.xlsx b/data-raw/rsi_translation.xlsx index 08823cfb..d3631792 100644 Binary files a/data-raw/rsi_translation.xlsx and b/data-raw/rsi_translation.xlsx differ diff --git a/data/antibiotics.rda b/data/antibiotics.rda index c7bc3ab8..83aaa270 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/data/rsi_translation.rda b/data/rsi_translation.rda index d68a81a2..c30ad0de 100644 Binary files a/data/rsi_translation.rda and b/data/rsi_translation.rda differ diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index 615a0c1a..67a17c3e 100644 --- a/inst/tinytest/test-mo_property.R +++ b/inst/tinytest/test-mo_property.R @@ -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"))) diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 04cb8b05..f72b59b3 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -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}