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library ( dplyr )
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# got EARS-Net codes (= ECDC/WHO codes) from here:
# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
# and exported table 'DRGLST' to MS Excel
library ( readxl )
DRGLST <- read_excel ( " DRGLST.xlsx" )
abx <- DRGLST %>%
select ( ab = WHON5_CODE ,
name = ANTIBIOTIC ) %>%
# remove the ones without WHONET code
filter ( ! is.na ( ab ) ) %>%
distinct ( name , .keep_all = TRUE ) %>%
# add the ones without WHONET code
bind_rows (
DRGLST %>%
select ( ab = WHON5_CODE ,
name = ANTIBIOTIC ) %>%
filter ( is.na ( ab ) ) %>%
distinct ( name , .keep_all = TRUE )
# add new ab code later
) %>%
arrange ( name )
# add old ATC codes
ab_old <- AMR :: antibiotics %>%
mutate ( official = gsub ( " ( and |, )" , " /" , official ) ,
abbr = tolower ( paste ( ifelse ( is.na ( abbr ) , " " , abbr ) ,
ifelse ( is.na ( certe ) , " " , certe ) ,
ifelse ( is.na ( umcg ) , " " , umcg ) ,
sep = " |" ) ) )
for ( i in 1 : nrow ( ab_old ) ) {
abbr <- ab_old [i , " abbr" ]
abbr <- strsplit ( abbr , " |" , fixed = TRUE ) %>% unlist ( ) %>% unique ( )
abbr <- abbr [abbr != " " ]
#print(abbr)
if ( length ( abbr ) == 0 ) {
ab_old [i , " abbr" ] <- NA_character_
} else {
ab_old [i , " abbr" ] <- paste ( abbr , collapse = " |" )
}
}
# create reference data set: to be able to map ab to atc
abx_atc1 <- abx %>%
mutate ( name_lower = tolower ( name ) ) %>%
left_join ( ab_old %>%
select ( ears_net , atc ) , by = c ( ab = " ears_net" ) ) %>%
rename ( atc1 = atc ) %>%
left_join ( ab_old %>%
mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
rename ( atc2 = atc ) %>%
left_join ( ab_old %>%
mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " f" , " ph" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
rename ( atc3 = atc ) %>%
left_join ( ab_old %>%
mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " t" , " th" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
rename ( atc4 = atc ) %>%
left_join ( ab_old %>%
mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " f" , " ph" , official ) ) %>%
mutate ( official = gsub ( " t" , " th" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
rename ( atc5 = atc ) %>%
left_join ( ab_old %>%
mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " f" , " ph" , official ) ) %>%
mutate ( official = gsub ( " t" , " th" , official ) ) %>%
mutate ( official = gsub ( " ine$" , " in" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
rename ( atc6 = atc ) %>%
mutate ( atc = case_when ( ! is.na ( atc1 ) ~ atc1 ,
! is.na ( atc2 ) ~ atc2 ,
! is.na ( atc3 ) ~ atc3 ,
! is.na ( atc4 ) ~ atc4 ,
! is.na ( atc4 ) ~ atc5 ,
TRUE ~ atc6 ) ) %>%
distinct ( ab , name , .keep_all = TRUE ) %>%
select ( ab , atc , name )
abx_atc2 <- ab_old %>%
filter ( ! atc %in% abx_atc1 $ atc ,
is.na ( ears_net ) ,
! is.na ( atc_group1 ) ,
! atc_group1 %like% ( " virus|vaccin|viral|immun" ) ,
! official %like% " (combinations| with )" ) %>%
mutate ( ab = NA_character_ ) %>%
as.data.frame ( stringsAsFactors = FALSE ) %>%
select ( ab , atc , name = official )
abx2 <- bind_rows ( abx_atc1 , abx_atc2 )
rm ( abx_atc1 )
rm ( abx_atc2 )
abx2 $ ab [is.na ( abx2 $ ab ) ] <- toupper ( abbreviate ( gsub ( " [/0-9-]" ,
" " ,
abx2 $ name [is.na ( abx2 $ ab ) ] ) ,
minlength = 3 ,
method = " left.kept" ,
strict = TRUE ) )
n_distinct ( abx2 $ ab )
abx2 <- abx2 %>% arrange ( ab )
seqnr <- 0
# add follow up nrs
for ( i in 2 : nrow ( abx2 ) ) {
if ( abx2 [i , " ab" ] == abx2 [i - 1 , " ab" ] ) {
seqnr <- seqnr + 1
abx2 [i , " seqnr" ] <- seqnr
} else {
seqnr <- 0
}
}
for ( i in 2 : nrow ( abx2 ) ) {
if ( ! is.na ( abx2 [i , " seqnr" ] ) ) {
abx2 [i , " ab" ] <- paste0 ( abx2 [i , " ab" ] , abx2 [i , " seqnr" ] )
}
}
abx2 <- abx2 %>% select ( - seqnr ) %>% arrange ( name )
# everything unique??
nrow ( abx2 ) == n_distinct ( abx2 $ ab )
# get ATC properties
abx2 <- abx2 %>%
left_join ( ab_old %>%
select ( atc , abbr , atc_group1 , atc_group2 ,
oral_ddd , oral_units , iv_ddd , iv_units ) )
abx2 $ abbr <- lapply ( as.list ( abx2 $ abbr ) , function ( x ) unlist ( strsplit ( x , " |" , fixed = TRUE ) ) )
# vector with official names, returns vector with CIDs
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get_CID <- function ( ab ) {
CID <- rep ( NA_integer_ , length ( ab ) )
p <- progress_estimated ( n = length ( ab ) , min_time = 0 )
for ( i in 1 : length ( ab ) ) {
p $ tick ( ) $ print ( )
CID [i ] <- tryCatch (
data.table :: fread ( paste0 ( " https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/" ,
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URLencode ( ab [i ] , reserved = TRUE ) ,
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" /cids/TXT?name_type=complete" ) ,
showProgress = FALSE ) [ [1 ] ] [1 ] ,
error = function ( e ) NA_integer_ )
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if ( is.na ( CID [i ] ) ) {
# try with removing the text in brackets
CID [i ] <- tryCatch (
data.table :: fread ( paste0 ( " https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/" ,
URLencode ( trimws ( gsub ( " [(].*[)]" , " " , ab [i ] ) ) , reserved = TRUE ) ,
" /cids/TXT?name_type=complete" ) ,
showProgress = FALSE ) [ [1 ] ] [1 ] ,
error = function ( e ) NA_integer_ )
}
if ( is.na ( CID [i ] ) ) {
# try match on word and take the lowest CID value (sorted)
ab [i ] <- gsub ( " [^a-z0-9]+" , " " , ab [i ] , ignore.case = TRUE )
CID [i ] <- tryCatch (
data.table :: fread ( paste0 ( " https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/" ,
URLencode ( ab [i ] , reserved = TRUE ) ,
" /cids/TXT?name_type=word" ) ,
showProgress = FALSE ) [ [1 ] ] [1 ] ,
error = function ( e ) NA_integer_ )
}
Sys.sleep ( 0.1 )
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}
CID
}
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# get CIDs (2-3 min)
CIDs <- get_CID ( abx2 $ name )
# These could not be found:
abx2 [is.na ( CIDs ) , ] %>% View ( )
# returns list with synonyms (brand names), with CIDs as names
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get_synonyms <- function ( CID , clean = TRUE ) {
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synonyms <- rep ( NA_character_ , length ( CID ) )
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p <- progress_estimated ( n = length ( CID ) , min_time = 0 )
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for ( i in 1 : length ( CID ) ) {
p $ tick ( ) $ print ( )
synonyms_txt <- " "
if ( is.na ( CID [i ] ) ) {
next
}
synonyms_txt <- tryCatch (
data.table :: fread ( paste0 ( " https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/" ,
CID [i ] ,
" /synonyms/TXT" ) ,
sep = " \n" ,
showProgress = FALSE ) [ [1 ] ] ,
error = function ( e ) NA_character_ )
Sys.sleep ( 0.1 )
if ( clean == TRUE ) {
# remove text between brackets
synonyms_txt <- trimws ( gsub ( " [(].*[)]" , " " ,
gsub ( " [[].*[]]" , " " ,
gsub ( " [(].*[]]" , " " ,
gsub ( " [[].*[)]" , " " , synonyms_txt ) ) ) ) )
synonyms_txt <- gsub ( " Co-" , " Co" , synonyms_txt , fixed = TRUE )
# only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand)
synonyms_txt <- synonyms_txt [nchar ( synonyms_txt ) %in% c ( 6 : 20 )
& ! grepl ( " [-&{},_0-9/]" , synonyms_txt )
& grepl ( " ^[A-Z]" , synonyms_txt , ignore.case = FALSE ) ]
synonyms_txt <- unlist ( strsplit ( synonyms_txt , " ;" , fixed = TRUE ) )
}
synonyms_txt <- unique ( trimws ( synonyms_txt [tolower ( synonyms_txt ) %in% unique ( tolower ( synonyms_txt ) ) ] ) )
synonyms [i ] <- list ( sort ( synonyms_txt ) )
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}
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names ( synonyms ) <- CID
synonyms
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}
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# get brand names from PubChem (2-3 min)
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synonyms <- get_synonyms ( CIDs )
synonyms <- lapply ( synonyms ,
function ( x ) {
if ( length ( x ) == 0 | all ( is.na ( x ) ) ) {
" "
} else {
x
} } )
# add them to data set
antibiotics <- abx2 %>%
left_join ( DRGLST %>%
select ( ab = WHON5_CODE , CLASS , SUBCLASS ) %>%
distinct ( ab , .keep_all = TRUE ) , by = " ab" ) %>%
transmute ( ab ,
atc ,
cid = CIDs ,
# no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam
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name = name %>%
gsub ( " ([/-])([A-Z])" , " \\1\\L\\2" , ., perl = TRUE ) %>%
gsub ( " edta" , " EDTA" , ., ignore.case = TRUE ) ,
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group = case_when (
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " am(ph|f)enicol" ~ " Amphenicols" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " aminoglycoside" ~ " Aminoglycosides" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " carbapenem" | name %like% " (imipenem|meropenem)" ~ " Carbapenems" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " First-generation cephalosporin" ~ " Cephalosporins (1st gen.)" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " Second-generation cephalosporin" ~ " Cephalosporins (2nd gen.)" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " Third-generation cephalosporin" ~ " Cephalosporins (3rd gen.)" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " Fourth-generation cephalosporin" ~ " Cephalosporins (4th gen.)" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " (tuberculosis|mycobacter)" ~ " Antimycobacterials" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " cephalosporin" ~ " Cephalosporins" ,
name %like% " ^Ce" & is.na ( atc_group1 ) & paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " beta-?lactam" ~ " Cephalosporins" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " (beta-?lactam|penicillin)" ~ " Beta-lactams/penicillins" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " quinolone" ~ " Quinolones" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " glycopeptide" ~ " Glycopeptides" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " macrolide" ~ " Macrolides/lincosamides" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " tetracycline" ~ " Tetracyclines" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " trimethoprim" ~ " Trimethoprims" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " polymyxin" ~ " Polymyxins" ,
paste ( atc_group1 , atc_group2 , CLASS , SUBCLASS ) %like% " (fungal|mycot)" ~ " Antifungals/antimycotics" ,
TRUE ~ " Other antibacterials"
) ,
atc_group1 , atc_group2 ,
abbreviations = unname ( abbr ) ,
synonyms = unname ( synonyms ) ,
oral_ddd , oral_units ,
iv_ddd , iv_units ) %>%
as.data.frame ( stringsAsFactors = FALSE )
# some exceptions
antibiotics [which ( antibiotics $ ab == " DOX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " dox" , " doxy" ) )
antibiotics [which ( antibiotics $ ab == " FLC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " clox" ) )
antibiotics [which ( antibiotics $ ab == " CEC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CEC" ) , " abbreviations" ] [ [1 ] ] , " CFC" ) ) # cefaclor old WHONET4 code
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antibiotics [which ( antibiotics $ ab == " AMX" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " AMX" ) , " synonyms" ] [ [1 ] ] , " Amoxy" ) ) )
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# 'Polymixin B' (POL) and 'Polymyxin B' (PLB) both exist, so:
antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] , " POL" , " Polymixin" , " Polymixin B" ) )
antibiotics <- filter ( antibiotics , ab != " POL" )
# 'Latamoxef' (LTM) and 'Moxalactam (Latamoxef)' (MOX) both exist, so:
antibiotics [which ( antibiotics $ ab == " LTM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " MOX" , " moxa" ) )
antibiotics <- filter ( antibiotics , ab != " MOX" )
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# RFP and RFP1 (the J0 one) both mean 'rifapentine', although 'rifp' is not recognised, so:
antibiotics <- filter ( antibiotics , ab != " RFP" )
antibiotics [which ( antibiotics $ ab == " RFP1" ) , " ab" ] <- " RFP"
antibiotics [which ( antibiotics $ ab == " RFP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " rifp" ) )
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# Rifampicin is better known as a drug than Rifampin (Rifampin is still listed as a brand name), so:
antibiotics [which ( antibiotics $ ab == " RIF" ) , " name" ] <- " Rifampicin"
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# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
antibiotics <- filter ( antibiotics , ab != " PME" )
antibiotics [which ( antibiotics $ ab == " PVM1" ) , " ab" ] <- " PME"
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# Remove Sinecatechins
antibiotics <- filter ( antibiotics , ab != " SNC" )
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# ESBL E-test codes:
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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antibiotics [which ( antibiotics $ ab == " CPC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " xpml" ) )
antibiotics [which ( antibiotics $ ab == " FEP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FEP" ) , " abbreviations" ] [ [1 ] ] , " xpm" ) )
antibiotics [which ( antibiotics $ ab == " CTC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " xctl" ) )
antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] , " xct" ) )
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# High level Gentamcin and Streptomycin
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antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " gehl" , " gentamicin high" , " genta high" ) )
antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " sthl" , " streptomycin high" , " strepto high" ) )
# add imi to imipenem
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antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " imip" , " imi" , " imp" ) )
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## new ATC codes
# ceftaroline
antibiotics [which ( antibiotics $ ab == " CPT" ) , " atc" ] <- " J01DI02"
# faropenem
antibiotics [which ( antibiotics $ ab == " FAR" ) , " atc" ] <- " J01DI03"
# ceftobiprole
antibiotics [which ( antibiotics $ ab == " BPR" ) , " atc" ] <- " J01DI01"
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# typo
antibiotics [which ( antibiotics $ ab == " RXT" ) , " name" ] <- " Roxithromycin"
antibiotics [which ( antibiotics $ ab == " PEN" ) , " atc" ] <- " J01CE01"
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antibiotics <- antibiotics %>% arrange ( name )
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# set cephalosporins groups for the ones that could not be determined automatically:
antibiotics <- antibiotics %>%
mutate ( group = case_when (
name == " Cefcapene" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefcapene pivoxil" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefditoren pivoxil" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefepime/clavulanic acid" ~ " Cephalosporins (4th gen.)" ,
name == " Cefepime/tazobactam" ~ " Cephalosporins (4th gen.)" ,
name == " Cefetamet pivoxil" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefetecol (Cefcatacol)" ~ " Cephalosporins (4th gen.)" ,
name == " Cefetrizole" ~ " Cephalosporins (unclassified gen.)" ,
name == " Cefoselis" ~ " Cephalosporins (4th gen.)" ,
name == " Cefotaxime/clavulanic acid" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefotaxime/sulbactam" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefotiam hexetil" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefovecin" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefozopran" ~ " Cephalosporins (4th gen.)" ,
name == " Cefpimizole" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefpodoxime proxetil" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefpodoxime/clavulanic acid" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefquinome" ~ " Cephalosporins (4th gen.)" ,
name == " Cefsumide" ~ " Cephalosporins (unclassified gen.)" ,
name == " Ceftaroline" ~ " Cephalosporins (5th gen.)" ,
name == " Ceftaroline/avibactam" ~ " Cephalosporins (5th gen.)" ,
name == " Ceftazidime/avibactam" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefteram" ~ " Cephalosporins (3rd gen.)" ,
name == " Cefteram pivoxil" ~ " Cephalosporins (3rd gen.)" ,
name == " Ceftiofur" ~ " Cephalosporins (3rd gen.)" ,
name == " Ceftizoxime alapivoxil" ~ " Cephalosporins (3rd gen.)" ,
name == " Ceftobiprole" ~ " Cephalosporins (5th gen.)" ,
name == " Ceftobiprole medocaril" ~ " Cephalosporins (5th gen.)" ,
name == " Ceftolozane/enzyme inhibitor" ~ " Cephalosporins (5th gen.)" ,
name == " Ceftolozane/tazobactam" ~ " Cephalosporins (5th gen.)" ,
name == " Cefuroxime axetil" ~ " Cephalosporins (2nd gen.)" ,
TRUE ~ group ) )
# set as data.frame again
antibiotics <- as.data.frame ( antibiotics , stringsAsFactors = FALSE )
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class ( antibiotics $ ab ) <- " ab"
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dim ( antibiotics ) # for R/data.R
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usethis :: use_data ( antibiotics , overwrite = TRUE )
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rm ( antibiotics )