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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
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# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
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# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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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 %>%
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select (
ab = WHON5_CODE ,
name = ANTIBIOTIC
) %>%
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# remove the ones without WHONET code
filter ( ! is.na ( ab ) ) %>%
distinct ( name , .keep_all = TRUE ) %>%
# add the ones without WHONET code
bind_rows (
DRGLST %>%
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select (
ab = WHON5_CODE ,
name = ANTIBIOTIC
) %>%
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filter ( is.na ( ab ) ) %>%
distinct ( name , .keep_all = TRUE )
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# add new ab code later
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) %>%
arrange ( name )
# add old ATC codes
ab_old <- AMR :: antibiotics %>%
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mutate (
official = gsub ( " ( and |, )" , " /" , official ) ,
abbr = tolower ( paste ( ifelse ( is.na ( abbr ) , " " , abbr ) ,
ifelse ( is.na ( certe ) , " " , certe ) ,
ifelse ( is.na ( umcg ) , " " , umcg ) ,
sep = " |"
) )
)
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for ( i in 1 : nrow ( ab_old ) ) {
abbr <- ab_old [i , " abbr" ]
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abbr <- strsplit ( abbr , " |" , fixed = TRUE ) %>%
unlist ( ) %>%
unique ( )
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abbr <- abbr [abbr != " " ]
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# print(abbr)
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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 %>%
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select ( ears_net , atc ) , by = c ( ab = " ears_net" ) ) %>%
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rename ( atc1 = atc ) %>%
left_join ( ab_old %>%
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mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
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rename ( atc2 = atc ) %>%
left_join ( ab_old %>%
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mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " f" , " ph" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
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rename ( atc3 = atc ) %>%
left_join ( ab_old %>%
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mutate ( official = gsub ( " , combinations" , " " , official , fixed = TRUE ) ) %>%
mutate ( official = gsub ( " t" , " th" , official ) ) %>%
transmute ( official = tolower ( official ) , atc ) , by = c ( name_lower = " official" ) ) %>%
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rename ( atc4 = atc ) %>%
left_join ( ab_old %>%
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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" ) ) %>%
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rename ( atc5 = atc ) %>%
left_join ( ab_old %>%
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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" ) ) %>%
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rename ( atc6 = atc ) %>%
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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
) ) %>%
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distinct ( ab , name , .keep_all = TRUE ) %>%
select ( ab , atc , name )
abx_atc2 <- ab_old %>%
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filter (
! atc %in% abx_atc1 $ atc ,
is.na ( ears_net ) ,
! is.na ( atc_group1 ) ,
atc_group1 %unlike% ( " virus|vaccin|viral|immun" ) ,
official %unlike% " (combinations| with )"
) %>%
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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 )
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abx2 $ ab [is.na ( abx2 $ ab ) ] <- toupper ( abbreviate (
gsub (
" [/0-9-]" ,
" " ,
abx2 $ name [is.na ( abx2 $ ab ) ]
) ,
minlength = 3 ,
method = " left.kept" ,
strict = TRUE
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) )
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n_distinct ( abx2 $ ab )
abx2 <- abx2 %>% arrange ( ab )
seqnr <- 0
# add follow up nrs
for ( i in 2 : nrow ( abx2 ) ) {
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if ( abx2 [i , " ab" , drop = TRUE ] == abx2 [i - 1 , " ab" , drop = TRUE ] ) {
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seqnr <- seqnr + 1
abx2 [i , " seqnr" ] <- seqnr
} else {
seqnr <- 0
}
}
for ( i in 2 : nrow ( abx2 ) ) {
if ( ! is.na ( abx2 [i , " seqnr" ] ) ) {
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abx2 [i , " ab" ] <- paste0 ( abx2 [i , " ab" , drop = TRUE ] , abx2 [i , " seqnr" , drop = TRUE ] )
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}
}
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abx2 <- abx2 %>%
select ( - seqnr ) %>%
arrange ( name )
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# everything unique??
nrow ( abx2 ) == n_distinct ( abx2 $ ab )
# get ATC properties
abx2 <- abx2 %>%
left_join ( ab_old %>%
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select (
atc , abbr , atc_group1 , atc_group2 ,
oral_ddd , oral_units , iv_ddd , iv_units
) )
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abx2 $ abbr <- lapply ( as.list ( abx2 $ abbr ) , function ( x ) unlist ( strsplit ( x , " |" , fixed = TRUE ) ) )
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# Update Compound IDs and Synonyms ----
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# vector with official names, returns vector with CIDs
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get_CID <- function ( ab ) {
CID <- rep ( NA_integer_ , length ( ab ) )
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p <- AMR ::: progress_ticker ( n = length ( ab ) , min_time = 0 )
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for ( i in 1 : length ( ab ) ) {
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p $ tick ( )
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CID [i ] <- tryCatch (
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data.table :: fread (
paste0 (
" https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/" ,
URLencode ( ab [i ] , reserved = TRUE ) ,
" /cids/TXT?name_type=complete"
) ,
showProgress = FALSE
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) [ [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 (
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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
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) [ [1 ] ] [1 ] ,
error = function ( e ) NA_integer_
)
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}
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 (
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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
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) [ [1 ] ] [1 ] ,
error = function ( e ) NA_integer_
)
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}
Sys.sleep ( 0.1 )
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}
CID
}
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# get CIDs (4-5 min)
CIDs <- get_CID ( antibiotics $ name )
# take missing from previously found CIDs
CIDs [is.na ( CIDs ) & ! is.na ( antibiotics $ cid ) ] <- antibiotics $ cid [is.na ( CIDs ) & ! is.na ( antibiotics $ cid ) ]
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# These could not be found:
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antibiotics [is.na ( CIDs ) , ] %>% View ( )
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# 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 <- AMR ::: progress_ticker ( n = length ( CID ) , min_time = 0 )
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for ( i in 1 : length ( CID ) ) {
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p $ tick ( )
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synonyms_txt <- " "
if ( is.na ( CID [i ] ) ) {
next
}
synonyms_txt <- tryCatch (
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data.table :: fread (
paste0 (
" https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/" ,
CID [i ] ,
" /synonyms/TXT"
) ,
sep = " \n" ,
showProgress = FALSE
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) [ [1 ] ] ,
error = function ( e ) NA_character_
)
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Sys.sleep ( 0.1 )
if ( clean == TRUE ) {
# remove text between brackets
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synonyms_txt <- trimws ( gsub (
" [(].*[)]" , " " ,
gsub (
" [[].*[]]" , " " ,
gsub (
" [(].*[]]" , " " ,
gsub ( " [[].*[)]" , " " , synonyms_txt )
)
)
) )
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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)
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synonyms_txt <- synonyms_txt [nchar ( synonyms_txt ) %in% c ( 6 : 20 ) &
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! grepl ( " [-&{},_0-9/:]" , synonyms_txt ) &
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grepl ( " ^[A-Z]" , synonyms_txt , ignore.case = FALSE ) ]
synonyms_txt <- unlist ( strsplit ( synonyms_txt , " ;" , fixed = TRUE ) )
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}
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 (3-4 min)
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synonyms <- get_synonyms ( CIDs )
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synonyms.bak <- synonyms
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# add existing ones (will be cleaned later)
for ( i in seq_len ( length ( synonyms ) ) ) {
old <- antibiotics $ synonyms [ [i ] ]
if ( old %like% " ^c[()]" ) {
old <- eval ( parse ( text = old ) )
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}
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synonyms [ [i ] ] <- c ( synonyms [ [i ] ] , old )
}
antibiotics $ synonyms <- synonyms
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stop ( " remember to remove co-trimoxazole as synonyms from SXT (Sulfamethoxazole), so it only exists in SXT!" )
sulfa <- antibiotics [which ( antibiotics $ ab == " SMX" ) , " synonyms" , drop = TRUE ] [ [1 ] ]
cotrim <- antibiotics [which ( antibiotics $ ab == " SXT" ) , " synonyms" , drop = TRUE ] [ [1 ] ]
sulfa <- sulfa [ ! sulfa %in% cotrim ]
antibiotics [which ( antibiotics $ ab == " SMX" ) , " synonyms" ] [ [1 ] ] [ [1 ] ] <- sulfa
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# now go to end of this file
# -----
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# add them to data set
antibiotics <- abx2 %>%
left_join ( DRGLST %>%
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select ( ab = WHON5_CODE , CLASS , SUBCLASS ) %>%
distinct ( ab , .keep_all = TRUE ) , by = " ab" ) %>%
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transmute ( ab ,
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atc ,
cid = CIDs ,
# no capital after a slash: Ampicillin/Sulbactam -> Ampicillin/sulbactam
name = name %>%
gsub ( " ([/-])([A-Z])" , " \\1\\L\\2" , ., perl = TRUE ) %>%
gsub ( " edta" , " EDTA" , ., ignore.case = TRUE ) ,
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
) %>%
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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:
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antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] , " POL" , " Polymixin" , " Polymixin B" , " Poly B" ) )
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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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# GLIMS codes
antibiotics [which ( antibiotics $ ab == as.ab ( " cefuroxim" ) ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == as.ab ( " cefuroxim" ) ) , " abbreviations" ] [ [1 ] ] , " cfrx" ) )
antibiotics [which ( antibiotics $ ab == as.ab ( " cefotaxim" ) ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == as.ab ( " cefotaxim" ) ) , " abbreviations" ] [ [1 ] ] , " cftx" ) )
antibiotics [which ( antibiotics $ ab == as.ab ( " ceftazidime" ) ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == as.ab ( " ceftazidime" ) ) , " abbreviations" ] [ [1 ] ] , " cftz" ) )
antibiotics [which ( antibiotics $ ab == as.ab ( " cefepime" ) ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == as.ab ( " cefepime" ) ) , " abbreviations" ] [ [1 ] ] , " cfpi" ) )
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antibiotics [which ( antibiotics $ ab == as.ab ( " cefoxitin" ) ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == as.ab ( " cefoxitin" ) ) , " abbreviations" ] [ [1 ] ] , " cfxt" ) )
# Add cefoxitin screening
class ( antibiotics $ ab ) <- " character"
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antibiotics <- rbind ( antibiotics , data.frame (
ab = " FOX1" , atc = NA , cid = NA ,
name = " Cefoxitin screening" ,
group = " Cephalosporins (2nd gen.)" , atc_group1 = NA , atc_group2 = NA ,
abbreviations = " cfsc" , synonyms = NA ,
oral_ddd = NA , oral_units = NA , iv_ddd = NA , iv_units = NA ,
loinc = NA ,
stringsAsFactors = FALSE
) )
2020-04-13 21:09:56 +02:00
# More GLIMS codes
2021-05-04 12:47:33 +02:00
antibiotics [which ( antibiotics $ ab == " AMB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMB" ) , " abbreviations" ] [ [1 ] ] , " amf" ) )
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antibiotics [which ( antibiotics $ ab == " CAZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CAZ" ) , " abbreviations" ] [ [1 ] ] , " cftz" ) )
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antibiotics [which ( antibiotics $ ab == " COL" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " COL" ) , " abbreviations" ] [ [1 ] ] , " cst" ) )
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antibiotics [which ( antibiotics $ ab == " CRO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CRO" ) , " abbreviations" ] [ [1 ] ] , " cftr" ) )
antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] , " cftx" ) )
antibiotics [which ( antibiotics $ ab == " CXM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CXM" ) , " abbreviations" ] [ [1 ] ] , " cfrx" ) )
antibiotics [which ( antibiotics $ ab == " CZO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CZO" ) , " abbreviations" ] [ [1 ] ] , " cfzl" ) )
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antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] , " fcu" ) )
antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] , " fluy" ) )
antibiotics [which ( antibiotics $ ab == " FLU" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FLU" ) , " abbreviations" ] [ [1 ] ] , " flz" ) )
antibiotics [which ( antibiotics $ ab == " FOS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FOS" ) , " abbreviations" ] [ [1 ] ] , " fof" ) )
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antibiotics [which ( antibiotics $ ab == " FOX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FOX" ) , " abbreviations" ] [ [1 ] ] , " cfxt" ) )
2021-05-04 12:47:33 +02:00
antibiotics [which ( antibiotics $ ab == " FUS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FUS" ) , " abbreviations" ] [ [1 ] ] , " fa" ) )
antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] , " g_h" ) )
antibiotics [which ( antibiotics $ ab == " KAH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " KAH" ) , " abbreviations" ] [ [1 ] ] , " k_h" ) )
antibiotics [which ( antibiotics $ ab == " KET" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " KET" ) , " abbreviations" ] [ [1 ] ] , " ktc" ) )
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antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] , " pipc" ) )
antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] , " PIPC" ) )
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antibiotics [which ( antibiotics $ ab == " SPX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SPX" ) , " abbreviations" ] [ [1 ] ] , " spa" ) )
antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] , " s_h" ) )
antibiotics [which ( antibiotics $ ab == " STR1" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " STR1" ) , " abbreviations" ] [ [1 ] ] , " stm" ) )
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antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] , " COTRIM" ) )
antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] , " trsx" ) )
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antibiotics [which ( antibiotics $ ab == " TGC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TGC" ) , " abbreviations" ] [ [1 ] ] , " tig" ) )
antibiotics [which ( antibiotics $ ab == " TMP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TMP" ) , " abbreviations" ] [ [1 ] ] , " tri" ) )
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antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] , " PIPTAZ" ) )
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antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] , " pit" ) )
2020-04-13 21:09:56 +02:00
antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] , " pita" ) )
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antibiotics [which ( antibiotics $ ab == " VOR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " VOR" ) , " abbreviations" ] [ [1 ] ] , " vrc" ) )
2020-04-14 20:38:09 +02:00
# official RIVM codes (Dutch National Health Institute)
# https://www.rivm.nl/sites/default/files/2019-09/Bijlage_4_Lijst_antibiotica%202020%201.0.pdf
antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FCT" ) , " abbreviations" ] [ [1 ] ] , " 5flc" ) )
antibiotics [which ( antibiotics $ ab == " AMC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMC" ) , " abbreviations" ] [ [1 ] ] , " amcl" ) )
antibiotics [which ( antibiotics $ ab == " AMB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMB" ) , " abbreviations" ] [ [1 ] ] , " amfb" ) )
antibiotics [which ( antibiotics $ ab == " AMH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMH" ) , " abbreviations" ] [ [1 ] ] , " amhl" ) )
antibiotics [which ( antibiotics $ ab == " AMK" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMK" ) , " abbreviations" ] [ [1 ] ] , " amik" ) )
antibiotics [which ( antibiotics $ ab == " AMX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMX" ) , " abbreviations" ] [ [1 ] ] , " amox" ) )
antibiotics [which ( antibiotics $ ab == " AMP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AMP" ) , " abbreviations" ] [ [1 ] ] , " ampi" ) )
antibiotics [which ( antibiotics $ ab == " SAM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SAM" ) , " abbreviations" ] [ [1 ] ] , " amsu" ) )
antibiotics [which ( antibiotics $ ab == " ANI" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ANI" ) , " abbreviations" ] [ [1 ] ] , " anid" ) )
antibiotics [which ( antibiotics $ ab == " SAM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SAM" ) , " abbreviations" ] [ [1 ] ] , " apsu" ) )
antibiotics [which ( antibiotics $ ab == " AZM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AZM" ) , " abbreviations" ] [ [1 ] ] , " azit" ) )
antibiotics [which ( antibiotics $ ab == " AZL" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " AZL" ) , " abbreviations" ] [ [1 ] ] , " azlo" ) )
antibiotics [which ( antibiotics $ ab == " ATM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ATM" ) , " abbreviations" ] [ [1 ] ] , " aztr" ) )
antibiotics [which ( antibiotics $ ab == " PNV" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PNV" ) , " abbreviations" ] [ [1 ] ] , " bepe" ) )
antibiotics [which ( antibiotics $ ab == " CAP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CAP" ) , " abbreviations" ] [ [1 ] ] , " capr" ) )
antibiotics [which ( antibiotics $ ab == " CRB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CRB" ) , " abbreviations" ] [ [1 ] ] , " carb" ) )
antibiotics [which ( antibiotics $ ab == " CAS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CAS" ) , " abbreviations" ] [ [1 ] ] , " casp" ) )
antibiotics [which ( antibiotics $ ab == " CDC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CDC" ) , " abbreviations" ] [ [1 ] ] , " cecl" ) )
antibiotics [which ( antibiotics $ ab == " CXA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CXA" ) , " abbreviations" ] [ [1 ] ] , " cfax" ) )
antibiotics [which ( antibiotics $ ab == " CTB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTB" ) , " abbreviations" ] [ [1 ] ] , " cfbu" ) )
antibiotics [which ( antibiotics $ ab == " CEC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CEC" ) , " abbreviations" ] [ [1 ] ] , " cfcl" ) )
antibiotics [which ( antibiotics $ ab == " CFR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CFR" ) , " abbreviations" ] [ [1 ] ] , " cfdx" ) )
antibiotics [which ( antibiotics $ ab == " CEP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CEP" ) , " abbreviations" ] [ [1 ] ] , " cflt" ) )
antibiotics [which ( antibiotics $ ab == " LEX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LEX" ) , " abbreviations" ] [ [1 ] ] , " cflx" ) )
antibiotics [which ( antibiotics $ ab == " MAN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MAN" ) , " abbreviations" ] [ [1 ] ] , " cfmn" ) )
antibiotics [which ( antibiotics $ ab == " CPD" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CPD" ) , " abbreviations" ] [ [1 ] ] , " cfpd" ) )
antibiotics [which ( antibiotics $ ab == " FEP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FEP" ) , " abbreviations" ] [ [1 ] ] , " cfpi" ) )
antibiotics [which ( antibiotics $ ab == " CPO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CPO" ) , " abbreviations" ] [ [1 ] ] , " cfpr" ) )
antibiotics [which ( antibiotics $ ab == " CFP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CFP" ) , " abbreviations" ] [ [1 ] ] , " cfpz" ) )
antibiotics [which ( antibiotics $ ab == " CED" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CED" ) , " abbreviations" ] [ [1 ] ] , " cfrd" ) )
antibiotics [which ( antibiotics $ ab == " CPT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CPT" ) , " abbreviations" ] [ [1 ] ] , " cfro" ) )
antibiotics [which ( antibiotics $ ab == " CXM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CXM" ) , " abbreviations" ] [ [1 ] ] , " cfrx" ) )
antibiotics [which ( antibiotics $ ab == " CFS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CFS" ) , " abbreviations" ] [ [1 ] ] , " cfsl" ) )
antibiotics [which ( antibiotics $ ab == " CRO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CRO" ) , " abbreviations" ] [ [1 ] ] , " cftr" ) )
antibiotics [which ( antibiotics $ ab == " CTT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTT" ) , " abbreviations" ] [ [1 ] ] , " cftt" ) )
antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTX" ) , " abbreviations" ] [ [1 ] ] , " cftx" ) )
antibiotics [which ( antibiotics $ ab == " CAZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CAZ" ) , " abbreviations" ] [ [1 ] ] , " cftz" ) )
antibiotics [which ( antibiotics $ ab == " CFM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CFM" ) , " abbreviations" ] [ [1 ] ] , " cfxm" ) )
antibiotics [which ( antibiotics $ ab == " FOX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FOX" ) , " abbreviations" ] [ [1 ] ] , " cfxt" ) )
2020-05-27 16:37:49 +02:00
antibiotics [which ( antibiotics $ ab == " CZA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CZA" ) , " abbreviations" ] [ [1 ] ] , " cfav" ) )
2020-04-14 20:38:09 +02:00
antibiotics [which ( antibiotics $ ab == " CZO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CZO" ) , " abbreviations" ] [ [1 ] ] , " cfzl" ) )
antibiotics [which ( antibiotics $ ab == " CZX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CZX" ) , " abbreviations" ] [ [1 ] ] , " cfzx" ) )
antibiotics [which ( antibiotics $ ab == " CHL" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CHL" ) , " abbreviations" ] [ [1 ] ] , " chlo" ) )
antibiotics [which ( antibiotics $ ab == " CPC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CPC" ) , " abbreviations" ] [ [1 ] ] , " cicl" ) )
antibiotics [which ( antibiotics $ ab == " CIN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CIN" ) , " abbreviations" ] [ [1 ] ] , " cino" ) )
antibiotics [which ( antibiotics $ ab == " CIP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CIP" ) , " abbreviations" ] [ [1 ] ] , " cipr" ) )
antibiotics [which ( antibiotics $ ab == " CIX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CIX" ) , " abbreviations" ] [ [1 ] ] , " cipx" ) )
antibiotics [which ( antibiotics $ ab == " CLR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CLR" ) , " abbreviations" ] [ [1 ] ] , " clar" ) )
antibiotics [which ( antibiotics $ ab == " CLI" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CLI" ) , " abbreviations" ] [ [1 ] ] , " clin" ) )
antibiotics [which ( antibiotics $ ab == " CTR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTR" ) , " abbreviations" ] [ [1 ] ] , " clot" ) )
antibiotics [which ( antibiotics $ ab == " CLO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CLO" ) , " abbreviations" ] [ [1 ] ] , " clox" ) )
antibiotics [which ( antibiotics $ ab == " COL" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " COL" ) , " abbreviations" ] [ [1 ] ] , " coli" ) )
antibiotics [which ( antibiotics $ ab == " CTC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CTC" ) , " abbreviations" ] [ [1 ] ] , " cxcl" ) )
antibiotics [which ( antibiotics $ ab == " CYC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CYC" ) , " abbreviations" ] [ [1 ] ] , " cycl" ) )
antibiotics [which ( antibiotics $ ab == " CCV" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " CCV" ) , " abbreviations" ] [ [1 ] ] , " czcl" ) )
antibiotics [which ( antibiotics $ ab == " DAP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " DAP" ) , " abbreviations" ] [ [1 ] ] , " dapt" ) )
antibiotics [which ( antibiotics $ ab == " DIC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " DIC" ) , " abbreviations" ] [ [1 ] ] , " dicl" ) )
antibiotics [which ( antibiotics $ ab == " DOR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " DOR" ) , " abbreviations" ] [ [1 ] ] , " dori" ) )
antibiotics [which ( antibiotics $ ab == " DOX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " DOX" ) , " abbreviations" ] [ [1 ] ] , " doxy" ) )
antibiotics [which ( antibiotics $ ab == " ENX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ENX" ) , " abbreviations" ] [ [1 ] ] , " enox" ) )
antibiotics [which ( antibiotics $ ab == " ETP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ETP" ) , " abbreviations" ] [ [1 ] ] , " erta" ) )
antibiotics [which ( antibiotics $ ab == " ERY" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ERY" ) , " abbreviations" ] [ [1 ] ] , " eryt" ) )
antibiotics [which ( antibiotics $ ab == " PHE" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PHE" ) , " abbreviations" ] [ [1 ] ] , " fene" ) )
antibiotics [which ( antibiotics $ ab == " PHN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PHN" ) , " abbreviations" ] [ [1 ] ] , " fepe" ) )
antibiotics [which ( antibiotics $ ab == " FLE" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FLE" ) , " abbreviations" ] [ [1 ] ] , " fler" ) )
antibiotics [which ( antibiotics $ ab == " FLU" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FLU" ) , " abbreviations" ] [ [1 ] ] , " fluc" ) )
antibiotics [which ( antibiotics $ ab == " FLC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FLC" ) , " abbreviations" ] [ [1 ] ] , " flux" ) )
antibiotics [which ( antibiotics $ ab == " FOS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FOS" ) , " abbreviations" ] [ [1 ] ] , " fosf" ) )
antibiotics [which ( antibiotics $ ab == " FRM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FRM" ) , " abbreviations" ] [ [1 ] ] , " fram" ) )
antibiotics [which ( antibiotics $ ab == " FUS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " FUS" ) , " abbreviations" ] [ [1 ] ] , " fusi" ) )
antibiotics [which ( antibiotics $ ab == " GAT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " GAT" ) , " abbreviations" ] [ [1 ] ] , " gati" ) )
antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] , " gehl" ) )
antibiotics [which ( antibiotics $ ab == " GEN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " GEN" ) , " abbreviations" ] [ [1 ] ] , " gent" ) )
antibiotics [which ( antibiotics $ ab == " GRX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " GRX" ) , " abbreviations" ] [ [1 ] ] , " grep" ) )
antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] , " imci" ) )
antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] , " imip" ) )
antibiotics [which ( antibiotics $ ab == " ISV" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ISV" ) , " abbreviations" ] [ [1 ] ] , " isav" ) )
antibiotics [which ( antibiotics $ ab == " ITR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " ITR" ) , " abbreviations" ] [ [1 ] ] , " itra" ) )
antibiotics [which ( antibiotics $ ab == " KAH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " KAH" ) , " abbreviations" ] [ [1 ] ] , " kahl" ) )
antibiotics [which ( antibiotics $ ab == " KAN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " KAN" ) , " abbreviations" ] [ [1 ] ] , " kana" ) )
antibiotics [which ( antibiotics $ ab == " KET" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " KET" ) , " abbreviations" ] [ [1 ] ] , " keto" ) )
antibiotics [which ( antibiotics $ ab == " LVX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LVX" ) , " abbreviations" ] [ [1 ] ] , " levo" ) )
antibiotics [which ( antibiotics $ ab == " LIN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LIN" ) , " abbreviations" ] [ [1 ] ] , " linc" ) )
antibiotics [which ( antibiotics $ ab == " LNZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LNZ" ) , " abbreviations" ] [ [1 ] ] , " line" ) )
antibiotics [which ( antibiotics $ ab == " LOR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LOR" ) , " abbreviations" ] [ [1 ] ] , " lora" ) )
antibiotics [which ( antibiotics $ ab == " MEM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MEM" ) , " abbreviations" ] [ [1 ] ] , " mero" ) )
antibiotics [which ( antibiotics $ ab == " MET" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MET" ) , " abbreviations" ] [ [1 ] ] , " meti" ) )
antibiotics [which ( antibiotics $ ab == " MTR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MTR" ) , " abbreviations" ] [ [1 ] ] , " metr" ) )
antibiotics [which ( antibiotics $ ab == " MEZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MEZ" ) , " abbreviations" ] [ [1 ] ] , " mezl" ) )
antibiotics [which ( antibiotics $ ab == " MIF" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MIF" ) , " abbreviations" ] [ [1 ] ] , " mica" ) )
antibiotics [which ( antibiotics $ ab == " MCZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MCZ" ) , " abbreviations" ] [ [1 ] ] , " mico" ) )
antibiotics [which ( antibiotics $ ab == " MNO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MNO" ) , " abbreviations" ] [ [1 ] ] , " mino" ) )
2021-12-13 10:18:28 +01:00
antibiotics [which ( antibiotics $ ab == " LTM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " LTM" ) , " abbreviations" ] [ [1 ] ] , " moxa" , " moxalactam" ) )
2020-04-14 20:38:09 +02:00
antibiotics [which ( antibiotics $ ab == " MFX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " MFX" ) , " abbreviations" ] [ [1 ] ] , " moxi" ) )
antibiotics [which ( antibiotics $ ab == " NAL" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NAL" ) , " abbreviations" ] [ [1 ] ] , " nali" ) )
antibiotics [which ( antibiotics $ ab == " NEO" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NEO" ) , " abbreviations" ] [ [1 ] ] , " neom" ) )
antibiotics [which ( antibiotics $ ab == " NET" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NET" ) , " abbreviations" ] [ [1 ] ] , " neti" ) )
antibiotics [which ( antibiotics $ ab == " NIT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NIT" ) , " abbreviations" ] [ [1 ] ] , " nitr" ) )
antibiotics [which ( antibiotics $ ab == " NOR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NOR" ) , " abbreviations" ] [ [1 ] ] , " norf" ) )
antibiotics [which ( antibiotics $ ab == " NYS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " NYS" ) , " abbreviations" ] [ [1 ] ] , " nyst" ) )
antibiotics [which ( antibiotics $ ab == " OFX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " OFX" ) , " abbreviations" ] [ [1 ] ] , " oflo" ) )
antibiotics [which ( antibiotics $ ab == " OXA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " OXA" ) , " abbreviations" ] [ [1 ] ] , " oxal" ) )
antibiotics [which ( antibiotics $ ab == " PEF" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PEF" ) , " abbreviations" ] [ [1 ] ] , " pefl" ) )
antibiotics [which ( antibiotics $ ab == " PEN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PEN" ) , " abbreviations" ] [ [1 ] ] , " peni" ) )
antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PIP" ) , " abbreviations" ] [ [1 ] ] , " pipc" ) )
antibiotics [which ( antibiotics $ ab == " PPA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PPA" ) , " abbreviations" ] [ [1 ] ] , " pipz" ) )
antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] , " pita" ) )
antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PLB" ) , " abbreviations" ] [ [1 ] ] , " polb" ) )
antibiotics [which ( antibiotics $ ab == " POS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " POS" ) , " abbreviations" ] [ [1 ] ] , " posa" ) )
antibiotics [which ( antibiotics $ ab == " PRI" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " PRI" ) , " abbreviations" ] [ [1 ] ] , " pris" ) )
antibiotics [which ( antibiotics $ ab == " QDA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " QDA" ) , " abbreviations" ] [ [1 ] ] , " quda" ) )
antibiotics [which ( antibiotics $ ab == " RIF" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " RIF" ) , " abbreviations" ] [ [1 ] ] , " rifa" ) )
antibiotics [which ( antibiotics $ ab == " RXT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " RXT" ) , " abbreviations" ] [ [1 ] ] , " roxi" ) )
antibiotics [which ( antibiotics $ ab == " SMX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SMX" ) , " abbreviations" ] [ [1 ] ] , " sfmx" ) )
antibiotics [which ( antibiotics $ ab == " SLF4" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SLF4" ) , " abbreviations" ] [ [1 ] ] , " sfmz" ) )
antibiotics [which ( antibiotics $ ab == " SSS" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SSS" ) , " abbreviations" ] [ [1 ] ] , " sfna" ) )
antibiotics [which ( antibiotics $ ab == " SLF" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SLF" ) , " abbreviations" ] [ [1 ] ] , " sfsz" ) )
antibiotics [which ( antibiotics $ ab == " SPX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SPX" ) , " abbreviations" ] [ [1 ] ] , " spar" ) )
antibiotics [which ( antibiotics $ ab == " SPT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SPT" ) , " abbreviations" ] [ [1 ] ] , " spec" ) )
antibiotics [which ( antibiotics $ ab == " SPI" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SPI" ) , " abbreviations" ] [ [1 ] ] , " spir" ) )
antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] , " sthl" ) )
antibiotics [which ( antibiotics $ ab == " STR1" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " STR1" ) , " abbreviations" ] [ [1 ] ] , " stre" ) )
antibiotics [which ( antibiotics $ ab == " TAZ" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TAZ" ) , " abbreviations" ] [ [1 ] ] , " tazo" ) )
antibiotics [which ( antibiotics $ ab == " TEC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TEC" ) , " abbreviations" ] [ [1 ] ] , " teic" ) )
antibiotics [which ( antibiotics $ ab == " TLT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TLT" ) , " abbreviations" ] [ [1 ] ] , " teli" ) )
antibiotics [which ( antibiotics $ ab == " TMX" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TMX" ) , " abbreviations" ] [ [1 ] ] , " tema" ) )
antibiotics [which ( antibiotics $ ab == " TEM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TEM" ) , " abbreviations" ] [ [1 ] ] , " temo" ) )
antibiotics [which ( antibiotics $ ab == " TRB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TRB" ) , " abbreviations" ] [ [1 ] ] , " terb" ) )
antibiotics [which ( antibiotics $ ab == " TCY" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TCY" ) , " abbreviations" ] [ [1 ] ] , " tetr" ) )
antibiotics [which ( antibiotics $ ab == " TIC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TIC" ) , " abbreviations" ] [ [1 ] ] , " tica" ) )
antibiotics [which ( antibiotics $ ab == " TCC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TCC" ) , " abbreviations" ] [ [1 ] ] , " ticl" ) )
antibiotics [which ( antibiotics $ ab == " TGC" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TGC" ) , " abbreviations" ] [ [1 ] ] , " tige" ) )
antibiotics [which ( antibiotics $ ab == " TIN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TIN" ) , " abbreviations" ] [ [1 ] ] , " tini" ) )
antibiotics [which ( antibiotics $ ab == " TOB" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TOB" ) , " abbreviations" ] [ [1 ] ] , " tobr" ) )
antibiotics [which ( antibiotics $ ab == " TOH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TOH" ) , " abbreviations" ] [ [1 ] ] , " tohl" ) )
antibiotics [which ( antibiotics $ ab == " TMP" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TMP" ) , " abbreviations" ] [ [1 ] ] , " trim" ) )
antibiotics [which ( antibiotics $ ab == " TVA" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " TVA" ) , " abbreviations" ] [ [1 ] ] , " trov" ) )
antibiotics [which ( antibiotics $ ab == " SLT4" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SLT4" ) , " abbreviations" ] [ [1 ] ] , " trsm" ) )
antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " SXT" ) , " abbreviations" ] [ [1 ] ] , " trsx" ) )
antibiotics [which ( antibiotics $ ab == " VAN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " VAN" ) , " abbreviations" ] [ [1 ] ] , " vanc" ) )
antibiotics [which ( antibiotics $ ab == " VOR" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( antibiotics [which ( antibiotics $ ab == " VOR" ) , " abbreviations" ] [ [1 ] ] , " vori" ) )
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antibiotics [which ( antibiotics $ ab == " FOS" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " FOS" ) , " synonyms" ] [ [1 ] ] , " Monuril" ) ) )
antibiotics [which ( antibiotics $ ab == " FOS" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " FOS" ) , " synonyms" ] [ [1 ] ] , " Monurol" ) ) )
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antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " abbreviations" ] [ [1 ] ] , " piptazo" ) ) )
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antibiotics [which ( antibiotics $ ab == " RFP" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " RFP" ) , " abbreviations" ] [ [1 ] ] , " RPT" ) ) )
antibiotics [which ( antibiotics $ ab == " RTP" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " RTP" ) , " abbreviations" ] [ [1 ] ] , " RET" ) ) )
antibiotics [which ( antibiotics $ ab == " TYL1" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " TYL1" ) , " abbreviations" ] [ [1 ] ] , " TVN" ) ) )
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antibiotics <- antibiotics %>%
mutate ( ab = as.character ( ab ) ) %>%
rbind ( antibiotics %>%
filter ( ab == " GEH" ) %>%
mutate (
ab = " AMH" ,
name = " Amphotericin B-high" ,
abbreviations = list ( c ( " amhl" , " amfo b high" , " ampho b high" , " amphotericin high" ) )
) ) %>%
rbind ( antibiotics %>%
filter ( ab == " GEH" ) %>%
mutate (
ab = " TOH" ,
name = " Tobramycin-high" ,
abbreviations = list ( c ( " tohl" , " tobra high" , " tobramycin high" ) )
) ) %>%
rbind ( antibiotics %>%
filter ( ab == " BUT" ) %>%
mutate (
ab = " CIX" ,
atc = " D01AE14" ,
name = " Ciclopirox" ,
group = " Antifungals/antimycotics" ,
atc_group1 = " Antifungals for topical use" ,
atc_group2 = " Other antifungals for topical use" ,
abbreviations = list ( c ( " cipx" ) )
) )
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antibiotics [which ( antibiotics $ ab == " SSS" ) , " name" ] <- " Sulfonamide"
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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" ) )
2019-10-08 22:21:33 +02:00
# High level Gentamcin and Streptomycin
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antibiotics [which ( antibiotics $ ab == " GEH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " gehl" , " gentamicin high" , " genta high" , " gehi" ) )
antibiotics [which ( antibiotics $ ab == " STH" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " sthl" , " streptomycin high" , " strepto high" , " sthi" ) )
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# add imi and "imipenem/cilastatine" to imipenem
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antibiotics [which ( antibiotics $ ab == " IPM" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " imip" , " imi" , " imp" ) )
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antibiotics [which ( antibiotics $ ab == " IPM" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " IPM" ) , " synonyms" ] [ [1 ] ] , " imipenem/cilastatin" ) ) )
# add synonyms of ones not found
antibiotics [which ( antibiotics $ ab == " TZP" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( antibiotics [which ( antibiotics $ ab == " TZP" ) , " synonyms" ] [ [1 ] ] , " Tazocel" , " tazocillin" , " Tazocin" , " Zosyn" ) ) )
antibiotics [which ( antibiotics $ ab == " COL" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " COL" ) , " synonyms" ] [ [1 ] ] , " Colisticin" , " Polymyxin E" , " Colimycin" , " Coly-Mycin" , " Totazina" , " Colistimethate" , " Promixin" , " Colistimethate Sodium" ) ) ) )
# remove incorrect synonyms from rifampicin (RIF) and add them to the combination rifampicin/isoniazid (RFI)
old_sym <- antibiotics [which ( antibiotics $ ab == " RIF" ) , " synonyms" ] [ [1 ] ]
old_sym <- old_sym [ ! old_sym %in% c ( " Rifinah" , " Rimactazid" ) ]
antibiotics [which ( antibiotics $ ab == " RIF" ) , " synonyms" ] [ [1 ] ] <- list ( old_sym )
antibiotics [which ( antibiotics $ ab == " RFI" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( c ( " Rifinah" , " Rimactazid" ) ) )
# remove incorrect synonyms from sulfamethoxazole (SMX) and add them to the combination trimethoprim/sulfamethoxazole (SXT)
old_sym <- antibiotics [which ( antibiotics $ ab == " SMX" ) , " synonyms" ] [ [1 ] ]
old_sym <- old_sym [ ! old_sym %in% c ( " Cotrimoxazole" , " Bactrimel" ) ]
antibiotics [which ( antibiotics $ ab == " SMX" ) , " synonyms" ] [ [1 ] ] <- list ( old_sym )
antibiotics [which ( antibiotics $ ab == " SXT" ) , " synonyms" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " COL" ) , " synonyms" ] [ [1 ] ] , " Cotrimoxazole" , " Bactrimel" , " Septra" , " Bactrim" , " Cotrimazole" ) ) ) )
2020-09-24 00:30:11 +02:00
# Fix penicillins
antibiotics [which ( antibiotics $ ab == " PEN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " bepe" , " pg" , " pen" , " peni" , " peni g" , " penicillin" , " penicillin g" ) )
antibiotics [which ( antibiotics $ ab == " PEN" ) , " name" ] <- " Benzylpenicillin"
antibiotics [which ( antibiotics $ ab == " PHN" ) , " abbreviations" ] [ [1 ] ] <- list ( c ( " fepe" , " peni v" , " pv" , " penicillin v" , " PNV" ) )
antibiotics <- subset ( antibiotics , antibiotics $ ab != " PNV" )
2020-07-30 15:15:52 +02:00
# New DDDs
antibiotics [which ( antibiotics $ ab == " PEN" ) , " iv_ddd" ] <- 3.6
antibiotics [which ( antibiotics $ ab == " PEN" ) , " iv_units" ] <- " g"
2019-10-26 21:56:41 +02:00
## 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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# ceftazidime / avibactam
antibiotics [which ( antibiotics $ ab == " CZA" ) , " atc" ] <- " J01DD52"
antibiotics [which ( antibiotics $ ab == " CZA" ) , " cid" ] <- 90643431
antibiotics [which ( antibiotics $ ab == " CZA" ) , " atc_group1" ] <- " Other beta-lactam antibacterials"
antibiotics [which ( antibiotics $ ab == " CZA" ) , " atc_group2" ] <- " Third-generation cephalosporins"
antibiotics [which ( antibiotics $ ab == " CZA" ) , " iv_ddd" ] <- 6
antibiotics [which ( antibiotics $ ab == " CZA" ) , " iv_units" ] <- " g"
antibiotics [which ( antibiotics $ ab == " CZA" ) , " synonyms" ] <- list ( c ( " Avycaz" , " Zavicefta" ) )
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2019-10-27 00:31:59 +02:00
# typo
antibiotics [which ( antibiotics $ ab == " RXT" ) , " name" ] <- " Roxithromycin"
antibiotics [which ( antibiotics $ ab == " PEN" ) , " atc" ] <- " J01CE01"
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# WHONET cleanup
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antibiotics [which ( antibiotics $ ab == " BCZ" ) , " name" ] <- " Bicyclomycin"
antibiotics [which ( antibiotics $ ab == " CCL" ) , " name" ] <- " Cefetecol"
antibiotics [which ( antibiotics $ ab == " ENV" ) , " name" ] <- " Enviomycin"
antibiotics [which ( antibiotics $ ab == " KIT" ) , " name" ] <- " Kitasamycin"
antibiotics [which ( antibiotics $ ab == " LSP" ) , " name" ] <- " Linco-spectin"
antibiotics [which ( antibiotics $ ab == " MEC" ) , " name" ] <- " Mecillinam"
antibiotics [which ( antibiotics $ ab == " PMR" ) , " name" ] <- " Pimaricin"
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antibiotics [which ( antibiotics $ ab == " BCZ" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " BCZ" ) , " abbreviations" ] [ [1 ] ] , " Bicozamycin" ) ) ) )
antibiotics [which ( antibiotics $ ab == " CCL" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " CCL" ) , " abbreviations" ] [ [1 ] ] , " Cefcatacol" ) ) ) )
antibiotics [which ( antibiotics $ ab == " ENV" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " ENV" ) , " abbreviations" ] [ [1 ] ] , " Tuberactinomycin" ) ) ) )
antibiotics [which ( antibiotics $ ab == " KIT" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " KIT" ) , " abbreviations" ] [ [1 ] ] , " Leucomycin" ) ) ) )
antibiotics [which ( antibiotics $ ab == " LSP" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " LSP" ) , " abbreviations" ] [ [1 ] ] , " lincomycin/spectinomycin" ) ) ) )
antibiotics [which ( antibiotics $ ab == " MEC" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " MEC" ) , " abbreviations" ] [ [1 ] ] , " Amdinocillin" ) ) ) )
antibiotics [which ( antibiotics $ ab == " PMR" ) , " abbreviations" ] [ [1 ] ] <- list ( sort ( unique ( c ( antibiotics [which ( antibiotics $ ab == " PMR" ) , " abbreviations" ] [ [1 ] ] , " Natamycin" ) ) ) )
2019-08-11 19:07:26 +02:00
# set cephalosporins groups for the ones that could not be determined automatically:
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antibiotics <- antibiotics %>%
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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.)" ,
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TRUE ~ group
) )
2020-09-24 00:30:11 +02:00
antibiotics [which ( antibiotics $ ab %in% c ( " CYC" , " LNZ" , " THA" , " TZD" ) ) , " group" ] <- " Oxazolidinones"
2021-01-12 22:08:04 +01:00
# add pretomanid
antibiotics <- antibiotics %>%
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mutate ( ab = as.character ( ab ) ) %>%
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bind_rows ( antibiotics %>%
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mutate ( ab = as.character ( ab ) ) %>%
filter ( ab == " SMF" ) %>%
mutate (
ab = " PMD" ,
atc = " J04AK08" ,
cid = 456199 ,
name = " Pretomanid" ,
abbreviations = list ( " " ) ,
oral_ddd = NA_real_
) )
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# update ATC codes from WHOCC website -------------------------------------
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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 )
get_atcs <- function ( ab_name , url = " https://www.whocc.no/atc_ddd_index/" ) {
ab_name <- gsub ( " /" , " and " , tolower ( ab_name ) , fixed = TRUE )
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# we will do a search on their website, which means:
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# go to the url
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atc_tbl <- read_html ( url ) %>%
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# get all forms
html_form ( ) %>%
# get the second form (the first form is a global website form)
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.[ [2 ] ] %>%
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# set the name input box to our search parameter
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html_form_set ( name = ab_name ) %>%
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# hit Submit
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html_form_submit ( ) %>%
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# read the resulting page
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read_html ( ) %>%
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# retrieve the table on it
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html_node ( " table" ) %>%
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# transform it to an R data set
html_table ( header = FALSE )
# and get the ATCs (first column) of only exact hits
unique ( as.character ( atc_tbl [which ( tolower ( atc_tbl [ , 2 , drop = TRUE ] ) == ab_name ) , 1 , drop = TRUE ] ) )
}
# this takes around 4 minutes (some are skipped and go faster)
for ( i in seq_len ( nrow ( antibiotics ) ) ) {
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message ( percentage ( i / nrow ( antibiotics ) , digits = 1 ) ,
" - Downloading " , antibiotics $ name [i ] ,
appendLF = FALSE
)
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atcs <- get_atcs ( antibiotics $ name [i ] )
if ( length ( atcs ) > 0 ) {
updated_atc [ [i ] ] <- atcs
message ( " (" , length ( atcs ) , " results)" )
# let the WHO server rest for a second - they might have a limitation on the queries per second
Sys.sleep ( 1 )
} else {
message ( " (skipping)" )
}
}
antibiotics $ atc <- updated_atc
# update DDDs from WHOCC website ------------------------------------------
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# last time checked: 2022-10-29
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ddd_oral <- rep ( NA_real_ , nrow ( antibiotics ) )
ddd_oral_units <- rep ( NA_character_ , nrow ( antibiotics ) )
ddd_iv <- rep ( NA_real_ , nrow ( antibiotics ) )
ddd_iv_units <- rep ( NA_character_ , nrow ( antibiotics ) )
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progress <- progress_ticker ( nrow ( antibiotics ) )
for ( i in seq_len ( nrow ( antibiotics ) ) ) {
on.exit ( close ( progress ) )
progress $ tick ( )
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atcs <- antibiotics $ atc [ [i ] ]
if ( ! all ( is.na ( atcs ) ) ) {
for ( j in seq_len ( length ( atcs ) ) ) {
# oral
if ( is.na ( ddd_oral [i ] ) ) {
ddd_oral [i ] <- atc_online_ddd ( atcs [j ] , administration = " O" )
if ( ! is.na ( ddd_oral [i ] ) ) {
ddd_oral_units [i ] <- atc_online_ddd_units ( atcs [j ] , administration = " O" )
}
}
# parenteral
if ( is.na ( ddd_iv [i ] ) ) {
ddd_iv [i ] <- atc_online_ddd ( atcs [j ] , administration = " P" )
if ( ! is.na ( ddd_iv [i ] ) ) {
ddd_iv_units [i ] <- atc_online_ddd_units ( atcs [j ] , administration = " P" )
}
}
}
}
if ( ! is.na ( ddd_oral [i ] ) | ! is.na ( ddd_iv [i ] ) ) {
# let the WHO server rest for 0.25 second - they might have a limitation on the queries per second
Sys.sleep ( 0.25 )
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}
}
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antibiotics $ oral_ddd <- ddd_oral
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antibiotics $ oral_units <- ddd_oral_units
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antibiotics $ iv_ddd <- ddd_iv
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antibiotics $ iv_units <- ddd_iv_units
# Wrap up -----------------------------------------------------------------
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# set as data.frame again
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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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# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
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for ( i in 1 : nrow ( antibiotics ) ) {
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abb <- as.character ( sort ( unique ( tolower ( antibiotics [i , " abbreviations" , drop = TRUE ] [ [1 ] ] ) ) ) )
abb <- abb [abb != " " & abb %unlike% " :" ]
syn <- as.character ( sort ( unique ( tolower ( antibiotics [i , " synonyms" , drop = TRUE ] [ [1 ] ] ) ) ) )
syn <- syn [syn != " " & syn %unlike% " :" ]
antibiotics [i , " abbreviations" ] [ [1 ] ] <- ifelse ( length ( abb ) == 0 , list ( " " ) , list ( abb ) )
antibiotics [i , " synonyms" ] [ [1 ] ] <- ifelse ( length ( syn ) == 0 , list ( " " ) , list ( syn ) )
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if ( " loinc" %in% colnames ( antibiotics ) ) {
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loinc <- as.character ( sort ( unique ( tolower ( antibiotics [i , " loinc" , drop = TRUE ] [ [1 ] ] ) ) ) )
loinc <- loinc [loinc != " " ]
antibiotics [i , " loinc" ] [ [1 ] ] <- ifelse ( length ( loinc ) == 0 , list ( " " ) , list ( loinc ) )
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}
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}
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# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
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usethis :: use_data ( antibiotics , overwrite = TRUE , version = 2 , compress = " xz" )
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rm ( antibiotics )