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163 new trade names, added ab_tradenames

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dr. M.S. (Matthijs) Berends
2018-08-29 12:27:37 +02:00
parent 972fc4f6c7
commit 029157b3be
20 changed files with 139 additions and 314 deletions
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14
R/ab_property.R
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@ -22,6 +22,7 @@
#' @param x a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}
#' @param property one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}
#' @rdname ab_property
#' @return A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
#' @export
#' @importFrom dplyr %>% left_join pull
#' @seealso \code{\link{antibiotics}}
@ -82,3 +83,16 @@ ab_certe <- function(x) {
ab_umcg <- function(x) {
ab_property(x, "umcg")
}
#' @rdname ab_property
#' @export
ab_tradenames <- function(x) {
res <- ab_property(x, "trade_name")
res <- strsplit(res, "|", fixed = TRUE)
if (length(x) == 1) {
res <- unlist(res)
} else {
names(res) <- x
}
res
}

11
R/abname.R
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@ -23,6 +23,7 @@
#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"certe"} and \code{"umcg"}. When using \code{to = "atc"}, the ATC code will be searched using \code{\link{as.atc}}.
#' @param textbetween text to put between multiple returned texts
#' @param tolower return output as lower case with function \code{\link{tolower}}.
#' @details \strong{The \code{\link{ab_property}} functions are faster and more concise}, but do not support concatenated strings, like \code{abname("AMCL+GENT"}.
#' @keywords ab antibiotics
#' @source \code{\link{antibiotics}}
#' @export
@ -100,29 +101,29 @@ abname <- function(abcode,
}
if (from %in% c("atc", "guess")) {
if (abcode[i] %in% abx$atc) {
abcode[i] <- abx[which(abx$atc == abcode[i]),] %>% pull(to)
abcode[i] <- abx[which(abx$atc == abcode[i]),] %>% pull(to) %>% .[1]
next
}
}
if (from %in% c("certe", "guess")) {
if (abcode[i] %in% abx$certe) {
abcode[i] <- abx[which(abx$certe == abcode[i]),] %>% pull(to)
abcode[i] <- abx[which(abx$certe == abcode[i]),] %>% pull(to) %>% .[1]
next
}
}
if (from %in% c("umcg", "guess")) {
if (abcode[i] %in% abx$umcg) {
abcode[i] <- abx[which(abx$umcg == abcode[i]),] %>% pull(to)
abcode[i] <- abx[which(abx$umcg == abcode[i]),] %>% pull(to) %>% .[1]
next
}
}
if (from %in% c("trade_name", "guess")) {
if (abcode[i] %in% abx$trade_name) {
abcode[i] <- abx[which(abx$trade_name == abcode[i]),] %>% pull(to)
abcode[i] <- abx[which(abx$trade_name == abcode[i]),] %>% pull(to) %>% .[1]
next
}
if (sum(abx$trade_name %like% abcode[i]) > 0) {
abcode[i] <- abx[which(abx$trade_name %like% abcode[i]),] %>% pull(to)
abcode[i] <- abx[which(abx$trade_name %like% abcode[i]),] %>% pull(to) %>% .[1]
next
}
}

14
R/atc.R
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@ -64,6 +64,13 @@ as.atc <- function(x) {
x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
}
# try ATC in code form, even if it does not exist in the antibiotics data set YET
if (length(found) == 0 & x[i] %like% '[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]') {
warning("ATC code ", x[i], " is not yet in the `antibiotics` data set.")
fail <- FALSE
x.new[is.na(x.new) & x.bak == x[i]] <- x[i]
}
# try abbreviation of certe and glims
found <- AMR::antibiotics[which(tolower(AMR::antibiotics$certe) == tolower(x[i])),]$atc
if (length(found) > 0) {
@ -83,6 +90,13 @@ as.atc <- function(x) {
x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
}
# try exact official Dutch
found <- AMR::antibiotics[which(tolower(AMR::antibiotics$official_nl) == tolower(x[i])),]$atc
if (length(found) > 0) {
fail <- FALSE
x.new[is.na(x.new) & x.bak == x[i]] <- found[1L]
}
# try trade name
found <- AMR::antibiotics[which(paste0("(", AMR::antibiotics$trade_name, ")") %like% x[i]),]$atc
if (length(found) > 0) {

4
R/bactid.R
View File

@ -205,12 +205,12 @@ as.bactid <- function(x, Becker = FALSE, Lancefield = FALSE) {
failures <- c(failures, x_backup[i])
next
}
if (x_backup[i] %in% MOs$bactid) {
if (x_backup[i] %in% AMR::microorganisms$bactid) {
# is already a valid bactid
x[i] <- x_backup[i]
next
}
if (x_trimmed[i] %in% MOs$bactid) {
if (x_trimmed[i] %in% AMR::microorganisms$bactid) {
# is already a valid bactid
x[i] <- x_trimmed[i]
next

231
R/data.R
View File

@ -16,10 +16,10 @@
# GNU General Public License for more details. #
# ==================================================================== #
#' Dataset with 420 antibiotics
#' Dataset with 423 antibiotics
#'
#' A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source.
#' @format A data.frame with 420 observations and 18 variables:
#' A dataset containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDD's. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.
#' @format A data.frame with 423 observations and 18 variables:
#' \describe{
#' \item{\code{atc}}{ATC code, like \code{J01CR02}}
#' \item{\code{certe}}{Certe code, like \code{amcl}}
@ -28,7 +28,7 @@
#' \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and beta-lactamase inhibitor"}}
#' \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
#' \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
#' \item{\code{trade_name}}{Trade name as used by many countries, used internally by \code{\link{as.atc}}}
#' \item{\code{trade_name}}{Trade name as used by many countries (a total of 294), used internally by \code{\link{as.atc}}}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{ddd_units}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
@ -61,177 +61,7 @@
# paste() %>%
# .[. %like% "StringValueList"] %>%
# gsub("[</]+StringValueList[>]", "", .)
# abbr and trade_name created with:
# https://hs.unr.edu/Documents/dhs/chs/NVPHTC/antibiotic_refeference_guide.pdf
# antibiotics %>%
# mutate(abbr =
# case_when(
# official == 'Amikacin' ~ 'Ak|AN|AMI|AMK',
# official == 'Amoxicillin' ~ 'AMX|AMOX|AC',
# official == 'Amoxicillin and beta-lactamase inhibitor' ~ 'AUG|A/C|XL|AML',
# official == 'Ampicillin' ~ 'AM|AMP',
# official == 'Ampicillin and beta-lactamase inhibitor' ~ 'A/S|SAM|AMS|AB',
# official == 'Azithromycin' ~ 'Azi|AZM|AZ',
# official == 'Azlocillin' ~ 'AZ|AZL',
# official == 'Aztreonam' ~ 'Azt|ATM|AT|AZM',
# official == 'Carbenicillin' ~ 'Cb|BAR',
# official == 'Cefaclor' ~ 'Ccl|CEC|Cfr|FAC|CF',
# official == 'Cefadroxil' ~ 'CFR|FAD',
# official == 'Cefazolin' ~ 'Cfz|CZ|FAZ|KZ',
# official == 'Cefdinir' ~ 'Cdn|CDR|DIN|CD|CFD',
# official == 'Cefditoren' ~ 'CDN',
# official == 'Cefepime' ~ 'Cpe|FEP|PM|CPM',
# official == 'Cefixime' ~ 'Cfe|DCFM|FIX|IX',
# official == 'Cefoperazone' ~ 'Cfp|CPZ|PER|FOP|CP',
# official == 'Cefotaxime' ~ 'Cft|CTX|TAX|FOT|CT',
# official == 'Cefotetan' ~ 'Ctn|CTT|CTE|TANS|CN',
# official == 'Cefoxitin' ~ 'Cfx|FOX|CX|FX',
# official == 'Cefpodoxime' ~ 'Cpd|POD|PX',
# official == 'Cefprozil' ~ 'Cpz|CPR|FP',
# official == 'Ceftaroline' ~ 'CPT',
# official == 'Ceftazidime' ~ 'Caz|TAZ|TZ',
# official == 'Ceftibuten' ~ 'CTB|TIB|CB',
# official == 'Ceftizoxime' ~ 'Cz|ZOX|CZX|CZ|CTZ|TIZ',
# official == 'Ceftriaxone' ~ 'Cax|CRO|CTR|FRX|AXO|TX',
# official == 'Cefuroxime' ~ 'Crm|CXM|CFX|ROX|FUR|XM',
# official == 'Cephalexin' ~ 'CN|LX|CFL',
# official == 'Cephalothin' ~ 'Cf',
# official == 'Chloramphenicol' ~ 'C|CHL|CL',
# official == 'Ciprofloxacin' ~ 'Cp|CIP|CI',
# official == 'Clarithromycin' ~ 'Cla|CLR|CLM|CH',
# official == 'Clindamycin' ~ 'Cd|CC|CM|CLI|DA',
# official == 'Colistin' ~ 'CL|CS|CT',
# official == 'Daptomycin' ~ 'Dap',
# official == 'Doxycycline' ~ 'Dox',
# official == 'Doripenem' ~ 'DOR|Dor',
# official == 'Ertapenem' ~ 'Etp',
# official == 'Erythromycin' ~ 'E|ERY|EM',
# official == 'Fosfomycin' ~ 'FOS|FF|FO|FM',
# official == 'Flucloxacillin' ~ 'CLOX',
# official == 'Gentamicin' ~ 'Gm|CN|GEN',
# official == 'Imipenem' ~ 'Imp|IPM|IMI|IP',
# official == 'Kanamycin' ~ 'K|KAN|HLK|KM',
# official == 'Levofloxacin' ~ 'Lvx|LEV|LEVO|LE',
# official == 'Linezolid' ~ 'Lzd|LNZ|LZ',
# official == 'Lomefloxacin' ~ 'Lmf|LOM',
# official == 'Meropenem' ~ 'Mer|MEM|MERO|MRP|MP',
# official == 'Metronidazole' ~ 'MNZ',
# official == 'Mezlocillin' ~ 'Mz|MEZ',
# official == 'Minocycline' ~ 'Min|MI|MN|MNO|MC|MH',
# official == 'Moxifloxacin' ~ 'Mox|MXF',
# official == 'Mupirocin' ~ 'MUP',
# official == 'Nafcillin' ~ 'Naf|NF',
# official == 'Nalidixic acid' ~ 'NA|NAL',
# official == 'Nitrofurantoin' ~ 'Fd|F/M|FT|NIT|NI|F',
# official == 'Norfloxacin' ~ 'Nxn|NOR|NX',
# official == 'Ofloxacin' ~ 'Ofl|OFX|OF',
# official == 'Oxacillin' ~ 'Ox|OXS|OXA',
# official == 'Benzylpenicillin' ~ 'P|PEN|PV',
# official == 'Penicillins, combinations with other antibacterials' ~ 'P|PEN|PV',
# official == 'Piperacillin' ~ 'Pi|PIP|PP',
# official == 'Piperacillin and beta-lactamase inhibitor' ~ 'PT|TZP|PTZ|P/T|PTc',
# official == 'Polymyxin B' ~ 'PB',
# official == 'Quinupristin/dalfopristin' ~ 'Syn|Q/D|QDA|RP',
# official == 'Rifampin' ~ 'Rif|RA|RI|RD',
# official == 'Spectinomycin' ~ 'SPT|SPE|SC',
# official == 'Streptomycin' ~ 'S|STR',
# official == 'Teicoplanin' ~ 'Tei|TEC|TPN|TP|TPL',
# official == 'Telavancin' ~ 'TLV',
# official == 'Telithromcyin' ~ 'Tel',
# official == 'Tetracycline' ~ 'Te|TET|TC',
# official == 'Ticarcillin' ~ 'Ti|TIC|TC',
# official == 'Ticarcillin and beta-lactamase inhibitor' ~ 'Tim|T/C|TCC|TLc',
# official == 'Tigecycline' ~ 'TGC',
# official == 'Tobramycin' ~ 'To|NN|TM|TOB',
# official == 'Trimethoprim' ~ 'T|TMP|TR|W',
# official == 'Sulfamethoxazole and trimethoprim' ~ 'T/S|SXT|SxT|TS|COT',
# official == 'Vancomycin' ~ 'Va|VAN',
# TRUE ~ NA_character_),
#
# trade_name =
# case_when(
# official == 'Amikacin' ~ 'Amikin',
# official == 'Amoxicillin' ~ 'Amoxil|Dispermox|Larotid|Trimox',
# official == 'Amoxicillin and beta-lactamase inhibitor' ~ 'Augmentin',
# official == 'Ampicillin' ~ 'Pfizerpen-A|Principen',
# official == 'Ampicillin and beta-lactamase inhibitor' ~ 'Unasyn',
# official == 'Azithromycin' ~ 'Zithromax',
# official == 'Azlocillin' ~ 'Azlin',
# official == 'Aztreonam' ~ 'Azactam',
# official == 'Carbenicillin' ~ 'Geocillin',
# official == 'Cefaclor' ~ 'Ceclor',
# official == 'Cefadroxil' ~ 'Duricef',
# official == 'Cefazolin' ~ 'Ancef',
# official == 'Cefdinir' ~ 'Omnicef',
# official == 'Cefditoren' ~ 'Spectracef',
# official == 'Cefepime' ~ 'Maxipime',
# official == 'Cefixime' ~ 'Suprax',
# official == 'Cefoperazone' ~ 'Cefobid',
# official == 'Cefotaxime' ~ 'Claforan',
# official == 'Cefotetan' ~ 'Cefotan',
# official == 'Cefoxitin' ~ 'Mefoxin',
# official == 'Cefpodoxime' ~ 'Vantin',
# official == 'Cefprozil' ~ 'Cefzil',
# official == 'Ceftaroline' ~ 'Teflaro',
# official == 'Ceftazidime' ~ 'Fortaz|Tazicef|Tazidime',
# official == 'Ceftibuten' ~ 'Cedax',
# official == 'Ceftizoxime' ~ 'Cefizox',
# official == 'Ceftriaxone' ~ 'Rocephin',
# official == 'Cefuroxime' ~ 'Ceftin|Zinacef',
# official == 'Cephalexin' ~ 'Keflex|Panixine',
# official == 'Cephalothin' ~ 'Keflin',
# official == 'Chloramphenicol' ~ 'Chloromycetin',
# official == 'Ciprofloxacin' ~ 'Cipro|Ciloxan|Ciproxin',
# official == 'Clarithromycin' ~ 'Biaxin',
# official == 'Clindamycin' ~ 'Cleocin|Clinda-Derm|Clindagel|Clindesse|Clindets|Evoclin',
# official == 'Colistin' ~ 'Coly-Mycin',
# official == 'Daptomycin' ~ 'Cubicin',
# official == 'Doxycycline' ~ 'Doryx|Monodox|Vibramycin|Atridox|Oracea|Periostat|Vibra-Tabs',
# official == 'Doripenem' ~ 'Doribax',
# official == 'Ertapenem' ~ 'Invanz',
# official == 'Erythromycin' ~ 'Eryc|EryPed|Erythrocin|E-Base|E-Glades|E-Mycin|E.E.S.|Ery-Tab|Eryderm|Erygel|Erythra-derm|Eryzole|Pediamycin',
# official == 'Fosfomycin' ~ 'Monurol',
# official == 'Flucloxacillin' ~ 'Flopen|Floxapen|Fluclox|Sesamol|Softapen|Staphylex',
# official == 'Gentamicin' ~ 'Garamycin|Genoptic',
# official == 'Imipenem' ~ 'Primaxin',
# official == 'Kanamycin' ~ 'Kantrex',
# official == 'Levofloxacin' ~ 'Levaquin|Quixin',
# official == 'Linezolid' ~ 'Zyvox',
# official == 'Lomefloxacin' ~ 'Maxaquin',
# official == 'Meropenem' ~ 'Merrem',
# official == 'Metronidazole' ~ 'Flagyl|MetroGel|MetroCream|MetroLotion',
# official == 'Mezlocillin' ~ 'Mezlin',
# official == 'Minocycline' ~ 'Arestin|Solodyn',
# official == 'Moxifloxacin' ~ 'Avelox|Vigamox',
# official == 'Mupirocin' ~ 'Bactroban|Centany',
# official == 'Nafcillin' ~ 'Unipen',
# official == 'Nalidixic acid' ~ 'NegGram',
# official == 'Nitrofurantoin' ~ 'Furadantin|Macrobid|Macrodantin',
# official == 'Norfloxacin' ~ 'Noroxin',
# official == 'Ofloxacin' ~ 'Floxin|Ocuflox|Ophthalmic',
# official == 'Oxacillin' ~ 'Bactocill',
# official == 'Benzylpenicillin' ~ 'Permapen|Pfizerpen|Veetids',
# official == 'Penicillins, combinations with other antibacterials' ~ 'Permapen|Pfizerpen|Veetids',
# official == 'Piperacillin' ~ 'Pipracil',
# official == 'Piperacillin and beta-lactamase inhibitor' ~ 'Zosyn',
# official == 'Polymyxin B' ~ 'Poly-RX',
# official == 'Quinupristin/dalfopristin' ~ 'Synercid',
# official == 'Rifampin' ~ 'Rifadin|Rifamate|Rimactane',
# official == 'Spectinomycin' ~ 'Trobicin',
# official == 'Streptomycin' ~ 'Streptomycin Sulfate',
# official == 'Teicoplanin' ~ 'Targocid',
# official == 'Telavancin' ~ 'Vibativ',
# official == 'Telithromcyin' ~ 'Ketek',
# official == 'Tetracycline' ~ 'Sumycin|Bristacycline|Tetrex',
# official == 'Ticarcillin' ~ 'Ticar',
# official == 'Ticarcillin and beta-lactamase inhibitor' ~ 'Timentin',
# official == 'Tigecycline' ~ 'Tygacil',
# official == 'Tobramycin' ~ 'Tobi|Aktob|Tobre',
# official == 'Trimethoprim' ~ 'Primsol|Proloprim',
# official == 'Sulfamethoxazole and trimethoprim' ~ 'Bactrim|Septra|Sulfatrim',
# official == 'Vancomycin' ~ 'Vancocin|Vancomycin Hydrochloride',
# TRUE ~ NA_character_)
# )
# last two columns created with:
# antibiotics %>%
# mutate(useful_gramnegative =
@ -251,21 +81,44 @@
# NA
# )
# )
#
# ADD NEW TRADE NAMES FROM OTHER DATAFRAME
# antibiotics_add_to_property <- function(ab_df, atc, property, value) {
# if (length(atc) > 1L) {
# stop("only one atc at a time")
# }
# if (!property %in% c("abbr", "trade_name")) {
# stop("only possible for abbr and trade_name")
# }
#
# value <- gsub(ab_df[which(ab_df$atc == atc),] %>% pull("official"), "", value, fixed = TRUE)
# value <- gsub("||", "|", value, fixed = TRUE)
# value <- gsub("[äáàâ]", "a", value)
# value <- gsub("[ëéèê]", "e", value)
# value <- gsub("[ïíìî]", "i", value)
# value <- gsub("[öóòô]", "o", value)
# value <- gsub("[üúùû]", "u", value)
# if (!atc %in% ab_df$atc) {
# message("SKIPPING - UNKNOWN ATC: ", atc)
# }
# if (is.na(value)) {
# message("SKIPPING - VALUE MISSES: ", atc)
# }
# if (atc %in% ab_df$atc & !is.na(value)) {
# current <- ab_df[which(ab_df$atc == atc),] %>% pull(property)
# if (!is.na(current)) {
# value <- paste(current, value, sep = "|")
# }
# value <- strsplit(value, "|", fixed = TRUE) %>% unlist() %>% unique() %>% paste(collapse = "|")
# value <- gsub("||", "|", value, fixed = TRUE)
# # print(value)
# ab_df[which(ab_df$atc == atc), property] <- value
# message("Added ", value, " to ", ab_official(atc), " (", atc, ", ", ab_certe(atc), ")")
# }
# ab_df
# }
#
"antibiotics"
antibiotics_add_to_property <- function(antibiotics, atc, property, value) {
if (length(atc) > 1L) {
stop("only one atc at a time")
}
if (!property %in% c("abbr", "trade_name")) {
stop("only possible for abbr and trade_name")
}
if (atc %in% antibiotics$atc) {
current <- antibiotics[which(antibiotics$atc == atc), property]
antibiotics[which(antibiotics$atc == atc), property] <- paste(current, value, sep = "|")
message("done")
}
antibiotics
}
#' Dataset with ~2650 microorganisms
#'