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(v1.3.0.9004) data sets, as.disk() improvement

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  1. 4
      DESCRIPTION
  2. 13
      NEWS.md
  3. 6
      R/aa_helper_functions.R
  4. 4
      R/data.R
  5. 23
      R/disk.R
  6. 41
      R/rsi.R
  7. 4
      README.md
  8. 3
      _pkgdown.yml
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  36. 9
      docs/404.html
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      docs/articles/datasets.html
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      docs/articles/datasets_files/accessible-code-block-0.0.1/empty-anchor.js
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      docs/reference/as.rsi.html
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  48. 9
      docs/reference/intrinsic_resistant.html
  49. 13
      docs/reference/rsi_translation.html
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  52. 29
      index.md
  53. 8
      man/as.rsi.Rd
  54. 2
      man/rsi_translation.Rd
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      pkgdown/extra.css
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      vignettes/datasets.Rmd

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0.9003
Date: 2020-08-15
Version: 1.3.0.9004
Date: 2020-08-16
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

13
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# AMR 1.3.0.9003
## <small>Last updated: 15 August 2020</small>
# AMR 1.3.0.9004
## <small>Last updated: 16 August 2020</small>
### New
* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
@ -11,7 +11,7 @@ @@ -11,7 +11,7 @@
intrinsic_resistant %>%
filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
pull(microorganism)
# [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
```
### Changed
@ -27,6 +27,13 @@ @@ -27,6 +27,13 @@
your_data %>% mutate(across(where(is.disk), as.rsi))
```
* Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.
* Added parameter 'add_intrinsic_resistance' (defaults to `FALSE`), that considers intrinsic resistance according to EUCAST
* Added intelligent data cleaning to `as.disk()`, so numbers can also be extracted from text and decimal numbers will always be rounded up:
```r
as.disk(c("disk zone: 23.4 mm", 23.4))
#> Class <disk>
#> [1] 24 24
```
* Overall speed improvement by tweaking joining functions
# AMR 1.3.0

6
R/aa_helper_functions.R

@ -575,3 +575,9 @@ isFALSE <- function(x) { @@ -575,3 +575,9 @@ isFALSE <- function(x) {
deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
paste(deparse(expr, width.cutoff, ...), collapse = collapse)
}
file.size <- function (...) {
base::file.info(...)$size
}
file.mtime <- function (...) {
base::file.info(...)$mtime
}

4
R/data.R

@ -221,7 +221,7 @@ catalogue_of_life <- list( @@ -221,7 +221,7 @@ catalogue_of_life <- list(
#' Data set for R/SI interpretation
#'
#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
#' @format A [`data.frame`] with `r format(nrow(rsi_translation), big.mark = ",")` observations and `r ncol(rsi_translation)` variables:
#' - `guideline`\cr Name of the guideline
#' - `method`\cr Either "MIC" or "DISK"
@ -234,6 +234,8 @@ catalogue_of_life <- list( @@ -234,6 +234,8 @@ catalogue_of_life <- list(
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
#'
#'
#' @inheritSection AMR Read more on our website!
#' @seealso [intrinsic_resistant]
"rsi_translation"

23
R/disk.R

@ -62,8 +62,27 @@ as.disk <- function(x, na.rm = FALSE) { @@ -62,8 +62,27 @@ as.disk <- function(x, na.rm = FALSE) {
na_before <- length(x[is.na(x)])
# force it to be integer
x <- suppressWarnings(as.integer(x))
# heavily based on the function from our cleaner package:
clean_double2 <- function(x, remove = "[^0-9.,-]", fixed = FALSE) {
x <- gsub(",", ".", x)
# remove ending dot/comma
x <- gsub("[,.]$", "", x)
# only keep last dot/comma
reverse <- function(x) sapply(lapply(strsplit(x, NULL), rev), paste, collapse = "")
x <- sub("{{dot}}", ".",
gsub(".", "",
reverse(sub(".", "}}tod{{",
reverse(x),
fixed = TRUE)),
fixed = TRUE),
fixed = TRUE)
x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
# remove everything that is not a number or dot
as.numeric(gsub("[^0-9.]+", "", x_clean))
}
# round up and make it an integer
x <- as.integer(ceiling(clean_double2(x)))
# disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
x[x < 6 | x > 50] <- NA_integer_

41
R/rsi.R

@ -31,6 +31,7 @@ @@ -31,6 +31,7 @@
#' @inheritParams first_isolate
#' @param guideline defaults to the latest included EUCAST guideline, see Details for all options
#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a logical to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... parameters passed on to methods
#' @details
@ -108,6 +109,9 @@ @@ -108,6 +109,9 @@
#'
#' # the dplyr way
#' library(dplyr)
#' df %>% mutate_if(is.mic, as.rsi)
#' df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.rsi)
#' df %>% mutate(across(where(is.mic), as.rsi))
#' df %>% mutate_at(vars(AMP:TOB), as.rsi)
#' df %>% mutate(across(AMP:TOB), as.rsi)
#'
@ -282,6 +286,7 @@ as.rsi.mic <- function(x, @@ -282,6 +286,7 @@ as.rsi.mic <- function(x,
guideline = "EUCAST",
uti = FALSE,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
...) {
# for dplyr's across()
@ -339,7 +344,8 @@ as.rsi.mic <- function(x, @@ -339,7 +344,8 @@ as.rsi.mic <- function(x,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti,
conserve_capped_values = conserve_capped_values) # exec_as.rsi will return message(font_blue(" OK."))
conserve_capped_values = conserve_capped_values,
add_intrinsic_resistance = add_intrinsic_resistance) # exec_as.rsi will return message(font_blue(" OK."))
result
}
@ -350,6 +356,7 @@ as.rsi.disk <- function(x, @@ -350,6 +356,7 @@ as.rsi.disk <- function(x,
ab = deparse(substitute(x)),
guideline = "EUCAST",
uti = FALSE,
add_intrinsic_resistance = FALSE,
...) {
# for dplyr's across()
@ -405,7 +412,9 @@ as.rsi.disk <- function(x, @@ -405,7 +412,9 @@ as.rsi.disk <- function(x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti) # exec_as.rsi will return message(font_blue(" OK."))
uti = uti,
conserve_capped_values = FALSE,
add_intrinsic_resistance = add_intrinsic_resistance) # exec_as.rsi will return message(font_blue(" OK."))
result
}
@ -416,6 +425,7 @@ as.rsi.data.frame <- function(x, @@ -416,6 +425,7 @@ as.rsi.data.frame <- function(x,
guideline = "EUCAST",
uti = NULL,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
...) {
# try to find columns based on type
# -- mo
@ -534,7 +544,15 @@ get_guideline <- function(guideline) { @@ -534,7 +544,15 @@ get_guideline <- function(guideline) {
}
exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_values) {
exec_as.rsi <- function(method,
x,
mo,
ab,
guideline,
uti,
conserve_capped_values,
add_intrinsic_resistance) {
x_bak <- data.frame(x_mo = paste0(x, mo))
df <- unique(data.frame(x, mo), stringsAsFactors = FALSE)
x <- df$x
@ -580,10 +598,23 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_value @@ -580,10 +598,23 @@ exec_as.rsi <- function(method, x, mo, ab, guideline, uti, conserve_capped_value
warning("Interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI).\n Use parameter 'uti' to set which isolates are from urine. See ?as.rsi.", call. = FALSE)
warned <- TRUE
}
for (i in seq_len(length(x))) {
if (isTRUE(add_intrinsic_resistance)) {
if (!guideline_coerced %like% "EUCAST") {
warning("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call. = FALSE)
} else {
get_record <- subset(intrinsic_resistant,
microorganism == mo_name(mo[i], language = NULL) & antibiotic == ab_name(ab, language = NULL))
if (nrow(get_record) > 0) {
new_rsi[i] <- "R"
next
}
}
}
get_record <- trans %>%
# no sebsetting to UTI for now
# no subsetting to UTI for now
subset(lookup %in% c(lookup_mo[i],
lookup_genus[i],
lookup_family[i],

4
README.md

@ -1,6 +1,10 @@ @@ -1,6 +1,10 @@
% AMR (for R)
# `AMR` (for R)
<img src="https://www.r-pkg.org/badges/version-ago/AMR" />
<img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" />
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.

3
_pkgdown.yml

@ -44,6 +44,9 @@ navbar: @@ -44,6 +44,9 @@ navbar:
- text: "Predict antimicrobial resistance"
icon: "fa-dice"
href: "articles/resistance_predict.html"
- text: "Download our free data sets"
icon: "fa-database"
href: "articles/datasets.html"
- text: "Conduct principal component analysis for AMR"
icon: "fa-compress"
href: "articles/PCA.html"

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160
data-raw/antivirals.txt

@ -1,31 +1,31 @@ @@ -1,31 +1,31 @@
"atc" "cid" "name" "atc_group" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units"
"J05AF06" "441300" "abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Abacavir\", \"Abacavir sulfate\", \"Ziagen\")" "0.6" "g"
"J05AB01" "135398513" "aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Acicloftal\", \"Aciclovier\", \"Aciclovir\", \"Aciclovirum\", \"Activir\", \"AcycloFoam\", \"Acycloguanosine\", \"Acyclovir\", \"Acyclovir Lauriad\", \"ACYCLOVIR SODIUM\", \"Avirax\", \"Cargosil\", \"Cyclovir\", \"Genvir\", \"Gerpevir\", \"Hascovir\", \"Herpevir\", \"Maynar\", \"Poviral\", \"Sitavig\", \"Sitavir\", \"Vipral\", \"Virolex\", \"Viropump\", \"Virorax\", \"Zovirax\", \"Zovirax topical\", \"Zyclir\")" "4" "g" "4" "g"
"J05AF08" "60871" "adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Adefovir di ester\", \"Adefovir dipivoxil\", \"Adefovir Dipivoxil\", \"Adefovir dipivoxyl\", \"Adefovir pivoxil\", \"Adefovirdipivoxl\", \"Bisadenine\", \"BISADENINE\", \"BisPMEA\", \"Hepsera\", \"Preveon\", \"YouHeDing\")" "10" "mg"
"J05AE05" "65016" "amprenavir" "Protease inhibitors" "c(\"Agenerase\", \"Amprenavir\", \"Amprenavirum\", \"Prozei\", \"Vertex\")" "1.2" "g"
"J05AP06" "16076883" "asunaprevir" "Antivirals for treatment of HCV infections" "c(\"Asunaprevir\", \"Sunvepra\")"
"J05AE08" "148192" "atazanavir" "Protease inhibitors" "c(\"Atazanavir\", \"Atazanavir Base\", \"Latazanavir\", \"Reyataz\", \"Zrivada\")" "0.3" "g"
"J05AR15" "86583336" "atazanavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR23" "atazanavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "" "0.3" "g"
"J05AP03" "10324367" "boceprevir" "Antivirals for treatment of HCV infections" "c(\"Bocepravir\", \"Boceprevir\", \"Victrelis\")" "2.4" "g"
"J05AB15" "446727" "brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Bridic\", \"Brivox\", \"Brivudin\", \"Brivudina\", \"Brivudine\", \"Brivudinum\", \"BrVdUrd\", \"Helpin\", \"Zerpex\", \"Zostex\")" "0.125" "g"
"J05AB12" "60613" "cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cidofovir\", \"Cidofovir anhydrous\", \"Cidofovir gel\", \"Cidofovirum\", \"Forvade\", \"Vistide\")" "25" "mg"
"J05AF12" "73115" "clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Clevudine\", \"Levovir\", \"Revovir\")" "30" "mg"
"J05AP07" "25154714" "daclatasvir" "Antivirals for treatment of HCV infections" "c(\"Daclatasvir\", \"Daklinza\")" "60" "mg"
"J05AE10" "213039" "darunavir" "Protease inhibitors" "c(\"Darunavir\", \"Darunavirum\", \"Prezista\", \"Prezista Naive\")" "1.2" "g"
"J05AF06" 441300 "abacavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Abacavir\", \"Abacavir sulfate\", \"Ziagen\")" 0.6 "g"
"J05AB01" 135398513 "aciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Acicloftal\", \"Aciclovier\", \"Aciclovir\", \"Aciclovirum\", \"Activir\", \"AcycloFoam\", \"Acycloguanosine\", \"Acyclovir\", \"Acyclovir Lauriad\", \"ACYCLOVIR SODIUM\", \"Avirax\", \"Cargosil\", \"Cyclovir\", \"Genvir\", \"Gerpevir\", \"Hascovir\", \"Herpevir\", \"Maynar\", \"Poviral\", \"Sitavig\", \"Sitavir\", \"Vipral\", \"Virolex\", \"Viropump\", \"Virorax\", \"Zovirax\", \"Zovirax topical\", \"Zyclir\")" 4 "g" 4 "g"
"J05AF08" 60871 "adefovir dipivoxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Adefovir di ester\", \"Adefovir dipivoxil\", \"Adefovir Dipivoxil\", \"Adefovir dipivoxyl\", \"Adefovir pivoxil\", \"Adefovirdipivoxl\", \"Bisadenine\", \"BISADENINE\", \"BisPMEA\", \"Hepsera\", \"Preveon\", \"YouHeDing\")" 10 "mg"
"J05AE05" 65016 "amprenavir" "Protease inhibitors" "c(\"Agenerase\", \"Amprenavir\", \"Amprenavirum\", \"Prozei\", \"Vertex\")" 1.2 "g"
"J05AP06" 16076883 "asunaprevir" "Antivirals for treatment of HCV infections" "c(\"Asunaprevir\", \"Sunvepra\")"
"J05AE08" 148192 "atazanavir" "Protease inhibitors" "c(\"Atazanavir\", \"Atazanavir Base\", \"Latazanavir\", \"Reyataz\", \"Zrivada\")" 0.3 "g"
"J05AR15" 86583336 "atazanavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR23" "atazanavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "" 0.3 "g"
"J05AP03" 10324367 "boceprevir" "Antivirals for treatment of HCV infections" "c(\"Bocepravir\", \"Boceprevir\", \"Victrelis\")" 2.4 "g"
"J05AB15" 446727 "brivudine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Bridic\", \"Brivox\", \"Brivudin\", \"Brivudina\", \"Brivudine\", \"Brivudinum\", \"BrVdUrd\", \"Helpin\", \"Zerpex\", \"Zostex\")" 0.125 "g"
"J05AB12" 60613 "cidofovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cidofovir\", \"Cidofovir anhydrous\", \"Cidofovir gel\", \"Cidofovirum\", \"Forvade\", \"Vistide\")" 25 "mg"
"J05AF12" 73115 "clevudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Clevudine\", \"Levovir\", \"Revovir\")" 30 "mg"
"J05AP07" 25154714 "daclatasvir" "Antivirals for treatment of HCV infections" "c(\"Daclatasvir\", \"Daklinza\")" 60 "mg"
"J05AE10" 213039 "darunavir" "Protease inhibitors" "c(\"Darunavir\", \"Darunavirum\", \"Prezista\", \"Prezista Naive\")" 1.2 "g"
"J05AR14" "darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AP09" "56640146" "dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" "0.5" "g"
"J05AP09" 56640146 "dasabuvir" "Antivirals for treatment of HCV infections" "Dasabuvir" 0.5 "g"
"J05AP52" "dasabuvir, ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AG02" "5625" "delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"BHAP der\", \"Delavirdin\", \"Delavirdina\", \"Delavirdine\", \"Delavirdinum\", \"PIPERAZINE\", \"Rescriptor\")" "1.2" "g"
"J05AF02" "135398739" "didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Didanosina\", \"Didanosine\", \"Didanosinum\", \"Dideoxyinosine\", \"DIDEOXYINOSINE\", \"Hypoxanthine ddN\", \"Videx\", \"Videx EC\")" "0.4" "g"
"J05AX12" "54726191" "dolutegravir" "Other antivirals" "c(\"Dolutegravir\", \"Dolutegravir Sodium\", \"Soltegravir\", \"Tivicay\")" "50" "mg"
"J05AR21" "131801472" "dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AG06" "58460047" "doravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Doravirine\", \"Pifeltro\")"
"J05AG03" "64139" "efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Efavirenz\", \"Efavirenzum\", \"Eravirenz\", \"Stocrin\", \"Strocin\", \"Sustiva\")" "0.6" "g"
"J05AP54" "91669168" "elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
"J05AX11" "5277135" "elvitegravir" "Other antivirals" "c(\"Elvitegravir\", \"Vitekta\")"
"J05AF09" "60877" "emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Coviracil\", \"Emtricitabin\", \"Emtricitabina\", \"Emtricitabine\", \"Emtricitabinum\", \"Emtritabine\", \"Emtriva\", \"Racivir\")" "0.2" "g"
"J05AR17" "90469070" "emtricitabine and tenofovir alafenamide" "Antivirals for treatment of HIV infections, combinations" ""
"J05AG02" 5625 "delavirdine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"BHAP der\", \"Delavirdin\", \"Delavirdina\", \"Delavirdine\", \"Delavirdinum\", \"PIPERAZINE\", \"Rescriptor\")" 1.2 "g"
"J05AF02" 135398739 "didanosine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Didanosina\", \"Didanosine\", \"Didanosinum\", \"Dideoxyinosine\", \"DIDEOXYINOSINE\", \"Hypoxanthine ddN\", \"Videx\", \"Videx EC\")" 0.4 "g"
"J05AX12" 54726191 "dolutegravir" "Other antivirals" "c(\"Dolutegravir\", \"Dolutegravir Sodium\", \"Soltegravir\", \"Tivicay\")" 50 "mg"
"J05AR21" 131801472 "dolutegravir and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AG06" 58460047 "doravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Doravirine\", \"Pifeltro\")"
"J05AG03" 64139 "efavirenz" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Efavirenz\", \"Efavirenzum\", \"Eravirenz\", \"Stocrin\", \"Strocin\", \"Sustiva\")" 0.6 "g"
"J05AP54" 91669168 "elbasvir and grazoprevir" "Antivirals for treatment of HCV infections" ""
"J05AX11" 5277135 "elvitegravir" "Other antivirals" "c(\"Elvitegravir\", \"Vitekta\")"
"J05AF09" 60877 "emtricitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Coviracil\", \"Emtricitabin\", \"Emtricitabina\", \"Emtricitabine\", \"Emtricitabinum\", \"Emtritabine\", \"Emtriva\", \"Racivir\")" 0.2 "g"
"J05AR17" 90469070 "emtricitabine and tenofovir alafenamide" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR20" "emtricitabine, tenofovir alafenamide and bictegravir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR19" "emtricitabine, tenofovir alafenamide and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR22" "emtricitabine, tenofovir alafenamide, darunavir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
@ -33,71 +33,71 @@ @@ -33,71 +33,71 @@
"J05AR06" "emtricitabine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR08" "emtricitabine, tenofovir disoproxil and rilpivirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR09" "emtricitabine, tenofovir disoproxil, elvitegravir and cobicistat" "Antivirals for treatment of HIV infections, combinations" ""
"J05AX07" "16130199" "enfuvirtide" "Other antivirals" "c(\"Enfurvitide\", \"Enfuvirtide\", \"Fuzeon\", \"Pentafuside\")" "0.18" "g"
"J05AX17" "10089466" "enisamium iodide" "Other antivirals" "Enisamium iodide" "1.5" "g"
"J05AF10" "135398508" "entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Baraclude\", \"Entecavir\", \"Entecavir anhydrous\", \"Entecavirum\")" "0.5" "mg"
"J05AG04" "193962" "etravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"DAPY deriv\", \"Etravine\", \"Etravirine\", \"Intelence\")" "0.4" "g"
"J05AP04" "42601552" "faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
"J05AB09" "3324" "famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Famciclovir\", \"Famciclovirum\", \"Famvir\", \"Oravir\")" "0.75" "g"
"J05AE07" "131536" "fosamprenavir" "Protease inhibitors" "c(\"Amprenavir phosphate\", \"Fosamprenavir\", \"Lexiva\", \"Telzir\")" "1.4" "g"
"J05AD01" "3415" "foscarnet" "Phosphonic acid derivatives" "c(\"Forscarnet\", \"Forscarnet sodium\", \"Foscarmet\", \"Foscarnet\", \"Phosphonoformate\", \"Phosphonoformic acid\")" "6.5" "g"
"J05AD02" "546" "fosfonet" "Phosphonic acid derivatives" "c(\"Fosfonet\", \"Fosfonet sodium\", \"Fosfonet Sodium\", \"Fosfonoacetate\", \"Fosfonoacetic acid\", \"Phosphonacetate\", \"Phosphonacetic acid\")"
"J05AB06" "135398740" "ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Citovirax\", \"Cymevan\", \"Cymeven\", \"Cymevene\", \"Cytovene\", \"Cytovene IV\", \"Ganciclovir\", \"Ganciclovirum\", \"Gancyclovir\", \"Hydroxyacyclovir\", \"Virgan\", \"Vitrasert\", \"Zirgan\")" "3" "g" "0.5" "g"
"J05AX07" 16130199 "enfuvirtide" "Other antivirals" "c(\"Enfurvitide\", \"Enfuvirtide\", \"Fuzeon\", \"Pentafuside\")" 0.18 "g"
"J05AX17" 10089466 "enisamium iodide" "Other antivirals" "Enisamium iodide" 1.5 "g"
"J05AF10" 135398508 "entecavir" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Baraclude\", \"Entecavir\", \"Entecavir anhydrous\", \"Entecavirum\")" 0.5 "mg"
"J05AG04" 193962 "etravirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"DAPY deriv\", \"Etravine\", \"Etravirine\", \"Intelence\")" 0.4 "g"
"J05AP04" 42601552 "faldaprevir" "Antivirals for treatment of HCV infections" "Faldaprevir"
"J05AB09" 3324 "famciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Famciclovir\", \"Famciclovirum\", \"Famvir\", \"Oravir\")" 0.75 "g"
"J05AE07" 131536 "fosamprenavir" "Protease inhibitors" "c(\"Amprenavir phosphate\", \"Fosamprenavir\", \"Lexiva\", \"Telzir\")" 1.4 "g"
"J05AD01" 3415 "foscarnet" "Phosphonic acid derivatives" "c(\"Forscarnet\", \"Forscarnet sodium\", \"Foscarmet\", \"Foscarnet\", \"Phosphonoformate\", \"Phosphonoformic acid\")" 6.5 "g"
"J05AD02" 546 "fosfonet" "Phosphonic acid derivatives" "c(\"Fosfonet\", \"Fosfonet sodium\", \"Fosfonet Sodium\", \"Fosfonoacetate\", \"Fosfonoacetic acid\", \"Phosphonacetate\", \"Phosphonacetic acid\")"
"J05AB06" 135398740 "ganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Citovirax\", \"Cymevan\", \"Cymeven\", \"Cymevene\", \"Cytovene\", \"Cytovene IV\", \"Ganciclovir\", \"Ganciclovirum\", \"Gancyclovir\", \"Hydroxyacyclovir\", \"Virgan\", \"Vitrasert\", \"Zirgan\")" 3 "g" 0.5 "g"
"J05AP57" "glecaprevir and pibrentasvir" "Antivirals for treatment of HCV infections" ""
"J05AX23" "ibalizumab" "Other antivirals" ""
"J05AB02" "5905" "idoxuridine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Antizona\", \"Dendrid\", \"Emanil\", \"Heratil\", \"Herpesil\", \"Herpid\", \"Herpidu\", \"Herplex\", \"HERPLEX\", \"Herplex liquifilm\", \"Idexur\", \"Idossuridina\", \"Idoxene\", \"Idoxuridin\", \"Idoxuridina\", \"Idoxuridine\", \"Idoxuridinum\", \"Idu Oculos\", \"Iducher\", \"Idulea\", \"Iduoculos\", \"Iduridin\", \"Iduviran\", \"Iododeoxyridine\", \"Iododeoxyuridine\", \"Iodoxuridine\", \"Joddeoxiuridin\", \"Kerecid\", \"Kerecide\", \"Ophthalmadine\", \"Spectanefran\", \"Stoxil\", \"Synmiol\", \"Virudox\")"
"J05AE02" "5362440" "indinavir" "Protease inhibitors" "c(\"Compound J\", \"Crixivan\", \"Indinavir\", \"Indinavir anhydrous\", \"Propolis+Indinavir\")" "2.4" "g"
"J05AX05" "135449284" "inosine pranobex" "Other antivirals" "c(\"Aviral\", \"Delimmun\", \"Immunovir\", \"Imunovir\", \"Inosine pranobex\", \"Inosiplex\", \"Isoprinosin\", \"Isoprinosina\", \"Isoprinosine\", \"Isoviral\", \"Methisoprinol\", \"Methysoprinol\", \"Metisoprinol\", \"Viruxan\")" "3" "g"
"J05AF05" "60825" "lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epivir\", \"Hepitec\", \"Heptivir\", \"Heptodin\", \"Heptovir\", \"Lamivir\", \"Lamivudin\", \"Lamivudina\", \"Lamivudine\", \"Lamivudinum\", \"Zeffix\")" "0.3" "g"
"J05AB02" 5905 "idoxuridine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Antizona\", \"Dendrid\", \"Emanil\", \"Heratil\", \"Herpesil\", \"Herpid\", \"Herpidu\", \"Herplex\", \"HERPLEX\", \"Herplex liquifilm\", \"Idexur\", \"Idossuridina\", \"Idoxene\", \"Idoxuridin\", \"Idoxuridina\", \"Idoxuridine\", \"Idoxuridinum\", \"Idu Oculos\", \"Iducher\", \"Idulea\", \"Iduoculos\", \"Iduridin\", \"Iduviran\", \"Iododeoxyridine\", \"Iododeoxyuridine\", \"Iodoxuridine\", \"Joddeoxiuridin\", \"Kerecid\", \"Kerecide\", \"Ophthalmadine\", \"Spectanefran\", \"Stoxil\", \"Synmiol\", \"Virudox\")"
"J05AE02" 5362440 "indinavir" "Protease inhibitors" "c(\"Compound J\", \"Crixivan\", \"Indinavir\", \"Indinavir anhydrous\", \"Propolis+Indinavir\")" 2.4 "g"
"J05AX05" 135449284 "inosine pranobex" "Other antivirals" "c(\"Aviral\", \"Delimmun\", \"Immunovir\", \"Imunovir\", \"Inosine pranobex\", \"Inosiplex\", \"Isoprinosin\", \"Isoprinosina\", \"Isoprinosine\", \"Isoviral\", \"Methisoprinol\", \"Methysoprinol\", \"Metisoprinol\", \"Viruxan\")" 3 "g"
"J05AF05" 60825 "lamivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epivir\", \"Hepitec\", \"Heptivir\", \"Heptodin\", \"Heptovir\", \"Lamivir\", \"Lamivudin\", \"Lamivudina\", \"Lamivudine\", \"Lamivudinum\", \"Zeffix\")" 0.3 "g"
"J05AR02" "lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR16" "73386700" "lamivudine and raltegravir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR16" 73386700 "lamivudine and raltegravir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR12" "lamivudine and tenofovir disoproxil" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR13" "lamivudine, abacavir and dolutegravir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR24" "lamivudine, tenofovir disoproxil and doravirine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR11" "lamivudine, tenofovir disoproxil and efavirenz" "Antivirals for treatment of HIV infections, combinations" ""
"J05AX18" "45138674" "letermovir" "Other antivirals" "c(\"Letermovir\", \"Prevymis\")" "0.48" "g" "0.48" "g"
"J05AR10" "11979606" "lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "c(\"Aluvia\", \"Kaletra\")" "0.8" "g"
"J05AX02" "24839946" "lysozyme" "Other antivirals" "c(\"Lysozyme chloride\", \"Lysozyme Chloride\", \"Lysozyme G\")"
"J05AX09" "3002977" "maraviroc" "Other antivirals" "c(\"Celsentri\", \"Maraviroc\", \"Selzentry\")" "0.6" "g"
"J05AX10" "471161" "maribavir" "Other antivirals" "c(\"Benzimidavir\", \"Camvia\", \"Maribavir\")"
"J05AA01" "667492" "metisazone" "Thiosemicarbazones" "c(\"Kemoviran\", \"Marboran\", \"Marborane\", \"Methisazon\", \"Methisazone\", \"Methsazone\", \"Metisazon\", \"Metisazona\", \"Metisazone\", \"Metisazonum\", \"Viruzona\")"
"J05AX01" "71655" "moroxydine" "Other antivirals" "c(\"Bimolin\", \"Flumidine\", \"Influmine\", \"Moroxidina\", \"Moroxydine\", \"Moroxydinum\", \"Vironil\", \"Virugon\", \"Virumin\", \"Wirumin\")" "0.3" "g"
"J05AE04" "64143" "nelfinavir" "Protease inhibitors" "c(\"Nelfinavir\", \"Viracept\")" "2.25" "g"
"J05AG01" "4463" "nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Nevirapine\", \"Nevirapine anhydrous\", \"Viramune\", \"Viramune IR\", \"Viramune XR\")" "0.4" "g"
"J05AX18" 45138674 "letermovir" "Other antivirals" "c(\"Letermovir\", \"Prevymis\")" 0.48 "g" 0.48 "g"
"J05AR10" 11979606 "lopinavir and ritonavir" "Antivirals for treatment of HIV infections, combinations" "c(\"Aluvia\", \"Kaletra\")" 0.8 "g"
"J05AX02" 24839946 "lysozyme" "Other antivirals" "c(\"Lysozyme chloride\", \"Lysozyme Chloride\", \"Lysozyme G\")"
"J05AX09" 3002977 "maraviroc" "Other antivirals" "c(\"Celsentri\", \"Maraviroc\", \"Selzentry\")" 0.6 "g"
"J05AX10" 471161 "maribavir" "Other antivirals" "c(\"Benzimidavir\", \"Camvia\", \"Maribavir\")"
"J05AA01" 667492 "metisazone" "Thiosemicarbazones" "c(\"Kemoviran\", \"Marboran\", \"Marborane\", \"Methisazon\", \"Methisazone\", \"Methsazone\", \"Metisazon\", \"Metisazona\", \"Metisazone\", \"Metisazonum\", \"Viruzona\")"
"J05AX01" 71655 "moroxydine" "Other antivirals" "c(\"Bimolin\", \"Flumidine\", \"Influmine\", \"Moroxidina\", \"Moroxydine\", \"Moroxydinum\", \"Vironil\", \"Virugon\", \"Virumin\", \"Wirumin\")" 0.3 "g"
"J05AE04" 64143 "nelfinavir" "Protease inhibitors" "c(\"Nelfinavir\", \"Viracept\")" 2.25 "g"
"J05AG01" 4463 "nevirapine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Nevirapine\", \"Nevirapine anhydrous\", \"Viramune\", \"Viramune IR\", \"Viramune XR\")" 0.4 "g"
"J05AP53" "ombitasvir, paritaprevir and ritonavir" "Antivirals for treatment of HCV infections" ""
"J05AH02" "65028" "oseltamivir" "Neuraminidase inhibitors" "c(\"Agucort\", \"Oseltamivir\", \"Tamiflu\", \"Tamvir\")" "0.15" "g"
"J05AB13" "135398748" "penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenovir\", \"Denavir\", \"Penciceovir\", \"Penciclovir\", \"Penciclovirum\", \"Pencyclovir\", \"Vectavir\")"
"J05AX21" "9942657" "pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" "90" "mg"
"J05AH03" "154234" "peramivir" "Neuraminidase inhibitors" "c(\"PeramiFlu\", \"Peramivir\", \"Rapiacta\", \"RAPIVAB\")"
"J05AX06" "1684" "pleconaril" "Other antivirals" "c(\"Picovir\", \"Pleconaril\", \"Pleconarilis\")"
"J05AX08" "54671008" "raltegravir" "Other antivirals" "c(\"Isentress\", \"Raltegravir\")" "0.8" "g"
"J05AP01" "37542" "ribavirin" "Antivirals for treatment of HCV infections" "c(\"Copegus\", \"Cotronak\", \"Drug: Ribavirin\", \"Ravanex\", \"Rebetol\", \"Rebetron\", \"Rebretron\", \"Ribacine\", \"Ribamide\", \"Ribamidil\", \"Ribamidyl\", \"Ribasphere\", \"Ribavirin\", \"Ribavirin Capsules\", \"Ribavirina\", \"Ribavirine\", \"Ribavirinum\", \"Ribovirin\", \"Tribavirin\", \"Varazid\", \"Vilona\", \"Viramid\", \"Viramide\", \"Virazid\", \"Virazide\", \"Virazole\")" "1" "g"
"J05AG05" "6451164" "rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Edurant\", \"Rilpivirine\")" "25" "mg"
"J05AC02" "5071" "rimantadine" "Cyclic amines" "c(\"Remantadine\", \"Riamantadine\", \"Rimant\", \"RIMANTADIN\", \"Rimantadin A\", \"Rimantadina\", \"Rimantadine\", \"Rimantadinum\")" "0.2" "g"
"J05AE03" "392622" "ritonavir" "Protease inhibitors" "c(\"Norvir\", \"Norvir Sec\", \"Norvir Softgel\", \"Ritonavir\", \"Ritonavire\", \"Ritonavirum\")" "1.2" "g"
"J05AE01" "441243" "saquinavir" "Protease inhibitors" "c(\"Fortovase\", \"Invirase\", \"Saquinavir\")" "1.8" "g"
"J05AP05" "24873435" "simeprevir" "Antivirals for treatment of HCV infections" "c(\"Olysio\", \"Simeprevir sodium\")" "0.15" "g"
"J05AP08" "45375808" "sofosbuvir" "Antivirals for treatment of HCV infections" "c(\"Hepcinat\", \"Hepcvir\", \"Sofosbuvir\", \"Sovaldi\", \"SOVALDI\", \"SoviHep\")" "0.4" "g"
"J05AP51" "72734365" "sofosbuvir and ledipasvir" "Antivirals for treatment of HCV infections" ""
"J05AP55" "91885554" "sofosbuvir and velpatasvir" "Antivirals for treatment of HCV infections" "Epclusa Tablet"
"J05AH02" 65028 "oseltamivir" "Neuraminidase inhibitors" "c(\"Agucort\", \"Oseltamivir\", \"Tamiflu\", \"Tamvir\")" 0.15 "g"
"J05AB13" 135398748 "penciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenovir\", \"Denavir\", \"Penciceovir\", \"Penciclovir\", \"Penciclovirum\", \"Pencyclovir\", \"Vectavir\")"
"J05AX21" 9942657 "pentanedioic acid imidazolyl ethanamide" "Other antivirals" "Ingamine" 90 "mg"
"J05AH03" 154234 "peramivir" "Neuraminidase inhibitors" "c(\"PeramiFlu\", \"Peramivir\", \"Rapiacta\", \"RAPIVAB\")"
"J05AX06" 1684 "pleconaril" "Other antivirals" "c(\"Picovir\", \"Pleconaril\", \"Pleconarilis\")"
"J05AX08" 54671008 "raltegravir" "Other antivirals" "c(\"Isentress\", \"Raltegravir\")" 0.8 "g"
"J05AP01" 37542 "ribavirin" "Antivirals for treatment of HCV infections" "c(\"Copegus\", \"Cotronak\", \"Drug: Ribavirin\", \"Ravanex\", \"Rebetol\", \"Rebetron\", \"Rebretron\", \"Ribacine\", \"Ribamide\", \"Ribamidil\", \"Ribamidyl\", \"Ribasphere\", \"Ribavirin\", \"Ribavirin Capsules\", \"Ribavirina\", \"Ribavirine\", \"Ribavirinum\", \"Ribovirin\", \"Tribavirin\", \"Varazid\", \"Vilona\", \"Viramid\", \"Viramide\", \"Virazid\", \"Virazide\", \"Virazole\")" 1 "g"
"J05AG05" 6451164 "rilpivirine" "Non-nucleoside reverse transcriptase inhibitors" "c(\"Edurant\", \"Rilpivirine\")" 25 "mg"
"J05AC02" 5071 "rimantadine" "Cyclic amines" "c(\"Remantadine\", \"Riamantadine\", \"Rimant\", \"RIMANTADIN\", \"Rimantadin A\", \"Rimantadina\", \"Rimantadine\", \"Rimantadinum\")" 0.2 "g"
"J05AE03" 392622 "ritonavir" "Protease inhibitors" "c(\"Norvir\", \"Norvir Sec\", \"Norvir Softgel\", \"Ritonavir\", \"Ritonavire\", \"Ritonavirum\")" 1.2 "g"
"J05AE01" 441243 "saquinavir" "Protease inhibitors" "c(\"Fortovase\", \"Invirase\", \"Saquinavir\")" 1.8 "g"
"J05AP05" 24873435 "simeprevir" "Antivirals for treatment of HCV infections" "c(\"Olysio\", \"Simeprevir sodium\")" 0.15 "g"
"J05AP08" 45375808 "sofosbuvir" "Antivirals for treatment of HCV infections" "c(\"Hepcinat\", \"Hepcvir\", \"Sofosbuvir\", \"Sovaldi\", \"SOVALDI\", \"SoviHep\")" 0.4 "g"
"J05AP51" 72734365 "sofosbuvir and ledipasvir" "Antivirals for treatment of HCV infections" ""
"J05AP55" 91885554 "sofosbuvir and velpatasvir" "Antivirals for treatment of HCV infections" "Epclusa Tablet"
"J05AP56" "sofosbuvir, velpatasvir and voxilaprevir" "Antivirals for treatment of HCV infections" ""
"J05AF04" "18283" "stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Estavudina\", \"Sanilvudine\", \"Stavudin\", \"Stavudine\", \"Stavudinum\", \"Zerit Xr\", \"Zerut XR\")" "80" "mg"
"J05AR07" "15979285" "stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
"J05AP02" "3010818" "telaprevir" "Antivirals for treatment of HCV infections" "c(\"Incivek\", \"Incivo\", \"Telaprevir\", \"Telavic\")" "2.25" "g"
"J05AF11" "159269" "telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epavudine\", \"Sebivo\", \"Telbivudin\", \"Telbivudine\", \"Tyzeka\")" "0.6" "g"
"J05AF13" "9574768" "tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" "25" "mg"
"J05AF07" "5481350" "tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"BisPMPA\", \"PMPA prodrug\", \"Tenofovir\", \"Viread\")" "0.245" "g"
"J05AF04" 18283 "stavudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Estavudina\", \"Sanilvudine\", \"Stavudin\", \"Stavudine\", \"Stavudinum\", \"Zerit Xr\", \"Zerut XR\")" 80 "mg"
"J05AR07" 15979285 "stavudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" "STAVUDIINE"
"J05AP02" 3010818 "telaprevir" "Antivirals for treatment of HCV infections" "c(\"Incivek\", \"Incivo\", \"Telaprevir\", \"Telavic\")" 2.25 "g"
"J05AF11" 159269 "telbivudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Epavudine\", \"Sebivo\", \"Telbivudin\", \"Telbivudine\", \"Tyzeka\")" 0.6 "g"
"J05AF13" 9574768 "tenofovir alafenamide" "Nucleoside and nucleotide reverse transcriptase inhibitors" "Vemlidy" 25 "mg"
"J05AF07" 5481350 "tenofovir disoproxil" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"BisPMPA\", \"PMPA prodrug\", \"Tenofovir\", \"Viread\")" 0.245 "g"
"J05AR03" "tenofovir disoproxil and emtricitabine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AX19" "5475" "tilorone" "Other antivirals" "c(\"Amiksin\", \"Amixin\", \"Amixin IC\", \"Amyxin\", \"Tiloron\", \"Tilorona\", \"Tilorone\", \"Tiloronum\")" "0.125" "g"
"J05AE09" "54682461" "tipranavir" "Protease inhibitors" "c(\"Aptivus\", \"Tipranavir\")" "1" "g"
"J05AC03" "64377" "tromantadine" "Cyclic amines" "c(\"Tromantadina\", \"Tromantadine\", \"Tromantadinum\", \"Viruserol\")"
"J05AX13" "131411" "umifenovir" "Other antivirals" "c(\"Arbidol\", \"Arbidol base\", \"Umifenovir\")" "0.8" "g"
"J05AB11" "135398742" "valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Talavir\", \"Valaciclovir\", \"Valaciclovirum\", \"ValACV\", \"Valcivir\", \"Valcyclovir\", \"Valtrex\", \"Virval\", \"Zelitrex\")" "3" "g"
"J05AB14" "135413535" "valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cymeval\", \"Valganciclovir\")" "0.9" "g"
"J05AB03" "21704" "vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenine arabinoside\", \"Araadenosine\", \"Arabinoside adenine\", \"Arabinosyl adenine\", \"Arabinosyladenine\", \"Spongoadenosine\", \"Vidarabin\", \"Vidarabina\", \"Vidarabine\", \"Vidarabine anhydrous\", \"Vidarabinum\", \"Vira A\", \"Vira ATM\")"
"J05AF03" "24066" "zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Dideoxycytidine\", \"Interferon AD + ddC\", \"Zalcitabine\", \"Zalcitibine\")" "2.25" "mg"
"J05AH01" "60855" "zanamivir" "Neuraminidase inhibitors" "c(\"MODIFIED SIALIC ACID\", \"Relenza\", \"Zanamavir\", \"Zanamir\", \"Zanamivi\", \"Zanamivir\", \"Zanamivir hydrate\")"
"J05AF01" "35370" "zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Azidothymidine\", \"AZT Antiviral\", \"Beta interferon\", \"Compound S\", \"Propolis+AZT\", \"Retrovir\", \"Zidovudina\", \"Zidovudine\", \"ZIDOVUDINE\", \"Zidovudine EP III\", \"Zidovudinum\")" "0.6" "g" "0.6" "g"
"J05AX19" 5475 "tilorone" "Other antivirals" "c(\"Amiksin\", \"Amixin\", \"Amixin IC\", \"Amyxin\", \"Tiloron\", \"Tilorona\", \"Tilorone\", \"Tiloronum\")" 0.125 "g"
"J05AE09" 54682461 "tipranavir" "Protease inhibitors" "c(\"Aptivus\", \"Tipranavir\")" 1 "g"
"J05AC03" 64377 "tromantadine" "Cyclic amines" "c(\"Tromantadina\", \"Tromantadine\", \"Tromantadinum\", \"Viruserol\")"
"J05AX13" 131411 "umifenovir" "Other antivirals" "c(\"Arbidol\", \"Arbidol base\", \"Umifenovir\")" 0.8 "g"
"J05AB11" 135398742 "valaciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Talavir\", \"Valaciclovir\", \"Valaciclovirum\", \"ValACV\", \"Valcivir\", \"Valcyclovir\", \"Valtrex\", \"Virval\", \"Zelitrex\")" 3 "g"
"J05AB14" 135413535 "valganciclovir" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Cymeval\", \"Valganciclovir\")" 0.9 "g"
"J05AB03" 21704 "vidarabine" "Nucleosides and nucleotides excl. reverse transcriptase inhibitors" "c(\"Adenine arabinoside\", \"Araadenosine\", \"Arabinoside adenine\", \"Arabinosyl adenine\", \"Arabinosyladenine\", \"Spongoadenosine\", \"Vidarabin\", \"Vidarabina\", \"Vidarabine\", \"Vidarabine anhydrous\", \"Vidarabinum\", \"Vira A\", \"Vira ATM\")"
"J05AF03" 24066 "zalcitabine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Dideoxycytidine\", \"Interferon AD + ddC\", \"Zalcitabine\", \"Zalcitibine\")" 2.25 "mg"
"J05AH01" 60855 "zanamivir" "Neuraminidase inhibitors" "c(\"MODIFIED SIALIC ACID\", \"Relenza\", \"Zanamavir\", \"Zanamir\", \"Zanamivi\", \"Zanamivir\", \"Zanamivir hydrate\")"
"J05AF01" 35370 "zidovudine" "Nucleoside and nucleotide reverse transcriptase inhibitors" "c(\"Azidothymidine\", \"AZT Antiviral\", \"Beta interferon\", \"Compound S\", \"Propolis+AZT\", \"Retrovir\", \"Zidovudina\", \"Zidovudine\", \"ZIDOVUDINE\", \"Zidovudine EP III\", \"Zidovudinum\")" 0.6 "g" 0.6 "g"
"J05AR01" "zidovudine and lamivudine" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR04" "zidovudine, lamivudine and abacavir" "Antivirals for treatment of HIV infections, combinations" ""
"J05AR05" "zidovudine, lamivudine and nevirapine" "Antivirals for treatment of HIV infections, combinations" ""

BIN
data-raw/antivirals.xlsx

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48
data-raw/internals.R

@ -73,13 +73,41 @@ rm(microorganisms.translation) @@ -73,13 +73,41 @@ rm(microorganisms.translation)
usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
devtools::load_all(quiet = TRUE)
# give official names to ABs and MOs
write.table(dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo)),
"data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character),
"data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character),
"data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
write.table(dplyr::mutate_all(antivirals, as.character),
"data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
write.table(intrinsic_resistant,
"data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE)
rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2)
write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
haven::write_sas(rsi, "data-raw/rsi_translation.sas")
haven::write_sav(rsi, "data-raw/rsi_translation.sav")
haven::write_dta(rsi, "data-raw/rsi_translation.dta")
openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx")
mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character)
saveRDS(mo, "data-raw/microorganisms.rds", version = 2)
write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
haven::write_sas(mo, "data-raw/microorganisms.sas")
haven::write_sav(mo, "data-raw/microorganisms.sav")
haven::write_dta(mo, "data-raw/microorganisms.dta")
openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx")
ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character)
saveRDS(ab, "data-raw/antibiotics.rds", version = 2)
write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
haven::write_sas(ab, "data-raw/antibiotics.sas")
haven::write_sav(ab, "data-raw/antibiotics.sav")
haven::write_dta(ab, "data-raw/antibiotics.dta")
openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx")
av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character)
saveRDS(av, "data-raw/antivirals.rds", version = 2)
write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
haven::write_sas(av, "data-raw/antivirals.sas")
haven::write_sav(av, "data-raw/antivirals.sav")
haven::write_dta(av, "data-raw/antivirals.dta")
openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx")
saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2)
write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE)
haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas")
haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav")
haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta")
openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx")

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data-raw/intrinsic_resistant.sav

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data-raw/intrinsic_resistant.xlsx

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data-raw/microorganisms.dta

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data-raw/microorganisms.rds

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data-raw/microorganisms.sas

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data-raw/microorganisms.sav

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data-raw/microorganisms.xlsx

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data-raw/rsi_translation.dta

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data-raw/rsi_translation.rds

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9
docs/404.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
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@ -117,6 +117,13 @@ @@ -117,6 +117,13 @@
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
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@ -117,6 +117,13 @@ @@ -117,6 +117,13 @@
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@ -0,0 +1,958 @@ @@ -0,0 +1,958 @@
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<h1 data-toc-skip>Data sets for download</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
</div>
<p>This package contains a lot of reference data sets that are all reliable, up-to-date and free to download. You can even use them outside of R, for example to train your laboratory information system (LIS) about intrinsic resistance!</p>
<p>We included them in our <code>AMR</code> package, but also automatically ‘mirror’ them to our public repository in different software formats. On this page, we explain how to download them and how the structure of the data sets look like. The tab separated files <strong>allow for machine reading taxonomic data and EUCAST and CLSI interpretation guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI.</p>
<p><em>Note: Years and dates of updates mentioned on this page, are from on <code>AMR</code> package version 1.3.0.9004, online released on 16 August 2020. <strong>If you are reading this page from within R, please <a href="https://msberends.github.io/AMR/articles/datasets.html">visit our website</a> for the latest update.</strong></em></p>
<div id="microorganisms" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms" class="anchor"></a>Microorganisms</h2>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<div id="source" class="section level4">
<h4 class="hasAnchor">
<a href="#source" class="anchor"></a>Source</h4>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, included version: May 2020)</li>
</ul>
</div>
<div id="structure" class="section level4">
<h4 class="hasAnchor">
<a href="#structure" class="anchor"></a>Structure</h4>
<p>A data set with 67,151 rows and 16 columns, containing the following column names:</p>
<p><em>mo, fullname, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, species_id, source, prevalence, snomed</em>.</p>
<p>Included per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
<th align="center">Kingdom</th>
<th align="center">Number of (sub)species</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">(unknown kingdom)</td>
<td align="center">1</td>
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">2,153</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">697</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">19,244</td>
</tr>
<tr class="odd">
<td align="center">Chromista</td>
<td align="center">32,164</td>
</tr>
<tr class="even">
<td align="center">Fungi</td>
<td align="center">9,582</td>
</tr>
</tbody>
</table>
</div>
<div id="download" class="section level4">
<h4 class="hasAnchor">
<a href="#download" class="anchor"></a>Download</h4>
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 28 July 2020 20:52:40 CEST.</p>
<ul>
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.rds">from GitLab</a> (file size: 2.7 MB)</p></li>
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.xlsx">from GitLab</a> (file size: 6.1 MB)</p></li>
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.sav">from GitLab</a> (file size: 28.2 MB)</p></li>
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.sav">from GitLab</a> (file size: 28.2 MB)</p></li>
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.dta">from GitLab</a> (file size: 25.2 MB)</p></li>
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/microorganisms.txt">from GitLab</a> (file size: 13.3 MB)</p></li>
</ul>
</div>
<div id="example" class="section level4">
<h4 class="hasAnchor">
<a href="#example" class="anchor"></a>Example</h4>
<p>Example rows when filtering on genus <em>Escherichia</em>:</p>
<table class="table">
<colgroup>
<col width="5%">
<col width="9%">
<col width="3%">
<col width="6%">
<col width="8%">
<col width="6%">
<col width="7%">
<col width="5%">
<col width="4%">
<col width="4%">
<col width="3%">
<col width="9%">
<col width="13%">
<col width="3%">
<col width="4%">
<col width="4%">
</colgroup>
<thead><tr class="header">
<th align="center">mo</th>
<th align="center">fullname</th>
<th align="center">kingdom</th>
<th align="center">phylum</th>
<th align="center">class</th>
<th align="center">order</th>
<th align="center">family</th>
<th align="center">genus</th>
<th align="center">species</th>
<th align="center">subspecies</th>
<th align="center">rank</th>
<th align="center">ref</th>
<th align="center">species_id</th>
<th align="center">source</th>
<th align="center">prevalence</th>
<th align="center">snomed</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">B_ESCHR</td>
<td align="center">Escherichia</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">genus</td>
<td align="center"></td>
<td align="center">bc4fdde6867d5ecfc728000b0bfb49a3</td>
<td align="center">CoL</td>
<td align="center">1</td>
<td align="center">64735005</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_ALBR</td>
<td align="center">Escherichia albertii</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">albertii</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Huys et al., 2003</td>
<td align="center">36618b1ed3b8b7e5a61f40eb9386e63c</td>
<td align="center">CoL</td>
<td align="center">1</td>
<td align="center">419388003</td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_COLI</td>
<td align="center">Escherichia coli</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Castellani et al., 1919</td>
<td align="center">3254b3db31bf16fdde669ac57bf8c4fe</td>
<td align="center">CoL</td>
<td align="center">1</td>
<td align="center">112283007</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_FRGS</td>
<td align="center">Escherichia fergusonii</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">fergusonii</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Farmer et al., 1985</td>
<td align="center">82d98b10c456ce5f4c8c515f4e1567e2</td>
<td align="center">CoL</td>
<td align="center">1</td>
<td align="center">72461005</td>
</tr>
<tr class="odd">
<td align="center">B_ESCHR_HRMN</td>
<td align="center">Escherichia hermannii</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">hermannii</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Brenner et al., 1983</td>
<td align="center">b16086aee36e3b46b565510083ab4b65</td>
<td align="center">CoL</td>
<td align="center">1</td>
<td align="center">85786000</td>
</tr>
<tr class="even">
<td align="center">B_ESCHR_MRMT</td>
<td align="center">Escherichia marmotae</td>
<td align="center">Bacteria</td>
<td align="center">Proteobacteria</td>
<td align="center">Gammaproteobacteria</td>
<td align="center">Enterobacterales</td>
<td align="center">Enterobacteriaceae</td>
<td align="center">Escherichia</td>
<td align="center">marmotae</td>
<td align="center"></td>
<td align="center">species</td>
<td align="center">Liu et al., 2015</td>
<td align="center">792928</td>
<td align="center">DSMZ</td>
<td align="center">1</td>
<td align="center"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<div id="source-1" class="section level4">
<h4 class="hasAnchor">
<a href="#source-1" class="anchor"></a>Source</h4>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is frelly available from the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
<li><a href="https://whonet.org">WHONET software 2019</a></li>
</ul>
</div>
<div id="structure-1" class="section level4">
<h4 class="hasAnchor">
<a href="#structure-1" class="anchor"></a>Structure</h4>
<p>A data set with 456 rows and 14 columns, containing the following column names:</p>
<p><em>ab, atc, cid, name, group, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc</em>.</p>
</div>
<div id="download-1" class="section level4">
<h4 class="hasAnchor">
<a href="#download-1" class="anchor"></a>Download</h4>
<p>Download the data set preferably in the software you use, so the data file already has the correct data structure. Below files were updated on 31 July 2020 12:12:13 CEST.</p>
<ul>
<li><p>R file (.rds): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.rds">from GitLab</a> (file size: 37.3 kB)</p></li>
<li><p>Excel workbook (.xlsx): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.xlsx">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.xlsx">from GitLab</a> (file size: 64.5 kB)</p></li>
<li><p>SPSS file (.sav): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.sav">from GitLab</a> (file size: 1.3 MB)</p></li>
<li><p>Stata file (.dta): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.sav">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.sav">from GitLab</a> (file size: 1.3 MB)</p></li>
<li><p>SAS file (.sas): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.dta">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.dta">from GitLab</a> (file size: 321.8 kB)</p></li>
<li><p>Tab separated file (.txt): <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.txt">from GitHub</a>, <a href="https://gitlab.com/msberends/AMR/-/raw/master/data-raw/../data-raw/antibiotics.txt">from GitLab</a> (file size: 146.1 kB)</p></li>
</ul>
</div>
<div id="example-1" class="section level4">
<h4 class="hasAnchor">
<a href="#example-1" class="anchor"></a>Example</h4>
<p>Example rows:</p>
<table class="table">
<colgroup>
<col width="1%">
<col width="2%">
<col width="3%">
<col width="9%">
<col width="8%">
<col width="14%">
<col width="19%">
<col width="6%">
<col width="11%">
<col width="3%">
<col width="3%">
<col width="2%">
<col width="3%">
<col width="10%">
</colgroup>
<thead><tr class="header">
<th align="center">ab</th>
<th align="center">atc</th>
<th align="center">cid</th>
<th align="center">name</th>
<th align="center">group</th>
<th align="center">atc_group1</th>
<th align="center">atc_group2</th>
<th align="center">abbreviations</th>
<th align="center">synonyms</th>
<th align="center">oral_ddd</th>
<th align="center">oral_units</th>
<th align="center">iv_ddd</th>
<th align="center">iv_units</th>
<th align="center">loinc</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">AMK</td>
<td align="center">J01GB06</td>
<td align="center">37768</td>
<td align="center">Amikacin</td>
<td align="center">Aminoglycosides</td>
<td align="center">Aminoglycoside antibacterials</td>
<td align="center">Other aminoglycosides</td>
<td align="center">ak, ami, amik, …</td>
<td align="center">amicacin, amikacillin, amikacin, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">1.0</td>
<td align="center">g</td>
<td align="center">13546-7, 15098-7, 17798-0, …</td>
</tr>
<tr class="even">
<td align="center">AMX</td>
<td align="center">J01CA04</td>
<td align="center">33613</td>
<td align="center">Amoxicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">ac, amox, amx</td>
<td align="center">actimoxi, amoclen, amolin, …</td>
<td align="center">1.0</td>
<td align="center">g</td>
<td align="center">1.0</td>
<td align="center">g</td>
<td align="center">16365-9, 25274-2, 3344-9, …</td>
</tr>
<tr class="odd">
<td align="center">AMC</td>
<td align="center">J01CR02</td>
<td align="center">23665637</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Combinations of penicillins, incl. beta-lactamase inhibitors</td>
<td align="center">a/c, amcl, aml, …</td>
<td align="center">amocla, amoclan, amoclav, …</td>
<td align="center">1.0</td>
<td align="center">g</td>
<td align="center">3.0</td>
<td align="center">g</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="center">AMP</td>
<td align="center">J01CA01</td>
<td align="center">6249</td>
<td align="center">Ampicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
<td align="center">am, amp, ampi</td>
<td align="center">acillin, adobacillin, amblosin, …</td>
<td align="center">2.0</td>
<td align="center">g</td>
<td align="center">2.0</td>
<td align="center">g</td>
<td align="center">21066-6, 3355-5, 33562-0, …</td>
</tr>
<tr class="odd">
<td align="center">AZM</td>
<td align="center">J01FA10</td>
<td align="center">447043</td>
<td align="center">Azithromycin</td>
<td align="center">Macrolides/lincosamides</td>
<td align="center">Macrolides, lincosamides and streptogramins</td>
<td align="center">Macrolides</td>
<td align="center">az, azi, azit, …</td>
<td align="center">aritromicina, azasite, azenil, …</td>
<td align="center">0.3</td>
<td align="center">g</td>
<td align="center">0.5</td>
<td align="center">g</td>
<td align="center">16420-2, 25233-8</td>
</tr>
<tr class="even">
<td align="center">CZO</td>
<td align="center">J01DB04</td>
<td align="center">33255</td>
<td align="center">Cefazolin</td>
<td align="center">Cephalosporins (1st gen.)</td>
<td align="center">Other beta-lactam antibacterials</td>
<td align="center">First-generation cephalosporins</td>
<td align="center">cfz, cfzl, cz, …</td>
<td align="center">atirin, cefamezin, cefamezine, …</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">3.0</td>
<td align="center">g</td>
<td align="center">16566-2, 25235-3, 3442-1, …</td>