v 1.0.0

.gitignore

@@ -22,3 +22,4 @@ packrat/lib*/
 packrat/src/
 data-raw/taxon.tab
 data-raw/DSMZ_bactnames.xlsx
+data-raw/country_analysis_url_token.R

.gitlab-ci.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

.gitlab-ci.yml

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.9.0
-Date: 2019-11-29
+Version: 1.0.0
+Date: 2020-02-17
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -8,7 +8,7 @@ Authors@R: c(
     person(role = c("aut", "ctb"),
            family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
     person(role = c("aut", "ths"),
-           family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
+           family = "Friedrich", given = c("Alexander", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
     person(role = c("aut", "ths"),
            family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
     person(role = c("aut", "ths"),
@@ -63,5 +63,5 @@ BugReports: https://gitlab.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.1
+RoxygenNote: 7.0.2
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -66,6 +66,7 @@ export(ab_cid)
 export(ab_ddd)
 export(ab_group)
 export(ab_info)
+export(ab_loinc)
 export(ab_name)
 export(ab_property)
 export(ab_synonyms)
@@ -85,7 +86,6 @@ export(availability)
 export(brmo)
 export(bug_drug_combinations)
 export(catalogue_of_life_version)
-export(clear_mo_history)
 export(count_I)
 export(count_IR)
 export(count_R)
@@ -156,6 +156,7 @@ export(mo_rank)
 export(mo_ref)
 export(mo_renamed)
 export(mo_shortname)
+export(mo_snomed)
 export(mo_species)
 export(mo_subspecies)
 export(mo_synonyms)
@@ -327,5 +328,3 @@ importFrom(tidyr,pivot_wider)
 importFrom(utils,adist)
 importFrom(utils,browseURL)
 importFrom(utils,menu)
-importFrom(utils,read.csv)
-importFrom(utils,write.csv)

NEWS.md

@@ -1,3 +1,51 @@
+# AMR 1.0.0
+
+This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
+
+### New
+* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
+* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
+* Support for LOINC and SNOMED codes
+  * Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
+    ```r
+    ab_loinc("ampicillin")
+    #> [1] "21066-6" "3355-5"  "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"
+    ab_name("21066-6")
+    #> [1] "Ampicillin"
+    ab_atc("21066-6")
+    #> [1] "J01CA01"
+    ```
+  * Support for SNOMED CT codes in the `microorganisms` data set. Use `mo_snomed()` to retrieve SNOMED codes, or use a SNOMED code for input in any `mo_*` function:
+    ```r
+    mo_snomed("S. aureus")
+    #> [1] 115329001   3092008 113961008
+    mo_name(115329001)
+    #> [1] "Staphylococcus aureus"
+    mo_gramstain(115329001)
+    #> [1] "Gram-positive"
+    ```
+
+### Changes
+* The `as.mo()` function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the function `clear_mo_history()` was removed.
+* Bugfix for some WHONET microorganism codes that were not interpreted correctly when using `as.rsi()`
+* Improvements for the algorithm used by `as.mo()` (and consequently all `mo_*` functions, that use `as.mo()` internally):
+  * Support for missing spaces, e.g. in `as.mo("Methicillin-resistant S.aureus")`
+  * Better support for determination of *Salmonella* biovars
+  * Speed improvements, especially for the *G. species* format (G for genus), like *E. coli* and *K pneumoniae*
+  * Support for more common codes used in laboratory information systems
+* Input values for `as.disk()` limited to a maximum of 50 millimeters
+* Added a lifecycle state to every function, following [the lifecycle circle of the `tidyverse`](https://www.tidyverse.org/lifecycle)
+* For in `as.ab()`: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
+* Changes to the `antibiotics` data set (thanks to Peter Dutey):
+  * Added more synonyms to colistin, imipenem and piperacillin/tazobactam
+  * Moved synonyms Rifinah and Rimactazid from rifampicin (`RIF`) to rifampicin/isoniazid (`RFI`). Please note that [the combination rifampicin/isoniazid has no DDDs defined](https://www.whocc.no/atc_ddd_index/?code=J04AM02&showdescription=no), so e.g. `ab_ddd("Rimactazid")` will now return `NA`.
+  * Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (`SMX`) to trimethoprim/sulfamethoxazole (`SXT`)
+
+### Other
+* Add a `CITATION` file
+* Full support for the upcoming R 4.0
+* Removed unnecessary `AMR::` calls
+
 # AMR 0.9.0
 
 ### Breaking

R/ab.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Transform to antibiotic ID
 #'
 #' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param x character vector to determine to antibiotic ID
 #' @param ... arguments passed on to internal functions
 #' @rdname as.ab
@@ -42,7 +43,7 @@
 #' @inheritSection AMR Read more on our website!
 #' @export
 #' @examples
-#' # These examples all return "ERY", the ID of Erythromycin:
+#' # these examples all return "ERY", the ID of erythromycin:
 #' as.ab("J01FA01")
 #' as.ab("J 01 FA 01")
 #' as.ab("Erythromycin")
@@ -53,17 +54,26 @@
 #' as.ab("eritromicine") # spelled wrong, yet works
 #' as.ab("Erythrocin")   # trade name
 #' as.ab("Romycin")      # trade name
+#' 
+#' # spelling from different languages and dyslexia are no problem
+#' ab_atc("ceftriaxon")
+#' ab_atc("cephtriaxone")     # small spelling error
+#' ab_atc("cephthriaxone")    # or a bit more severe
+#' ab_atc("seephthriaaksone") # and even this works
 #'
-#' # Use ab_* functions to get a specific properties (see ?ab_property);
+#' # use ab_* functions to get a specific properties (see ?ab_property);
 #' # they use as.ab() internally:
 #' ab_name("J01FA01")    # "Erythromycin"
 #' ab_name("eryt")       # "Erythromycin"
 as.ab <- function(x, ...) {
+  
+  check_dataset_integrity()
+  
   if (is.ab(x)) {
     return(x)
   }
 
-  if (all(toupper(x) %in% AMR::antibiotics$ab)) {
+  if (all(toupper(x) %in% antibiotics$ab)) {
     # valid AB code, but not yet right class
     return(structure(.Data = toupper(x),
                      class = "ab"))
@@ -86,6 +96,10 @@ as.ab <- function(x, ...) {
   # spaces around non-characters must be removed: amox + clav -> amox/clav
   x_bak_clean <- gsub("(.*[a-zA-Z0-9]) ([^a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
   x_bak_clean <- gsub("(.*[^a-zA-Z0-9]) ([a-zA-Z0-9].*)", "\\1\\2", x_bak_clean)
+  # remove hyphen after a starting "co"
+  x_bak_clean <- gsub("^co-", "co", x_bak_clean, ignore.case = TRUE)
+  # replace text 'and' with a slash
+  x_bak_clean <- gsub(" and ", "/", x_bak_clean, ignore.case = TRUE)
 
   x <- unique(x_bak_clean)
   x_new <- rep(NA_character_, length(x))
@@ -106,54 +120,67 @@ as.ab <- function(x, ...) {
     }
 
     # exact AB code
-    found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])), ]$ab
+    found <- antibiotics[which(antibiotics$ab == toupper(x[i])), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact ATC code
-    found <- AMR::antibiotics[which(AMR::antibiotics$atc == toupper(x[i])), ]$ab
+    found <- antibiotics[which(antibiotics$atc == toupper(x[i])), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact CID code
-    found <- AMR::antibiotics[which(AMR::antibiotics$cid == x[i]), ]$ab
+    found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact name
-    found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) == toupper(x[i])), ]$ab
+    found <- antibiotics[which(toupper(antibiotics$name) == toupper(x[i])), ]$ab
+    if (length(found) > 0) {
+      x_new[i] <- found[1L]
+      next
+    }
+    
+    # exact LOINC code
+    loinc_found <- unlist(lapply(antibiotics$loinc,
+                                   function(s) if (x[i] %in% s) {
+                                     TRUE
+                                   } else {
+                                     FALSE
+                                   }))
+    found <- antibiotics$ab[loinc_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact synonym
-    synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,
+    synonym_found <- unlist(lapply(antibiotics$synonyms,
                                    function(s) if (toupper(x[i]) %in% toupper(s)) {
                                      TRUE
                                    } else {
                                      FALSE
                                    }))
-    found <- AMR::antibiotics$ab[synonym_found == TRUE]
+    found <- antibiotics$ab[synonym_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
 
     # exact abbreviation
-    abbr_found <- unlist(lapply(AMR::antibiotics$abbreviations,
+    abbr_found <- unlist(lapply(antibiotics$abbreviations,
                                 function(a) if (toupper(x[i]) %in% toupper(a)) {
                                   TRUE
                                 } else {
                                   FALSE
                                 }))
-    found <- AMR::antibiotics$ab[abbr_found == TRUE]
+    found <- antibiotics$ab[abbr_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
@@ -161,7 +188,7 @@ as.ab <- function(x, ...) {
 
     # first >=4 characters of name
     if (nchar(x[i]) >= 4) {
-      found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) %like% paste0("^", x[i])), ]$ab
+      found <- antibiotics[which(toupper(antibiotics$name) %like% paste0("^", x[i])), ]$ab
       if (length(found) > 0) {
         x_new[i] <- found[1L]
         next
@@ -191,19 +218,19 @@ as.ab <- function(x, ...) {
     x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
   
     # try if name starts with it
-    found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)), ]$ab
+    found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
     }
     # and try if any synonym starts with it
-    synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,
+    synonym_found <- unlist(lapply(antibiotics$synonyms,
                                    function(s) if (any(s %like% paste0("^", x_spelling))) {
                                      TRUE
                                    } else {
                                      FALSE
                                    }))
-    found <- AMR::antibiotics$ab[synonym_found == TRUE]
+    found <- antibiotics$ab[synonym_found == TRUE]
     if (length(found) > 0) {
       x_new[i] <- found[1L]
       next
@@ -303,7 +330,7 @@ as.ab <- function(x, ...) {
 #' @rdname as.ab
 #' @export
 is.ab <- function(x) {
-  identical(class(x), "ab")
+  inherits(x, "ab")
 }
 
 #' @exportMethod print.ab
@@ -350,7 +377,7 @@ as.data.frame.ab <- function(x, ...) {
 "[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @exportMethod [[<-.ab
 #' @export
@@ -358,7 +385,7 @@ as.data.frame.ab <- function(x, ...) {
 "[[<-.ab" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 #' @exportMethod c.ab
 #' @export
@@ -366,7 +393,7 @@ as.data.frame.ab <- function(x, ...) {
 c.ab <- function(x, ...) {
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  class_integrity_check(y, "antimicrobial code", AMR::antibiotics$ab)
+  class_integrity_check(y, "antimicrobial code", antibiotics$ab)
 }
 
 #' @importFrom pillar type_sum

R/ab_property.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Property of an antibiotic
 #'
 #' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.ab()]
 #' @param tolower logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
 #' @param property one of the column names of one of the [antibiotics] data set
@@ -46,18 +47,18 @@
 #' ab_name("AMX")       # "Amoxicillin"
 #' ab_atc("AMX")        # J01CA04 (ATC code from the WHO)
 #' ab_cid("AMX")        # 33613 (Compound ID from PubChem)
-#'
 #' ab_synonyms("AMX")   # a list with brand names of amoxicillin
 #' ab_tradenames("AMX") # same
-#'
 #' ab_group("AMX")      # "Beta-lactams/penicillins"
 #' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
 #' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
 #'
+#' # smart lowercase tranformation
 #' ab_name(x = c("AMC", "PLB"))  # "Amoxicillin/clavulanic acid" "Polymyxin B"
 #' ab_name(x = c("AMC", "PLB"),
 #'         tolower = TRUE)       # "amoxicillin/clavulanic acid" "polymyxin B"
 #'
+#' # defined daily doses (DDD)
 #' ab_ddd("AMX", "oral")               #  1
 #' ab_ddd("AMX", "oral", units = TRUE) # "g"
 #' ab_ddd("AMX", "iv")                 #  1
@@ -65,12 +66,19 @@
 #'
 #' ab_info("AMX")       # all properties as a list
 #'
-#' # all ab_* functions use as.ab() internally:
-#' ab_name("Fluclox")   # "Flucloxacillin"
-#' ab_name("fluklox")   # "Flucloxacillin"
-#' ab_name("floxapen")  # "Flucloxacillin"
-#' ab_name(21319)       # "Flucloxacillin" (using CID)
-#' ab_name("J01CF05")   # "Flucloxacillin" (using ATC)
+#' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
+#' ab_atc("AMP")           # ATC code of AMP (ampicillin)
+#' ab_group("J01CA01")     # Drug group of ampicillins ATC code
+#' ab_loinc("ampicillin")  # LOINC codes of ampicillin
+#' ab_name("21066-6")      # "Ampicillin" (using LOINC)
+#' ab_name(6249)           # "Ampicillin" (using CID)
+#' ab_name("J01CA01")      # "Ampicillin" (using ATC)
+#' 
+#' # spelling from different languages and dyslexia are no problem
+#' ab_atc("ceftriaxon")
+#' ab_atc("cephtriaxone")
+#' ab_atc("cephthriaxone")
+#' ab_atc("seephthriaaksone")
 ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
   x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
   if (tolower == TRUE) {
@@ -130,6 +138,18 @@ ab_atc_group2 <- function(x, language = get_locale(), ...) {
   translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
 }
 
+#' @rdname ab_property
+#' @export
+ab_loinc <- function(x, ...) {
+  loincs <- ab_validate(x = x, property = "loinc", ...)
+  names(loincs) <- x
+  if (length(loincs) == 1) {
+    unname(unlist(loincs))
+  } else {
+    loincs
+  }
+}
+
 #' @rdname ab_property
 #' @export
 ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
@@ -148,7 +168,7 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
 #' @rdname ab_property
 #' @export
 ab_info <- function(x, language = get_locale(), ...) {
-  x <- AMR::as.ab(x, ...)
+  x <- as.ab(x, ...)
   base::list(ab = as.character(x),
              atc = ab_atc(x),
              cid = ab_cid(x),
@@ -169,7 +189,7 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
   if (length(property) != 1L) {
     stop("'property' must be of length 1.")
   }
-  if (!property %in% colnames(AMR::antibiotics)) {
+  if (!property %in% colnames(antibiotics)) {
     stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
   }
 
@@ -177,19 +197,17 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
 }
 
 ab_validate <- function(x, property, ...) {
-  if (!"AMR" %in% base::.packages()) {
-    library("AMR")
-    # check onLoad() in R/zzz.R: data tables are created there.
-  }
+  
+  check_dataset_integrity()
   
   # try to catch an error when inputting an invalid parameter
   # so the 'call.' can be set to FALSE
-  tryCatch(x[1L] %in% AMR::antibiotics[1, property],
+  tryCatch(x[1L] %in% antibiotics[1, property],
            error = function(e) stop(e$message, call. = FALSE))
   x_bak <- x
-  if (!all(x %in% AMR::antibiotics[, property])) {
-    x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
-      left_join(AMR::antibiotics, by = "ab") %>%
+  if (!all(x %in% antibiotics[, property])) {
+    x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %>%
+      left_join(antibiotics, by = "ab") %>%
       pull(property)
   }
   if (property == "ab") {

R/age.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Age in years of individuals
 #'
 #' Calculates age in years based on a reference date, which is the sytem date at default.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x date(s), will be coerced with [as.POSIXlt()]
 #' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()] and cannot be lower than `x`
 #' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
@@ -91,6 +92,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
 #' Split ages into age groups
 #'
 #' Split ages into age groups defined by the `split` parameter. This allows for easier demographic (antimicrobial resistance) analysis.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x age, e.g. calculated with [age()]
 #' @param split_at values to split `x` at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.
 #' @param na.rm a logical to indicate whether missing values should be removed

R/amr.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -38,15 +38,17 @@
 #' - Getting properties for any microorganism (like Gram stain, species, genus or family)
 #' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
 #' - Plotting antimicrobial resistance
-#' - Applying EUCAST expert rules
+#' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
+#' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
+#' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
 
 #' @section Read more on our website!:
-#' On our website <https://msberends.gitlab.io/AMR> you can find [a tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
+#' On our website <https://msberends.gitlab.io/AMR> you can find [a comprehensive tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
 #' @section Contact us:
 #' For suggestions, comments or questions, please contact us at:
 #'
 #' Matthijs S. Berends \cr
-#' m.s.berends at umcg dot nl \cr
+#' m.s.berends \[at\] umcg \[dot\] nl \cr
 #' Department of Medical Microbiology, University of Groningen \cr
 #' University Medical Center Groningen \cr
 #' Post Office Box 30001 \cr

R/atc_online.R

@@ -6,21 +6,22 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Get ATC properties from WHOCC website
 #'
+#' @inheritSection lifecycle Questioning lifecycle
 #' @description Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
 #' 
 #' **This function requires an internet connection.**
@@ -75,12 +76,14 @@ atc_online_property <- function(atc_code,
                                 property,
                                 administration = "O",
                                 url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no") {
+  
+  check_dataset_integrity()
 
   if (!all(c("curl", "rvest", "xml2") %in% rownames(utils::installed.packages()))) {
     stop("Packages 'xml2', 'rvest' and 'curl' are required for this function")
   }
 
-  if (!all(atc_code %in% AMR::antibiotics)) {
+  if (!all(atc_code %in% antibiotics)) {
     atc_code <- as.character(ab_atc(atc_code))
   }
 

R/availability.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Check availability of columns
 #'
-#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antimicrobial combination can be used for calculation with e.g. [resistance()].
+#' Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. [susceptibility()] and [resistance()].
+#' @inheritSection lifecycle Stable lifecycle
 #' @param tbl a [`data.frame`] or [`list`]
 #' @param width number of characters to present the visual availability, defaults to filling the width of the console
 #' @details The function returns a [`data.frame`] with columns `"resistant"` and `"visual_resistance"`. The values in that columns are calculated with [resistance()].

R/bug_drug_combinations.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Determine bug-drug combinations
 #' 
 #' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see Examples.
+#' @inheritSection lifecycle Stable lifecycle
 #' @inheritParams eucast_rules
 #' @param combine_IR logical to indicate whether values R and I should be summed
 #' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column

R/catalogue_of_life.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -91,20 +91,23 @@ NULL
 #' microorganisms %>% freq(kingdom)
 #' microorganisms %>% group_by(kingdom) %>% freq(phylum, nmax = NULL)
 catalogue_of_life_version <- function() {
+  
+  check_dataset_integrity()
+  
   # see the `catalogue_of_life` list in R/data.R
   lst <- list(catalogue_of_life =
                 list(version = gsub("{year}", catalogue_of_life$year, catalogue_of_life$version, fixed = TRUE),
                      url = gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE),
-                     n = nrow(filter(AMR::microorganisms, source == "CoL"))),
+                     n = nrow(filter(microorganisms, source == "CoL"))),
               deutsche_sammlung_von_mikroorganismen_und_zellkulturen =
                 list(version = "Prokaryotic Nomenclature Up-to-Date from DSMZ",
                      url = catalogue_of_life$url_DSMZ,
                      yearmonth = catalogue_of_life$yearmonth_DSMZ,
-                     n = nrow(filter(AMR::microorganisms, source == "DSMZ"))),
+                     n = nrow(filter(microorganisms, source == "DSMZ"))),
               total_included =
                 list(
-                  n_total_species = nrow(AMR::microorganisms),
-                  n_total_synonyms = nrow(AMR::microorganisms.old)))
+                  n_total_species = nrow(microorganisms),
+                  n_total_synonyms = nrow(microorganisms.old)))
 
   structure(.Data = lst,
             class = c("catalogue_of_life_version", "list"))

R/count.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -24,6 +24,7 @@
 #' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in [summarise()] and support grouped variables, see *Examples*.
 #'
 #' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed.
 #' @inheritParams proportion
 #' @inheritSection as.rsi Interpretation of R and S/I

R/data.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -23,7 +23,7 @@
 #'
 #' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
 #' @format
-#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 13 variables:
+#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 14 variables:
 #' - `ab`\cr Antibiotic ID as used in this package (like `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
 #' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
 #' - `cid`\cr Compound ID as found in PubChem
@@ -37,6 +37,7 @@
 #' - `oral_units`\cr Units of `oral_ddd`
 #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
 #' - `iv_units`\cr Units of `iv_ddd`
+#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
 #' 
 #' ### For the [antivirals] data set: a [`data.frame`] with 102 observations and 9 variables:
 #' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
@@ -51,6 +52,12 @@
 #' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
 #'
 #' Synonyms (i.e. trade names) are derived from the Compound ID (`cid`) and consequently only available where a CID is available.
+#' 
+#' ### Direct download
+#' These data sets are available as 'flat files' for use even without R - you can find the files here:
+#' 
+#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
+#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
 #' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
 #'
 #' WHONET 2019 software: <http://www.whonet.org/software.html>
@@ -68,7 +75,7 @@
 #'
 #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using [as.mo()].
 #' @inheritSection catalogue_of_life Catalogue of Life
-#' @format A [`data.frame`] with 69,447 observations and 16 variables:
+#' @format A [`data.frame`] with 69,447 observations and 17 variables:
 #' - `mo`\cr ID of microorganism as used by this package
 #' - `col_id`\cr Catalogue of Life ID
 #' - `fullname`\cr Full name, like `"Escherichia coli"`
@@ -78,6 +85,7 @@
 #' - `species_id`\cr ID of the species as used by the Catalogue of Life
 #' - `source`\cr Either "CoL", "DSMZ" (see Source) or "manually added"
 #' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()]
+#' - `snomed`\cr SNOMED code of the microorganism. Use [mo_snomed()] to retrieve it quickly, see [mo_property()].
 #' @details Manually added were:
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
@@ -86,6 +94,11 @@
 #' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not in the Catalogue of Life
 #' - 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
+#' 
+#'  ### Direct download
+#'  This data set is available as 'flat file' for use even without R - you can find the file here:
+#' 
+#' * <https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
 #' @section About the records from DSMZ (see source):
 #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
 #'
@@ -122,8 +135,8 @@ catalogue_of_life <- list(
 
 #' Translation table for common microorganism codes
 #'
-#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with [set_mo_source()].
-#' @format A [`data.frame`] with 5,433 observations and 2 variables:
+#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with [set_mo_source()]. They will all be searched when using [as.mo()] and consequently all the [`mo_*`][mo_property()] functions.
+#' @format A [`data.frame`] with 5,450 observations and 2 variables:
 #' - `code`\cr Commonly used code of a microorganism
 #' - `mo`\cr ID of the microorganism in the [microorganisms] data set
 #' @inheritSection catalogue_of_life Catalogue of Life
@@ -144,7 +157,7 @@ catalogue_of_life <- list(
 #' - `gender`\cr gender of the patient
 #' - `patient_id`\cr ID of the patient
 #' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms]
-#' - `PEN:RIF`\cr 40 different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in [antibiotics] data set and can be translated with [ab_name()]
+#' - `PEN:RIF`\cr 40 different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
 #' @inheritSection AMR Read more on our website!
 "example_isolates"
 
@@ -181,9 +194,9 @@ catalogue_of_life <- list(
 #' @inheritSection AMR Read more on our website!
 "WHONET"
 
-#' Data set for RSI interpretation
+#' Data set for R/SI interpretation
 #'
-#' Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use [as.rsi()] to transform MICs or disks measurements to RSI values.
+#' 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.
 #' @format A [`data.frame`] with 13,975 observations and 9 variables:
 #' - `guideline`\cr Name of the guideline
 #' - `method`\cr Either "MIC" or "DISK"
@@ -192,34 +205,8 @@ catalogue_of_life <- list(
 #' - `ab`\cr Antibiotic ID, see [as.ab()]
 #' - `ref_tbl`\cr Info about where the guideline rule can be found
 #' - `disk_dose`\cr Dose of the used disk diffusion method
-#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimeters that leads to "S"
-#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimeters that leads to "R"
+#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
+#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
+#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://gitlab.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. This file is updated automatically.
 #' @inheritSection AMR Read more on our website!
 "rsi_translation"
-
-# transforms data set to data.frame with only ASCII values, to comply with CRAN policies
-dataset_UTF8_to_ASCII <- function(df) {
-  trans <- function(vect) {
-    iconv(vect, from = "UTF-8", to = "ASCII//TRANSLIT")
-  }
-  df <- as.data.frame(df, stringsAsFactors = FALSE)
-  for (i in seq_len(NCOL(df))) {
-    col <- df[, i]
-    if (is.list(col)) {
-      for (j in seq_len(length(col))) {
-        col[[j]] <- trans(col[[j]])
-      }
-      df[, i] <- list(col)
-    } else {
-      if (is.factor(col)) {
-        levels(col) <- trans(levels(col))
-      } else if (is.character(col)) {
-        col <- trans(col)
-      } else {
-        col
-      }
-      df[, i] <- col
-    }
-  }
-  df
-}

R/deprecated.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Deprecated functions
 #'
 #' These functions are so-called '[Deprecated]'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
+#' @inheritSection lifecycle Retired lifecycle
 #' @inheritSection AMR Read more on our website!
 #' @export
 #' @keywords internal
@@ -29,7 +30,7 @@
 #' @rdname AMR-deprecated
 p.symbol <- function(...) {
   .Deprecated("p_symbol()", package = "AMR")
-  AMR::p_symbol(...)
+  p_symbol(...)
 }
 
 #' @rdname AMR-deprecated

R/disk.R

@@ -6,41 +6,50 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'disk'
 #'
-#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99.
+#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
+#' @inheritSection lifecycle Stable lifecycle
 #' @rdname as.disk
 #' @param x vector
 #' @param na.rm a logical indicating whether missing values should be removed
 #' @details Interpret disk values as RSI values with [as.rsi()]. It supports guidelines from EUCAST and CLSI.
-#' @return Ordered integer factor with new class [`disk`]
+#' @return An [`integer`] with additional new class [`disk`]
 #' @aliases disk
 #' @export
 #' @seealso [as.rsi()]
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' # interpret disk values
-#' as.rsi(x = 12,
-#'        mo = as.mo("S. pneumoniae"),
-#'        ab = "AMX",
+#' # transform existing disk zones to the `disk` class
+#' library(dplyr)
+#' df <- data.frame(microorganism = "E. coli",
+#'                  AMP = 20,
+#'                  CIP = 14,
+#'                  GEN = 18,
+#'                  TOB = 16)
+#' df <- df %>% mutate_at(vars(AMP:TOB), as.disk)
+#' df
+#' 
+#' # interpret disk values, see ?as.rsi
+#' as.rsi(x = as.disk(18),
+#'        mo = "Strep pneu",  # `mo` will be coerced with as.mo()
+#'        ab = "ampicillin",  # and `ab` with as.ab()
 #'        guideline = "EUCAST")
-#' as.rsi(x = 12,
-#'        mo = as.mo("S. pneumoniae"),
-#'        ab = "AMX",
-#'        guideline = "CLSI")
+#'        
+#' as.rsi(df)
 as.disk <- function(x, na.rm = FALSE) {
   if (is.disk(x)) {
     x
@@ -56,8 +65,8 @@ as.disk <- function(x, na.rm = FALSE) {
     # force it to be integer
     x <- suppressWarnings(as.integer(x))
 
-    # disks can never be less than 9 mm (size of a disk) or more than 50 mm
-    x[x < 6 | x > 99] <- NA_integer_
+    # disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
+    x[x < 6 | x > 50] <- NA_integer_
     na_after <- length(x[is.na(x)])
 
     if (na_before != na_after) {
@@ -80,7 +89,7 @@ as.disk <- function(x, na.rm = FALSE) {
 #' @export
 #' @importFrom dplyr %>%
 is.disk <- function(x) {
-  class(x) %>% identical(c("disk", "integer"))
+  inherits(x, "disk")
 }
 
 #' @exportMethod print.disk

R/eucast_rules.R

@@ -6,29 +6,30 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 # global variables
-EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
+EUCAST_VERSION_BREAKPOINTS <- "10.0, 2020"
 EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 
-#' EUCAST rules
+#' Apply EUCAST rules
 #' 
 #' @description
 #' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. 
 #' 
 #' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param x data with antibiotic columns, like e.g. `AMX` and `AMC`
 #' @param info print progress
 #' @param rules a character vector that specifies which rules should be applied - one or more of `c("breakpoints", "expert", "other", "all")`
@@ -48,6 +49,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
 #' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
 #' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
+#' 
 #' To *not* use these rules, please use `eucast_rules(..., rules = c("breakpoints", "expert"))`.
 #'
 #' The file containing all EUCAST rules is located here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
@@ -200,6 +202,8 @@ eucast_rules <- function(x,
                          verbose = FALSE,
                          ...) {
   
+  check_dataset_integrity()
+  
   if (verbose == TRUE & interactive()) {
     txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",
@@ -562,7 +566,7 @@ eucast_rules <- function(x,
       strsplit(",") %>%
       unlist() %>%
       trimws() %>%
-      sapply(function(x) if (x %in% AMR::antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
+      sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
       sort() %>%
       paste(collapse = ", ")
     x <- gsub("_", " ", x, fixed = TRUE)
@@ -651,9 +655,11 @@ eucast_rules <- function(x,
         cat(bold(
           case_when(
             rule_group_current %like% "breakpoint" ~
-              paste0("\nEUCAST Clinical Breakpoints (v", EUCAST_VERSION_BREAKPOINTS, ")\n"),
+              paste0("\nEUCAST Clinical Breakpoints (",
+                     red(paste0("v", EUCAST_VERSION_BREAKPOINTS)), ")\n"),
             rule_group_current %like% "expert" ~
-              paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"),
+              paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (", 
+                     red(paste0("v", EUCAST_VERSION_EXPERT_RULES)), ")\n"),
             TRUE ~
               "\nOther rules by this AMR package\n"
           )
@@ -662,8 +668,8 @@ eucast_rules <- function(x,
       # Print rule  -------------------------------------------------------------
       if (rule_current != rule_previous) {
         # is new rule within group, print its name
-        if (rule_current %in% c(AMR::microorganisms$family,
-                                AMR::microorganisms$fullname)) {
+        if (rule_current %in% c(microorganisms$family,
+                                microorganisms$fullname)) {
           cat(italic(rule_current))
         } else {
           cat(rule_current)
@@ -679,7 +685,7 @@ eucast_rules <- function(x,
     # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
     if (eucast_rules_df[i, 3] %like% "coagulase-") {
       suppressWarnings(
-        all_staph <- AMR::microorganisms %>%
+        all_staph <- microorganisms %>%
           filter(genus == "Staphylococcus") %>%
           mutate(CNS_CPS = mo_name(mo, Becker = "all"))
       )

R/extended.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Extended functions
 #'
 #' These functions are extensions of functions in other packages.
+#' @inheritSection lifecycle Stable lifecycle
 #' @inheritSection AMR Read more on our website!
 #' @export
 #' @keywords internal

R/filter_ab_class.R

@@ -6,24 +6,25 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Filter isolates on result in antibiotic class
 #'
 #' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x a data set
-#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`AMR::antibiotics$group`][antibiotics]
+#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]
 #' @param result an antibiotic result: S, I or R (or a combination of more of them)
 #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
 #' @param ... parameters passed on to `filter_at` from the `dplyr` package
@@ -66,6 +67,9 @@ filter_ab_class <- function(x,
                             result = NULL,
                             scope = "any",
                             ...) {
+  
+  check_dataset_integrity()
+  
   scope <- scope[1L]
   if (is.null(result)) {
     result <- c("S", "I", "R")
@@ -275,7 +279,7 @@ filter_tetracyclines <- function(x,
 #' @importFrom dplyr %>% filter_at vars any_vars select
 ab_class_vars <- function(ab_class) {
   ab_class <- gsub("[^a-z0-9]+", ".*", ab_class)
-  ab_vars <- AMR::antibiotics %>%
+  ab_vars <- antibiotics %>%
     filter(group %like% ab_class) %>% 
     select(ab:name, abbreviations, synonyms) %>%
     unlist() %>%
@@ -288,7 +292,7 @@ ab_class_vars <- function(ab_class) {
   ab_vars <- ab_vars[!ab_vars %in% c(NA, "", "NA") & nchar(ab_vars) > 2]
   if (length(ab_vars) == 0) {
     # try again, searching atc_group1 and atc_group2 columns
-    ab_vars <- AMR::antibiotics %>%
+    ab_vars <- antibiotics %>%
       filter_at(vars(c("atc_group1", "atc_group2")), any_vars(. %like% ab_class)) %>% 
       select(ab:name, abbreviations, synonyms) %>%
       unlist() %>%
@@ -313,7 +317,7 @@ find_ab_group <- function(ab_class) {
                          "macrolide",
                          "tetracycline"),
          paste0(ab_class, "s"),
-         AMR::antibiotics %>%
+         antibiotics %>%
            filter(ab %in% ab_class_vars(ab_class)) %>%
            pull(group) %>%
            unique() %>%

R/first_isolate.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

R/freq.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -58,14 +58,14 @@ freq.mo <- function(x, ...) {
 freq.rsi <- function(x, ...) {
   x_name <- deparse(substitute(x))
   x_name <- gsub(".*[$]", "", x_name)
-  ab <- suppressMessages(suppressWarnings(AMR::as.ab(x_name)))
+  ab <- suppressMessages(suppressWarnings(as.ab(x_name)))
   if (!is.na(ab)) {
     freq.default(x = x, ...,
                  .add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"),
                                     group = ab_group(ab),
-                                    `%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
+                                    `%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
   } else {
     freq.default(x = x, ...,
-                 .add_header = list(`%SI` = AMR::susceptibility(x, minimum = 0, as_percent = TRUE)))
+                 .add_header = list(`%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
   }
 }

R/g.test.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' *G*-test for Count Data
 #'
 #' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable (1). A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**).
+#' @inheritSection lifecycle Questioning lifecycle
 #' @inherit stats::chisq.test params return
 #' @details If `x` is a matrix with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given.
 #'

R/ggplot_rsi.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' AMR plots with `ggplot2`
 #'
 #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal [ggplot2][ggplot2::ggplot()] functions.
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param data a [`data.frame`] with column(s) of class [`rsi`] (see [as.rsi()])
 #' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
 #' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
@@ -302,7 +303,7 @@ geom_rsi <- function(position = NULL,
   ggplot2::layer(geom = "bar", stat = "identity", position = position,
                  mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
                  params = list(...), data = function(x) {
-                   AMR::rsi_df(data = x,
+                   rsi_df(data = x,
                                translate_ab = translate_ab,
                                language = language,
                                combine_SI = combine_SI,

R/globals.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -25,6 +25,7 @@ globalVariables(c(".",
                   "ab_txt",
                   "abbreviations",
                   "antibiotic",
+                  "antibiotics",
                   "CNS_CPS",
                   "col_id",
                   "count",
@@ -35,6 +36,7 @@ globalVariables(c(".",
                   "first_isolate_row_index",
                   "fullname",
                   "fullname_lower",
+                  "g_species",
                   "genus",
                   "gramstain",
                   "group",
@@ -56,6 +58,7 @@ globalVariables(c(".",
                   "median",
                   "microorganisms",
                   "microorganisms.codes",
+                  "microorganisms.old",
                   "missing_names",
                   "mo",
                   "mono_count",
@@ -81,6 +84,7 @@ globalVariables(c(".",
                   "R",
                   "real_first_isolate",
                   "ref",
+                  "rsi_translation",
                   "rule_group",
                   "rule_name",
                   "S",

R/guess_ab_col.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Guess antibiotic column
 #'
 #' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param x a [`data.frame`]
 #' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
 #' @param verbose a logical to indicate whether additional info should be printed
@@ -125,7 +126,7 @@ get_column_abx <- function(x,
   # only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
   # or already have the rsi class (as.rsi) 
   # and that have no more than 50% invalid values
-  vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
+  vectr_antibiotics <- unique(toupper(unlist(antibiotics[, c("ab", "atc", "name", "abbreviations", "synonyms")])))
   vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
   x_columns <- sapply(colnames(x), function(col, df = x_bak) {
     if (toupper(col) %in% vectr_antibiotics | 
@@ -204,7 +205,7 @@ get_column_abx <- function(x,
       # missing a soft dependency may lower the reliability
       missing <- soft_dependencies[!soft_dependencies %in% names(x)]
       missing_txt <- data.frame(missing = missing,
-                                missing_names = AMR::ab_name(missing, tolower = TRUE),
+                                missing_names = ab_name(missing, tolower = TRUE),
                                 stringsAsFactors = FALSE) %>%
         mutate(txt = paste0(bold(missing), " (", missing_names, ")")) %>%
         arrange(missing_names) %>%

R/join_microorganisms.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Join a table with [microorganisms]
 #'
 #' Join the data set [microorganisms] easily to an existing table or character vector.
+#' @inheritSection lifecycle Stable lifecycle
 #' @rdname join
 #' @name join
 #' @aliases join inner_join
@@ -53,7 +54,7 @@ inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::inner_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::inner_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -68,7 +69,7 @@ left_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::left_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::left_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -83,7 +84,7 @@ right_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::right_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::right_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -98,7 +99,7 @@ full_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
   x <- checked$x
   by <- checked$by
   join <- suppressWarnings(
-    dplyr::full_join(x = x, y = AMR::microorganisms, by = by, suffix = suffix, ...)
+    dplyr::full_join(x = x, y = microorganisms, by = by, suffix = suffix, ...)
   )
   if (nrow(join) > nrow(x)) {
     warning("The newly joined tbl contains ", nrow(join) - nrow(x), " rows more that its original.")
@@ -113,7 +114,7 @@ semi_join_microorganisms <- function(x, by = NULL, ...) {
   x <- checked$x
   by <- checked$by
   suppressWarnings(
-    dplyr::semi_join(x = x, y = AMR::microorganisms, by = by, ...)
+    dplyr::semi_join(x = x, y = microorganisms, by = by, ...)
   )
 }
 
@@ -124,7 +125,7 @@ anti_join_microorganisms <- function(x, by = NULL, ...) {
   x <- checked$x
   by <- checked$by
   suppressWarnings(
-    dplyr::anti_join(x = x, y = AMR::microorganisms, by = by, ...)
+    dplyr::anti_join(x = x, y = microorganisms, by = by, ...)
   )
 }
 
@@ -148,7 +149,7 @@ joins_check_df <- function(x, by) {
     message('Joining, by = "', by, '"') # message same as dplyr::join functions
   }
   if (is.null(names(by))) {
-    joinby <- colnames(AMR::microorganisms)[1]
+    joinby <- colnames(microorganisms)[1]
     names(joinby) <- by
   } else {
     joinby <- by

R/key_antibiotics.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Key antibiotics for first *weighted* isolates
 #'
 #' These function can be used to determine first isolates (see [first_isolate()]). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first *weighted* isolates.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x table with antibiotics coloms, like `AMX` or `amox`
 #' @param y,z characters to compare
 #' @inheritParams first_isolate

R/kurtosis.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Kurtosis of the sample
 #'
 #' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
+#' @inheritSection lifecycle Questioning lifecycle
 #' @param x a vector of values, a [`matrix`] or a [`data.frame`]
 #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
 #' @exportMethod kurtosis

R/lifecycle.R

@@ -0,0 +1,56 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+###############
+# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add another dependency for such an easy job?
+###############
+
+#' Lifecycles of functions in the `AMR` package
+#' @name lifecycle
+#' @rdname lifecycle
+#' @description Our functions are categorised using [the lifecycle circle of the `tidyverse` as found on www.tidyverse.org/lifecycle](https://www.tidyverse.org/lifecycle).
+#' 
+#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height=200px style=margin-bottom:5px} \cr}
+#' This page contains a section for every lifecycle (with text borrowed from the aforementioned `tidyverse` website), so they can be used in the manual pages of our functions. 
+#' @section Experimental lifecycle:
+#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in the very early stages of development. The unlying code might be changing frequently as we rapidly iterate and explore variations in search of the best fit. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions will not be included in releases we submit to CRAN.
+#' @section Maturing lifecycle:
+#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.
+#' @section Stable lifecycle:
+#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+#' 
+#' If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+#' @section Retired lifecycle:
+#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. We will only make the necessary changes to ensure that retired functions remain available. No new arguments will be added, and only the most critical bugs will be fixed.
+#' @section Archived lifecycle:
+#' \if{html}{\figure{lifecycle_archived.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **archived**. The development of an archived function has ended, and it is no longer available in future package versions.
+#' @section Dormant lifecycle:
+#' \if{html}{\figure{lifecycle_dormant.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **dormant**. A dormant function is currently not under active development and has not reached a stable phase. We might return to it in the future. As with experimental functions, you are best off waiting until a function is more mature before you use it in production code.
+#' @section Questioning lifecycle:
+#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
+#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our `AMR` package at all.
+NULL

R/like.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Pattern Matching
 #'
-#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) to compare items of each index in both vectors, or can both have the same length to iterate over all cases.
+#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
 #' @param pattern a character string containing a regular expression (or [`character`] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible.  If a [`character`] vector of length 2 or more is supplied, the first element is used with a warning.
 #' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
@@ -44,15 +45,15 @@
 #'
 #' # also supports multiple patterns, length must be equal to x
 #' a <- c("Test case", "Something different", "Yet another thing")
-#' b <- c("case", "diff", "yet")
+#' b <- c(     "case",           "diff",      "yet")
 #' a %like% b
 #' #> TRUE TRUE TRUE
 #'
 #' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
 #' library(dplyr)
 #' example_isolates %>%
-#'   filter(mo_genus(mo) %like% '^ent') %>%
-#'   freq(mo_fullname(mo))
+#'   filter(mo_name(mo) %like% '^ent') %>%
+#'   freq(mo_genus(mo))
 like <- function(x, pattern, ignore.case = TRUE) {
   if (length(pattern) > 1) {
     if (length(x) != length(pattern)) {

R/mdro.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Determine multidrug-resistant organisms (MDRO)
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
 #' @param info a logical to indicate whether progress should be printed to the console
 #' @inheritParams eucast_rules
@@ -89,6 +90,8 @@ mdro <- function(x,
                  verbose = FALSE,
                  ...) {
   
+  check_dataset_integrity()
+  
   if (verbose == TRUE & interactive()) {
     txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",
@@ -146,7 +149,7 @@ mdro <- function(x,
   if (is.null(col_mo) & guideline$code == "tb") {
     message(blue("NOTE: No column found as input for `col_mo`,",
                  bold("assuming all records contain", italic("Mycobacterium tuberculosis.\n"))))
-    x$mo <- AMR::as.mo("Mycobacterium tuberculosis")
+    x$mo <- as.mo("Mycobacterium tuberculosis")
     col_mo <- "mo"
   }
   if (is.null(col_mo)) {

R/mic.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'mic'
 #'
 #' This transforms a vector to a new class [`mic`], which is an ordered [`factor`] with valid MIC values as levels. Invalid MIC values will be translated as `NA` with a warning.
+#' @inheritSection lifecycle Stable lifecycle
 #' @rdname as.mic
 #' @param x vector
 #' @param na.rm a logical indicating whether missing values should be removed
@@ -129,7 +130,7 @@ as.mic <- function(x, na.rm = FALSE) {
 #' @export
 #' @importFrom dplyr %>%
 is.mic <- function(x) {
-  class(x) %>% identical(c("mic", "ordered", "factor"))
+  inherits(x, "mic")
 }
 
 #' @exportMethod as.double.mic

R/misc.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -29,12 +29,26 @@ addin_insert_like <- function() {
   rstudioapi::insertText(" %like% ")
 }
 
-load_AMR_package <- function() {
-  if (!"package:AMR" %in% base::search()) {
-    require(AMR)
-    # check onLoad() in R/zzz.R: data tables are created there.
+check_dataset_integrity <- function() {
+  tryCatch({
+    check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
+                                  "class", "order", "family", "genus", 
+                                  "species", "subspecies", "rank",
+                                  "col_id", "species_id", "source",
+                                  "ref", "prevalence", "snomed") %in% colnames(microorganisms),
+                                na.rm = TRUE) & NROW(microorganisms) == NROW(microorganismsDT)
+    check_antibiotics <- all(c("ab", "atc", "cid", "name", "group", 
+                               "atc_group1", "atc_group2", "abbreviations",
+                               "synonyms", "oral_ddd", "oral_units", 
+                               "iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
+                             na.rm = TRUE)
+  }, error = function(e)
+    stop('Please use the command \'library("AMR")\' before using this function, to load the needed reference data.', call. = FALSE)
+  )
+  if (!check_microorganisms | !check_antibiotics) {
+    stop("Data set `microorganisms` or data set `antibiotics` is overwritten by your global environment and prevents the AMR package from working correctly. Please rename your object before using this function.", call. = FALSE)
   }
-  base::invisible()
+  invisible(TRUE)
 }
 
 #' @importFrom crayon blue bold red
@@ -117,7 +131,10 @@ search_type_in_df <- function(x, type) {
 stopifnot_installed_package <- function(package) {
   # no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
   # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
-  get(".packageName", envir = asNamespace(package))
+  tryCatch(get(".packageName", envir = asNamespace(package)),
+           error = function(e) stop("package '", package, "' required but not installed",
+                                    ' - try to install it with: install.packages("', package, '")',
+                                    call. = FALSE))
   return(invisible())
 }
 
@@ -141,3 +158,28 @@ class_integrity_check <- function(value, type, check_vector) {
   }
   value
 }
+
+# transforms data set to data.frame with only ASCII values, to comply with CRAN policies
+dataset_UTF8_to_ASCII <- function(df) {
+  trans <- function(vect) {
+    iconv(vect, from = "UTF-8", to = "ASCII//TRANSLIT")
+  }
+  df <- as.data.frame(df, stringsAsFactors = FALSE)
+  for (i in seq_len(NCOL(df))) {
+    col <- df[, i]
+    if (is.list(col)) {
+      col <- lapply(col, function(j) trans(j))
+      df[, i] <- list(col)
+    } else {
+      if (is.factor(col)) {
+        levels(col) <- trans(levels(col))
+      } else if (is.character(col)) {
+        col <- trans(col)
+      } else {
+        col
+      }
+      df[, i] <- col
+    }
+  }
+  df
+}

R/mo_history.R

@@ -1,199 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# SOURCE                                                               #
-# https://gitlab.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
-#                                                                      #
-# 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.                                        #
-#                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
-# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
-# ==================================================================== #
-
-# print successful as.mo coercions to a options entry
-#' @importFrom dplyr %>% distinct filter
-#' @importFrom utils write.csv
-set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FALSE) {
-  if (isTRUE(disable)) {
-    return(base::invisible())
-  }
-  
-  # don't save codes that are in a code data set already
-  mo <- mo[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
-  x <- x[!x %in% microorganisms.codes$code & !x %in% microorganisms.translation$mo_old]
-  
-  warning_new_write <- FALSE
-  
-  if (base::interactive() | force == TRUE) {
-    mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
-    df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
-      distinct(x, .keep_all = TRUE) %>%
-      filter(!is.na(x) & !is.na(mo))
-    if (nrow(df) == 0) {
-      return(base::invisible())
-    }
-    x <- toupper(df$x)
-    mo <- df$mo
-    for (i in seq_len(length(x))) {
-      # save package version too, as both the as.mo() algorithm and the reference data set may change
-      if (NROW(mo_hist[base::which(mo_hist$x == x[i] &
-                                   mo_hist$uncertainty_level >= uncertainty_level &
-                                   mo_hist$package_version == utils::packageVersion("AMR")), ]) == 0) {
-        if (is.null(mo_hist) & interactive()) {
-          warning_new_write <- TRUE
-        }
-        tryCatch(write.csv(rbind(mo_hist,
-                                 data.frame(
-                                   x = x[i],
-                                   mo = mo[i],
-                                   uncertainty_level = uncertainty_level,
-                                   package_version = base::as.character(utils::packageVersion("AMR")),
-                                   stringsAsFactors = FALSE)),
-                           row.names = FALSE,
-                           file = mo_history_file()),
-                 error = function(e) {
-                   warning_new_write <- FALSE; base::invisible()
-                 })
-      }
-    }
-  }
-  if (warning_new_write == TRUE) {
-    message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
-  }
-  return(base::invisible())
-}
-
-get_mo_history <- function(x, uncertainty_level, force = FALSE, disable = FALSE) {
-  if (isTRUE(disable)) {
-    return(to_class_mo(NA))
-  }
-  
-  history <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
-  if (base::is.null(history)) {
-    result <- NA
-  } else {
-    result <- data.frame(x = as.character(toupper(x)), stringsAsFactors = FALSE) %>%
-      left_join(history, by = "x") %>%
-      pull(mo)
-  }
-  to_class_mo(result)
-}
-
-#' @importFrom dplyr %>% filter distinct
-#' @importFrom utils read.csv
-read_mo_history <- function(uncertainty_level = 2, force = FALSE, unfiltered = FALSE, disable = FALSE) {
-  if (isTRUE(disable)) {
-    return(NULL)
-  }
-  
-  if ((!base::interactive() & force == FALSE)) {
-    return(NULL)
-  }
-  uncertainty_level_param <- uncertainty_level
-  
-  history <- tryCatch(read.csv(mo_history_file(), stringsAsFactors = FALSE),
-                      warning = function(w) invisible(),
-                      error = function(e) NULL)
-  if (is.null(history)) {
-    return(NULL)
-  }
-  # Below: filter on current package version.
-  # Even current fullnames may be replaced by new taxonomic names, so new versions of
-  # the Catalogue of Life must not lead to data corruption.
-  
-  if (unfiltered == FALSE) {
-    history <- history %>%
-      filter(package_version == as.character(utils::packageVersion("AMR")),
-             # only take unknowns if uncertainty_level_param is higher
-             ((mo == "UNKNOWN" & uncertainty_level_param == uncertainty_level) |
-                (mo != "UNKNOWN" & uncertainty_level_param >= uncertainty_level))) %>%
-      arrange(desc(uncertainty_level)) %>%
-      distinct(x, mo, .keep_all = TRUE)
-  }
-  
-  if (nrow(history) == 0) {
-    NULL
-  } else {
-    history
-  }
-}
-
-#' @rdname as.mo
-#' @importFrom crayon red
-#' @importFrom utils menu
-#' @export
-clear_mo_history <- function(...) {
-  if (!is.null(read_mo_history())) {
-    if (interactive() & !isTRUE(list(...)$force)) {
-      q <- menu(title = paste("This will clear all",
-                              format(nrow(read_mo_history(999, unfiltered = TRUE)), big.mark = ","),
-                              "previously determined microbial IDs. Are you sure?"),
-                choices = c("Yes", "No"),
-                graphics = FALSE)
-      if (q != 1) {
-        return(invisible())
-      }
-    }
-
-    success <- create_blank_mo_history()
-    if (!isFALSE(success)) {
-      cat(red(paste("File", mo_history_file(), "cleared.")))
-    }
-  }
-}
-
-#' @importFrom utils write.csv
-create_blank_mo_history <- function() {
-  tryCatch(
-    write.csv(x = data.frame(x = character(0),
-                             mo = character(0),
-                             uncertainty_level = integer(0),
-                             package_version = character(0),
-                             stringsAsFactors = FALSE),
-              row.names = FALSE,
-              file = mo_history_file()),
-    warning = function(w) invisible(),
-    error = function(e) TRUE)
-}
-
-
-# Borrowed all below code from the extrafont package,
-# https://github.com/wch/extrafont/blob/254c3f99b02f11adb59affbda699a92aec8624f5/R/utils.r
-inst_path <- function() {
-  envname <- environmentName(parent.env(environment()))
-  
-  # If installed in package, envname == "AMR"
-  # If loaded with load_all, envname == "package:AMR"
-  # (This is kind of strange)
-  if (envname == "AMR") {
-    system.file(package = "AMR")
-  } else {
-    srcfile <- attr(attr(inst_path, "srcref"), "srcfile")
-    file.path(dirname(dirname(srcfile$filename)), "inst")
-  }
-}
-
-
-# Get the path where extrafontdb is installed
-db_path <- function() {
-  system.file(package = "AMR")
-}
-
-# fonttable file
-mo_history_file <- function() {
-  file.path(mo_history_path(), "mo_history.csv")
-}
-
-# Path of fontmap directory
-mo_history_path <- function() {
-  file.path(db_path(), "mo_history")
-}

R/mo_property.R

@@ -6,22 +6,22 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Property of a microorganism
 #'
-#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
+#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
 #' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
 #' @param property one of the column names of the [microorganisms] data set or `"shortname"`
 #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
@@ -32,7 +32,7 @@
 #' - `mo_ref("Chlamydia psittaci")` will return `"Page, 1968"` (with a warning about the renaming)
 #' - `mo_ref("Chlamydophila psittaci")` will return `"Everett et al., 1999"` (without a warning)
 #'
-#' The Gram stain - [mo_gramstain()] - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value `NA`.
+#' The Gram stain - [mo_gramstain()] - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`.
 #'
 #' All output will be [translate]d where possible.
 #'
@@ -43,8 +43,9 @@
 #' @name mo_property
 #' @return
 #' - An [`integer`] in case of [mo_year()]
-#' - A [`list`] in case of [mo_taxonomy()]
+#' - A [`list`] in case of [mo_taxonomy()] and [mo_info()]
 #' - A named [`character`] in case of [mo_url()]
+#' - A [`double`] in case of [mo_snomed()]
 #' - A [`character`] in all other cases
 #' @export
 #' @seealso [microorganisms]
@@ -62,11 +63,12 @@
 #'
 #' # colloquial properties ----------------------------------------------------
 #' mo_name("E. coli")            # "Escherichia coli"
-#' mo_fullname("E. coli")        # "Escherichia coli", same as mo_name()
+#' mo_fullname("E. coli")        # "Escherichia coli" - same as mo_name()
 #' mo_shortname("E. coli")       # "E. coli"
 #'
 #' # other properties ---------------------------------------------------------
 #' mo_gramstain("E. coli")       # "Gram-negative"
+#' mo_snomed("E. coli")          # 112283007, 116395006, ... (SNOMED codes)
 #' mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
 #' mo_rank("E. coli")            # "species"
 #' mo_url("E. coli")             # get the direct url to the online database entry
@@ -143,7 +145,7 @@ mo_fullname <- mo_name
 #' @rdname mo_property
 #' @export
 mo_shortname <- function(x, language = get_locale(), ...) {
-  x.mo <- AMR::as.mo(x, ...)
+  x.mo <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   replace_empty <- function(x) {
@@ -221,7 +223,7 @@ mo_type <- function(x, language = get_locale(), ...) {
 #' @rdname mo_property
 #' @export
 mo_gramstain <- function(x, language = get_locale(), ...) {
-  x.mo <- AMR::as.mo(x, ...)
+  x.mo <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   x.phylum <- mo_phylum(x.mo)
@@ -249,6 +251,12 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
   translate_AMR(x, language = language, only_unknown = FALSE)
 }
 
+#' @rdname mo_property
+#' @export
+mo_snomed <- function(x, ...) {
+  mo_validate(x = x, property = "snomed", ...)
+}
+
 #' @rdname mo_property
 #' @export
 mo_ref <- function(x, ...) {
@@ -282,17 +290,17 @@ mo_rank <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 mo_taxonomy <- function(x, language = get_locale(),  ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
-  result <- base::list(kingdom = AMR::mo_kingdom(x, language = language),
-             phylum = AMR::mo_phylum(x, language = language),
-             class = AMR::mo_class(x, language = language),
-             order = AMR::mo_order(x, language = language),
-             family = AMR::mo_family(x, language = language),
-             genus = AMR::mo_genus(x, language = language),
-             species = AMR::mo_species(x, language = language),
-             subspecies = AMR::mo_subspecies(x, language = language))
+  result <- base::list(kingdom = mo_kingdom(x, language = language),
+             phylum = mo_phylum(x, language = language),
+             class = mo_class(x, language = language),
+             order = mo_order(x, language = language),
+             family = mo_family(x, language = language),
+             genus = mo_genus(x, language = language),
+             species = mo_species(x, language = language),
+             subspecies = mo_subspecies(x, language = language))
 
   load_mo_failures_uncertainties_renamed(metadata)
   result
@@ -301,12 +309,12 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
 #' @rdname mo_property
 #' @export
 mo_synonyms <- function(x, ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
-  IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL)
+  IDs <- mo_property(x = x, property = "col_id", language = NULL)
   syns <- lapply(IDs, function(col_id) {
-    res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"])
+    res <- sort(microorganisms.old[which(microorganisms.old$col_id_new == col_id), "fullname"])
     if (length(res) == 0) {
       NULL
     } else {
@@ -327,7 +335,7 @@ mo_synonyms <- function(x, ...) {
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_locale(),  ...) {
-  x <- AMR::as.mo(x, ...)
+  x <- as.mo(x, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   info <- lapply(x, function(y)
@@ -352,12 +360,12 @@ mo_info <- function(x, language = get_locale(),  ...) {
 #' @importFrom dplyr %>% left_join select mutate case_when
 #' @export
 mo_url <- function(x, open = FALSE, ...) {
-  mo <- AMR::as.mo(x = x, ... = ...)
-  mo_names <- AMR::mo_name(mo)
+  mo <- as.mo(x = x, ... = ...)
+  mo_names <- mo_name(mo)
   metadata <- get_mo_failures_uncertainties_renamed()
 
   df <- data.frame(mo, stringsAsFactors = FALSE) %>%
-    left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
+    left_join(select(microorganisms, mo, source, species_id), by = "mo") %>%
     mutate(url = case_when(source == "CoL" ~
                              paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
                            source == "DSMZ" ~
@@ -386,7 +394,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
   if (length(property) != 1L) {
     stop("'property' must be of length 1.")
   }
-  if (!property %in% colnames(AMR::microorganisms)) {
+  if (!property %in% colnames(microorganisms)) {
     stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
   }
 
@@ -395,7 +403,7 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
 
 mo_validate <- function(x, property, ...) {
   
-  load_AMR_package()
+  check_dataset_integrity()
 
   dots <- list(...)
   Becker <- dots$Becker
@@ -409,7 +417,7 @@ mo_validate <- function(x, property, ...) {
 
   # try to catch an error when inputting an invalid parameter
   # so the 'call.' can be set to FALSE
-  tryCatch(x[1L] %in% AMR::microorganisms[1, property],
+  tryCatch(x[1L] %in% microorganisms[1, property],
            error = function(e) stop(e$message, call. = FALSE))
   
   if (is.mo(x) 
@@ -418,7 +426,7 @@ mo_validate <- function(x, property, ...) {
     # this will not reset mo_uncertainties and mo_failures
     # because it's already a valid MO
     x <- exec_as.mo(x, property = property, initial_search = FALSE, ...)
-  } else if (!all(x %in% pull(AMR::microorganisms, property))
+  } else if (!all(x %in% pull(microorganisms, property))
              | Becker %in% c(TRUE, "all")
              | Lancefield %in% c(TRUE, "all")) {
     x <- exec_as.mo(x, property = property, ...)
@@ -428,6 +436,8 @@ mo_validate <- function(x, property, ...) {
     return(to_class_mo(x))
   } else if (property == "col_id") {
     return(as.integer(x))
+  } else if (property == "snomed") {
+    return(as.double(eval(parse(text = x))))
   } else {
     return(x)
   }

R/mo_source.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -24,6 +24,7 @@
 #' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
 #'
 #' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param path location of your reference file, see Details
 #' @rdname mo_source
 #' @name mo_source
@@ -40,12 +41,12 @@
 #' 
 #' Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
 #' ```
-#'   |         A          |      B      |
-#' --|--------------------|-------------|
-#' 1 | Organisation XYZ   | mo          |
-#' 2 | lab_mo_ecoli       | B_ESCHR_COL |
-#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
-#' 4 |                    |             |
+#'   |         A          |       B      |
+#' --|--------------------|--------------|
+#' 1 | Organisation XYZ   | mo           |
+#' 2 | lab_mo_ecoli       | B_ESCHR_COLI |
+#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
+#' 4 |                    |              |
 #' ```
 #'
 #' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
@@ -59,7 +60,7 @@
 #' And now we can use it in our functions:
 #' ```
 #' as.mo("lab_mo_ecoli")
-#' \[1\] B_ESCHR_COLI
+#' [1] B_ESCHR_COLI
 #'
 #' mo_genus("lab_mo_kpneumoniae")
 #' [1] "Klebsiella"
@@ -69,7 +70,7 @@
 #' [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
 #' ```
 #'
-#' If we edit the Excel file to, let's say, this:
+#' If we edit the Excel file to, let's say, by adding row 4 like this:
 #' ```
 #'   |         A          |       B      |
 #' --|--------------------|--------------|
@@ -80,7 +81,7 @@
 #' 5 |                    |              |
 #' ```
 #'
-#' ...any new usage of an MO function in this package will update your data:
+#' ...any new usage of an MO function in this package will update your data file:
 #' ```
 #' as.mo("lab_mo_ecoli")
 #' # Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
@@ -90,9 +91,8 @@
 #' [1] "Staphylococcus"
 #' ```
 #'
-#' To remove the reference completely, just use any of these:
+#' To remove the reference data file completely, just use `""` or `NULL` as input for `[set_mo_source()]`:
 #' ```
-#' set_mo_source("")
 #' set_mo_source(NULL)
 #' # Removed mo_source file '~/.mo_source.rds'.
 #' ```
@@ -126,9 +126,7 @@ set_mo_source <- function(path) {
 
   } else if (path %like% "[.]xlsx?$") {
     # is Excel file (old or new)
-    if (!"readxl" %in% utils::installed.packages()) {
-      stop("Install the 'readxl' package first.")
-    }
+    stopifnot_installed_package("readxl")
     df <- readxl::read_excel(path)
 
   } else if (path %like% "[.]tsv$") {
@@ -204,6 +202,9 @@ get_mo_source <- function() {
 }
 
 mo_source_isvalid <- function(x) {
+  
+  check_dataset_integrity()
+  
   if (deparse(substitute(x)) == "get_mo_source()") {
     return(TRUE)
   }
@@ -219,5 +220,5 @@ mo_source_isvalid <- function(x) {
   if (!"mo" %in% colnames(x)) {
     return(FALSE)
   }
-  all(x$mo %in% c("", AMR::microorganisms$mo))
+  all(x$mo %in% c("", microorganisms$mo, microorganisms.translation$mo_old), na.rm = TRUE)
 }

R/p_symbol.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Symbol of a p-value
 #'
 #' Return the symbol related to the p-value: 0 '`***`' 0.001 '`**`' 0.01 '`*`' 0.05 '`.`' 0.1 ' ' 1. Values above `p = 1` will return `NA`.
+#' @inheritSection lifecycle Questioning lifecycle
 #' @param p p value
 #' @param emptychar text to show when `p > 0.1`
 #' @return Text

R/proportion.R

@@ -6,24 +6,25 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Calculate microbial resistance
 #'
-#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in [dplyr::summarise()] and support grouped variables, please see *Examples*.
+#' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in `summarise()`][dplyr::summarise()] and also support grouped variables, please see *Examples*.
 #'
 #' [resistance()] should be used to calculate resistance, [susceptibility()] should be used to calculate susceptibility.\cr
+#' @inheritSection lifecycle Stable lifecycle
 #' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.
 #' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.
 #' @param as_percent a logical to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of `0.123456` will then be returned as `"12.3%"`.
@@ -39,11 +40,11 @@
 #'  
 #' **Remember that you should filter your table to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set.
 #'
-#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can infuence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).*
+#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the `count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` parameter).*
 #'
 #' The function [proportion_df()] takes any variable from `data` that has an [`rsi`] class (created with [as.rsi()]) and calculates the proportions R, I and S. The function [rsi_df()] works exactly like [proportion_df()], but adds the number of isolates.
 #' @section Combination therapy:
-#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Antibiotic A and Antibiotic B, about how [susceptibility()] works to calculate the %SI:
+#' When using more than one variable for `...` (= combination therapy)), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI:
 #'
 #' ```
 #' --------------------------------------------------------------------

R/read.4d.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 #
 #' Read data from 4D database
 #'
 #' This function is only useful for the MMB department of the UMCG. Use this function to **import data by just defining the `file` parameter**. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the MO codes with [as.mo()] and transform all antimicrobial columns with [as.rsi()].
+#' @inheritSection lifecycle Dormant lifecycle
 #' @inheritParams utils::read.table
 #' @param info a logical to indicate whether info about the import should be printed, defaults to `TRUE` in interactive sessions
 #' @details Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.

R/resistance_predict.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Predict antimicrobial resistance
 #'
 #' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
+#' @inheritSection lifecycle Maturing lifecycle
 #' @param col_ab column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`)
 #' @param col_date column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class
 #' @param year_min lowest year to use in the prediction model, dafaults to the lowest year in `col_date`

R/rsi.R

@@ -6,37 +6,40 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Class 'rsi'
 #'
 #' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
+#' @inheritSection lifecycle Stable lifecycle
 #' @rdname as.rsi
-#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimeters)
-#' @param mo a microorganism code, generated with [as.mo()]
-#' @param ab an antimicrobial code, generated with [as.ab()]
+#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
+#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
+#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
 #' @inheritParams first_isolate
-#' @param guideline defaults to the latest included EUCAST guideline, run `unique(AMR::rsi_translation$guideline)` for all options
+#' @param guideline defaults to the latest included EUCAST guideline, run `unique(rsi_translation$guideline)` for all options
 #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
 #' @param ... parameters passed on to methods
-#' @details Run `unique(AMR::rsi_translation$guideline)` for a list of all supported guidelines.
+#' @details Run `unique(rsi_translation$guideline)` for a list of all supported guidelines. The repository of this package contains [this machine readable version](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of these guidelines.
+#' 
+#' These guidelines are machine readable, since [](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt).
 #'
 #' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 #'
 #' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter.
 #' @section Interpretation of R and S/I:
-#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<http://www.eucast.org/newsiandr/>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
+#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<http://www.eucast.org/newsiandr/>).
 #'
 #' - **R = Resistant**\cr
 #'   A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
@@ -53,37 +56,50 @@
 #' @seealso [as.mic()]
 #' @inheritSection AMR Read more on our website!
 #' @examples
-#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
-#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
-#' is.rsi(rsi_data)
-#'
-#' # this can also coerce combined MIC/RSI values:
-#' as.rsi("<= 0.002; S") # will return S
-#'
-#' # interpret MIC values
+#' # For INTERPRETING disk diffusion and MIC values -----------------------
+#' 
+#' # single values
 #' as.rsi(x = as.mic(2),
 #'        mo = as.mo("S. pneumoniae"),
-#'        ab = "AMX",
-#'        guideline = "EUCAST")
-#' as.rsi(x = as.mic(4),
-#'        mo = as.mo("S. pneumoniae"),
-#'        ab = "AMX",
+#'        ab = "AMP",
 #'        guideline = "EUCAST")
 #'
+#' as.rsi(x = as.disk(18),
+#'        mo = "Strep pneu",  # `mo` will be coerced with as.mo()
+#'        ab = "ampicillin",  # and `ab` with as.ab()
+#'        guideline = "EUCAST")
+#'        
+#' # a whole data set, even with combined MIC values and disk zones
+#' df <- data.frame(microorganism = "E. coli",
+#'                  AMP = as.mic(8),
+#'                  CIP = as.mic(0.256),
+#'                  GEN = as.disk(18),
+#'                  TOB = as.disk(16))
+#' as.rsi(df)
+#'
+#'
+#' # For CLEANING existing R/SI values ------------------------------------
+#' 
+#' as.rsi(c("S", "I", "R", "A", "B", "C"))
+#' as.rsi("<= 0.002; S") # will return "S"
+#' 
+#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
+#' is.rsi(rsi_data)
 #' plot(rsi_data)    # for percentages
 #' barplot(rsi_data) # for frequencies
 #' freq(rsi_data)    # frequency table with informative header
 #'
-#' # using dplyr's mutate
 #' library(dplyr)
 #' example_isolates %>%
 #'   mutate_at(vars(PEN:RIF), as.rsi)
 #'
-#'
-#' # fastest way to transform all columns with already valid AB results to class `rsi`:
+#' # fastest way to transform all columns with already valid AMR results to class `rsi`:
 #' example_isolates %>%
-#'   mutate_if(is.rsi.eligible,
-#'             as.rsi)
+#'   mutate_if(is.rsi.eligible, as.rsi)
+#'   
+#' # note: from dplyr 1.0.0 on, this will be: 
+#' # example_isolates %>%
+#' #   mutate(across(is.rsi.eligible, as.rsi))
 #'
 #' # default threshold of `is.rsi.eligible` is 5%.
 #' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
@@ -185,7 +201,7 @@ as.rsi.disk <- function(x, mo, ab, guideline = "EUCAST", ...) {
 get_guideline <- function(guideline) {
   guideline_param <- toupper(guideline)
   if (guideline_param %in% c("CLSI", "EUCAST")) {
-    guideline_param <- AMR::rsi_translation %>%
+    guideline_param <- rsi_translation %>%
       filter(guideline %like% guideline_param) %>%
       pull(guideline) %>%
       sort() %>%
@@ -193,9 +209,9 @@ get_guideline <- function(guideline) {
       .[1]
   }
   
-  if (!guideline_param %in% AMR::rsi_translation$guideline) {
+  if (!guideline_param %in% rsi_translation$guideline) {
     stop(paste0("invalid guideline: '", guideline,
-                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(AMR::rsi_translation$guideline))), "'", collapse = ", ")),
+                "'.\nValid guidelines are: ", paste0("'", rev(sort(unique(rsi_translation$guideline))), "'", collapse = ", ")),
          call. = FALSE)
   }
   
@@ -219,23 +235,25 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
   mo_order <- as.mo(mo_order(mo))
   mo_becker <- as.mo(mo, Becker = TRUE)
   mo_lancefield <- as.mo(mo, Lancefield = TRUE)
+  mo_other <- as.mo("other")
   
   guideline_coerced <- get_guideline(guideline)
   if (guideline_coerced != guideline) {
     message(blue(paste0("Note: Using guideline ", bold(guideline_coerced), " as input for `guideline`.")))
   }
-
+  
   new_rsi <- rep(NA_character_, length(x))
-  trans <- AMR::rsi_translation %>%
+  trans <- rsi_translation %>%
     filter(guideline == guideline_coerced & method == method_param) %>%
     mutate(lookup = paste(mo, ab))
-
+  
   lookup_mo <- paste(mo, ab)
   lookup_genus <- paste(mo_genus, ab)
   lookup_family <- paste(mo_family, ab)
   lookup_order <- paste(mo_order, ab)
   lookup_becker <- paste(mo_becker, ab)
   lookup_lancefield <- paste(mo_lancefield, ab)
+  lookup_other <- paste(mo_other, ab)
   
   for (i in seq_len(length(x))) {
     get_record <- trans %>%
@@ -244,7 +262,8 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
                            lookup_family[i],
                            lookup_order[i],
                            lookup_becker[i],
-                           lookup_lancefield[i])) %>%
+                           lookup_lancefield[i],
+                           lookup_other[i])) %>%
       # be as specific as possible (i.e. prefer species over genus):
       arrange(desc(nchar(mo))) %>%
       .[1L, ]
@@ -303,7 +322,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
         message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
         next
       }
-      message(blue(paste0("Interpreting column `", bold(ab_cols[i]), "` (",
+      message(blue(paste0("Interpreting MIC values of column `", bold(ab_cols[i]), "` (",
                           ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
                           ab_name(ab_col_coerced, tolower = TRUE), ")...")),
               appendLF = FALSE)
@@ -324,7 +343,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
         message(red(paste0("Unknown drug: `", bold(ab_cols[i]), "`. Rename this column to a drug name or code, and check the output with as.ab().")))
         next
       }
-      message(blue(paste0("Interpreting column `", bold(ab_cols[i]), "` (",
+      message(blue(paste0("Interpreting disk zones of column `", bold(ab_cols[i]), "` (",
                           ifelse(ab_col_coerced != ab_cols[i], paste0(ab_col_coerced, ", "), ""),
                           ab_name(ab_col_coerced, tolower = TRUE), ")...")),
               appendLF = FALSE)
@@ -343,8 +362,7 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
 #' @rdname as.rsi
 #' @export
 is.rsi <- function(x) {
-  identical(class(x),
-            c("rsi", "ordered", "factor"))
+  inherits(x, "rsi")
 }
 
 #' @rdname as.rsi

R/rsi_calc.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -179,6 +179,8 @@ rsi_calc_df <- function(type, # "proportion" or "count"
                         combine_IR = FALSE,
                         combine_SI_missing = FALSE) {
   
+  check_dataset_integrity()
+  
   if (!"data.frame" %in% class(data)) {
     stop(paste0("`", type, "_df` must be called on a data.frame"), call. = FALSE)
   }
@@ -252,7 +254,7 @@ rsi_calc_df <- function(type, # "proportion" or "count"
     arrange(antibiotic, interpretation)
   
   if (!translate_ab == FALSE) {
-    res <- res %>% mutate(antibiotic = AMR::ab_property(antibiotic, property = translate_ab, language = language))
+    res <- res %>% mutate(antibiotic = ab_property(antibiotic, property = translate_ab, language = language))
   }
   
   as.data.frame(res, stringsAsFactors = FALSE)

R/rsi_df.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

R/skewness.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -24,6 +24,7 @@
 #' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
 #'
 #' When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.
+#' @inheritSection lifecycle Questioning lifecycle
 #' @param x a vector of values, a [`matrix`] or a [`data.frame`]
 #' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
 #' @exportMethod skewness

R/translate.R

@@ -6,22 +6,23 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
 #' Translate strings from AMR package
 #'
 #' For language-dependent output of AMR functions, like [mo_name()], [mo_type()] and [ab_name()].
+#' @inheritSection lifecycle Stable lifecycle
 #' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv>.
 #'
 #' Currently supported languages can be found if running: `unique(AMR:::translations_file$lang)`.

R/whocc.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

R/zzz.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -23,19 +23,14 @@
 .onLoad <- function(libname, pkgname) {
   # get new functions not available in older versions of R
   backports::import(pkgname)
-
+  
   # register data
-  microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
-  # for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
-  microorganisms.oldDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganisms.oldDT$fullname))
-  setkey(microorganisms.oldDT, prevalence, fullname)
-
   assign(x = "microorganismsDT",
          value = make_DT(),
          envir = asNamespace("AMR"))
 
   assign(x = "microorganisms.oldDT",
-         value = microorganisms.oldDT,
+         value = make_oldDT(),
          envir = asNamespace("AMR"))
 
   assign(x = "mo_codes_v0.5.0",
@@ -62,7 +57,9 @@ make_DT <- function() {
                                  # work with Viridans Group Streptococci, etc.
                                  tolower(trimws(ifelse(genus == "",
                                                        fullname,
-                                                       paste(genus, species, subspecies)))))) %>% 
+                                                       paste(genus, species, subspecies))))),
+           # add a column with only "e coli" like combinations
+           g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>% 
     as.data.table()
   
   # so arrange data on prevalence first, then kingdom, then full name
@@ -73,6 +70,25 @@ make_DT <- function() {
   microorganismsDT
 }
 
+#' @importFrom data.table as.data.table setkey
+#' @importFrom dplyr %>% mutate
+make_oldDT <- function() {
+  microorganisms.oldDT <- AMR::microorganisms.old %>% 
+    mutate(
+      # for fullname_lower: keep only dots, letters,
+      # numbers, slashes, spaces and dashes
+      fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", tolower(fullname)),
+      # add a column with only "e coli" like combinations
+      g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>% 
+    as.data.table()
+  
+  # so arrange data on prevalence first, then full name
+  setkey(microorganisms.oldDT,
+         prevalence,
+         fullname)
+  microorganisms.oldDT
+}
+
 make_trans_tbl <- function() {
   # conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
   c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC",

_pkgdown.yml

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -148,6 +148,7 @@ reference:
     - "`catalogue_of_life`"
     - "`catalogue_of_life_version`"
     - "`WHOCC`"
+    - "`lifecycle`"
   - title: Other functions
     desc: >
       These functions are mostly for internal use, but some of
@@ -171,7 +172,7 @@ authors:
     href: https://www.rug.nl/staff/m.s.berends/
   Christian F. Luz:
     href: https://www.rug.nl/staff/c.f.luz/
-  Alex W. Friedrich:
+  Alexander W. Friedrich:
     href: https://www.rug.nl/staff/a.w.friedrich/
   Bhanu N. M. Sinha:
     href: https://www.rug.nl/staff/b.sinha/
@@ -185,7 +186,3 @@ template:
   params:
     noindex: false
     bootswatch: "flatly"
-    docsearch:
-      # using algolia.com
-      api_key: "f737050abfd4d726c63938e18f8c496e"
-      index_name: "amr"

appveyor.yml

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

codecov.yml

@@ -1,3 +1,24 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
 codecov:
   notify:
     require_ci_to_pass: no # allow fail

cran-comments.md

@@ -1,7 +1,5 @@
-# Version 0.9.0
+# Version 0.10.0
 
 * For this specific version, nothing to mention.
 
 * Since version 0.3.0, CHECK returns a NOTE for having a data directory over 3 MB. This is needed to offer users reference data for the complete taxonomy of microorganisms - one of the most important features of this package.
-
-* Since version 0.8.0, this package writes lines to `[library path]/AMR/mo_history/mo_history.csv` when using the `as.mo()` function, in the exact same way (and borrowed from) the `extrafont` package on CRAN (version 0.17) writes to the user library path. Users are notified about this with a `message()`, and staged install on R >= 3.6.0 still works. The CSV file is never newly created or deleted by this package, it only changes this file to improve speed and reliability of the `as.mo()` function. See the source code of functions `set_mo_history()` and `clear_mo_history()` in file `R/mo_history.R`.

data-raw/antibiotics.txt

@@ -0,0 +1,507 @@
+"ab"	"atc"	"cid"	"name"	"group"	"atc_group1"	"atc_group2"	"abbreviations"	"synonyms"	"oral_ddd"	"oral_units"	"iv_ddd"	"iv_units"	"loinc"
+"AMA"	"J04AA01"	4649	"4-aminosalicylic acid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"		"c(\"Aminopar\", \"Aminosalicylic\", \"Aminosalicylic acid\", \"Aminosalicylic Acid\", \"Aminosalyl\", \"Aminox\", \"Apacil\", \"Deapasil\", \"Entepas\", \"Ferrosan\", \"Gabbropas\", \"Helipidyl\", \"Hellipidyl\", \"Neopasalate\", \"Osacyl\", \"Pamacyl\", \"Pamisyl\", \"Paramycin\", \"Parasal\", \"Parasalicil\", \"Parasalindon\", \"Pasalon\", \"Pasara\", \"Pascorbic\", \"Pasdium\", \"Paser Granules\", \"PASKALIUM\", \"Pasmed\", \"Pasnodia\", \"Pasolac\", \"Propasa\", \"Rezipas\", \"TEEBACIN\", \"WLN: ZR CQ DVQ\")"	12	"g"			
+"FCT"	"D01AE21"	3366	"5-fluorocytosine"	"Antifungals/antimycotics"	"Antifungals for topical use"	"Other antifungals for topical use"	"fluo"	"c(\"Alcobon\", \"Ancobon\", \"Ancotil\", \"Ancotyl\", \"Flucitosina\", \"Flucystine\", \"Flucytosin\", \"Flucytosine\", \"Flucytosinum\", \"Flucytosone\", \"Fluocytosine\", \"Fluorcytosine\")"					"c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")"
+"ACM"		6450012	"Acetylmidecamycin"	"Macrolides/lincosamides"				""					
+"ASP"		49787020	"Acetylspiramycin"	"Macrolides/lincosamides"				"c(\"Acetylspiramycin\", \"Foromacidin B\", \"Spiramycin II\")"					
+"ALS"	"J04BA03"	8954	"Aldesulfone sodium"	"Other antibacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"		"c(\"Adesulfone Sodium\", \"Aldapsone\", \"Aldesulfona sodica\", \"Aldesulfone\", \"Aldesulfone sodique\", \"Aldesulfone sodium\", \"Diamidin\", \"Diasone\", \"Diasone sodium\", \"DIASONE SODIUM\", \"Diazon\", \"Novotrone\", \"Sodium aldesulphone\", \"Sodium sulfoxone\", \"Sulfoxone sodium\", \"SULFOXONE SODIUM\")"	0.33	"g"			
+"AMK"	"J01GB06"	37768	"Amikacin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"ak\", \"an\", \"ami\", \"amk\", \"amik\")"	"c(\"Amicacin\", \"Amikacillin\", \"Amikacin\", \"Amikacin Base\", \"Amikacin Dihydrate\", \"AMIKACIN SULFATE\", \"Amikacina\", \"Amikacine\", \"Amikacinum\", \"Amikavet\", \"Amikin\", \"Amiklin\", \"Amikozit\", \"Amukin\", \"Arikace\", \"Briclin\", \"Lukadin\", \"Mikavir\", \"Pierami\", \"Potentox\")"			1	"g"	"c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
+"AKF"			"Amikacin/fosfomycin"	"Aminoglycosides"				""					
+"AMX"	"J01CA04"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"amx\", \"amox\", \"ac\")"	"c(\"Actimoxi\", \"Amoclen\", \"Amolin\", \"Amopen\", \"Amopenixin\", \"Amoxibiotic\", \"Amoxicaps\", \"Amoxicilina\", \"Amoxicillin\", \"Amoxicilline\", \"Amoxicillinum\", \"Amoxiden\", \"Amoxil\", \"Amoxivet\", \"Amoxy\", \"Amoxycillin\", \"Anemolin\", \"Aspenil\", \"Biomox\", \"Bristamox\", \"Cemoxin\", \"Clamoxyl\", \"Delacillin\", \"DisperMox\", \"Efpenix\", \"Flemoxin\", \"Hiconcil\", \"Histocillin\", \"Hydroxyampicillin\", \"Ibiamox\", \"Imacillin\", \"Lamoxy\", \"Metafarma capsules\", \"Metifarma capsules\", \"Moxacin\", \"Moxatag\", \"Ospamox\", \"Pamoxicillin\", 
+\"Piramox\", \"Robamox\", \"Sawamox PM\", \"Tolodina\", \"Unicillin\", \"Utimox\", \"Vetramox\")"	1	"g"	1	"g"	"c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")"
+"AMC"	"J01CR02"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"aug\", \"a/c\", \"xl\", \"aml\", \"amcl\")"	"c(\"Amocla\", \"Amoclan\", \"Amoclav\", \"Amoxsiklav\", \"Augmentan\", \"Augmentin\", \"Augmentin XR\", \"Augmentine\", \"Auspilic\", \"Clamentin\", \"Clamobit\", \"Clavamox\", \"Clavinex\", \"Clavoxilin Plus\", \"Clavulin\", \"Clavumox\", \"Coamoxiclav\", \"Eumetinex\", \"Kmoxilin\", \"Spectramox\", \"Spektramox\", \"Viaclav\", \"Xiclav\")"	1	"g"	3	"g"	
+"AXS"		465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"				""					
+"AMB"	"J02AA01"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Antibiotics"	"amph"	"c(\"Abelcet\", \"Abelecet\", \"Ambisome\", \"AmBisome\", \"Amfotericina B\", \"Amphocin\", \"Amphomoronal\", \"Amphortericin B\", \"Amphotec\", \"Amphotericin\", \"Amphotericin B\", \"Amphotericine B\", \"Amphotericinum B\", \"Amphozone\", \"Anfotericine B\", \"Fungilin\", \"Fungisome\", \"Fungisone\", \"Fungizone\", \"Halizon\")"			35	"mg"	"c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
+"AMP"	"J01CA01"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"am\", \"amp\", \"ampi\")"	"c(\"Acillin\", \"Adobacillin\", \"Amblosin\", \"Amcill\", \"Amfipen\", \"Amfipen V\", \"Amipenix S\", \"Ampichel\", \"Ampicil\", \"Ampicilina\", \"Ampicillin\", \"AMPICILLIN\", \"Ampicillin A\", \"Ampicillin acid\", \"Ampicillin anhydrate\", \"Ampicillin Anhydrous\", \"Ampicillin Base\", \"AMPICILLIN SODIUM\", \"Ampicillina\", \"Ampicilline\", \"Ampicillinum\", \"Ampicin\", \"Ampifarm\", \"Ampikel\", \"Ampimed\", \"Ampipenin\", \"Ampiscel\", \"Ampisyn\", \"Ampivax\", \"Ampivet\", \"Amplacilina\", \"Amplin\", \"Amplipenyl\", \"Amplisom\", \"Amplital\", \"Anhydrous ampicillin\", 
+\"Austrapen\", \"Binotal\", \"Bonapicillin\", \"Britacil\", \"Campicillin\", \"Copharcilin\", \"Delcillin\", \"Deripen\", \"Divercillin\", \"Doktacillin\", \"Duphacillin\", \"Grampenil\", \"Guicitrina\", \"Guicitrine\", \"Lifeampil\", \"Marcillin\", \"Morepen\", \"Norobrittin\", \"Nuvapen\", \"Olin Kid\", \"Omnipen\", \"OMNIPEN\", \"Orbicilina\", \"Pen A Oral\", \"Pen Ampil\", \"Penbristol\", \"Penbritin\", \"Penbritin paediatric\", \"Penbritin syrup\", \"Penbrock\", \"Penicline\", \"Penimic\", \"Pensyn\", \"Pentrex\", \"Pentrexl\", \"Pentrexyl\", \"Pentritin\", \"Pfizerpen A\", 
+\"Polycillin\", \"Polyflex\", \"Ponecil\", \"Princillin\", \"Principen\", \"QIDamp\", \"Racenacillin\", \"Rosampline\", \"Roscillin\", \"Semicillin\", \"Semicillin R\", \"Servicillin\", \"Sumipanto\", \"Synpenin\", \"Texcillin\", \"Tokiocillin\", \"Tolomol\", \"Totacillin\", \"Totalciclina\", \"Totapen\", \"Trifacilina\", \"Ukapen\", \"Ultrabion\", \"Ultrabron\", \"Vampen\", \"Viccillin\", \"Viccillin S\", \"Vidocillin\", \"Wypicil\")"	2	"g"	2	"g"	"c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
+"SAM"	"J01CR01"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"a/s\", \"sam\", \"ams\", \"ab\", \"amsu\")"	""			6	"g"	
+"AMR"		73341	"Amprolium"	"Other antibacterials"				"c(\"AMPROCIDUM\", \"Amprolio\", \"Amprolium\", \"Amprovine\")"					
+"ANI"	"J02AX06"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid"	"c(\"Anidulafungin\", \"Anidulafungina\", \"Anidulafungine\", \"Anidulafunginum\", \"Ecalta\", \"Eraxis\")"			0.1	"g"	"58420-1"
+"APL"		6602341	"Apalcillin"	"Beta-lactams/penicillins"				"c(\"Apalcilina\", \"Apalcillin\", \"Apalcilline\", \"Apalcillinum\")"					
+"APR"		3081545	"Apramycin"	"Aminoglycosides"				"c(\"Ambylan\", \"Apralan\", \"Apramicina\", \"Apramycin\", \"Apramycine\", \"Apramycinum\", \"Nebramycin II\")"					
+"ARB"		68682	"Arbekacin"	"Aminoglycosides"				"c(\"Arbekacin\", \"Arbekacina\", \"Arbekacine\", \"Arbekacini Sulfas\", \"Arbekacinum\", \"Habekacin\", \"Haberacin\")"					
+"APX"		71961	"Aspoxicillin"	"Beta-lactams/penicillins"				"c(\"Aspoxicilina\", \"Aspoxicillan\", \"Aspoxicillin\", \"Aspoxicilline\", \"Aspoxicillinum\")"					
+"AST"		5284517	"Astromicin"	"Aminoglycosides"				"c(\"Astromicin\", \"Astromicin A\", \"Astromicina\", \"Astromicine\", \"Astromicinum\", \"Fortimicin A\")"					
+"AVB"		9835049	"Avibactam"	"Beta-lactams/penicillins"				"c(\"Avibactam\", \"Avibactam free acid\")"					
+"AVI"		71674	"Avilamycin"	"Other antibacterials"				"c(\"Avilamycin\", \"Avilamycina\", \"Avilamycine\", \"Avilamycinum\", \"Surmax\")"					
+"AVO"		16131159	"Avoparcin"	"Glycopeptides"				""					
+"AZD"	"J01CE04"	15574941	"Azidocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Azidocilina\", \"Azidocillin\", \"Azidocillina\", \"Azidocilline\", \"Azidocillinum\")"	1.5	"g"			
+"AZM"	"J01FA10"	447043	"Azithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"azi\", \"azm\", \"az\", \"azit\")"	"c(\"Aritromicina\", \"Azasite\", \"Azenil\", \"Azifast\", \"Azigram\", \"Azimakrol\", \"Azithramycine\", \"Azithromycin\", \"Azithromycine\", \"Azithromycinum\", \"Azitrocin\", \"Azitromax\", \"Azitromicina\", \"Azitromicine\", \"Azitromin\", \"Aziwok\", \"Aztrin\", \"Azyter\", \"Azythromycin\", \"Hemomycin\", \"Misultina\", \"Mixoterin\", \"Setron\", \"Sumamed\", \"Tromix\", \"Trulimax\", \"Zentavion\", \"Zithrax\", \"Zithromac\", \"Zithromax\", \"Zithromax IV\", \"Zithromycin\", \"Zitrim\", \"Zitromax\", \"Zitrotek\", \"Zmax SR\")"	0.3	"g"	0.5	"g"	"c(\"16420-2\", \"25233-8\")"
+"AZL"	"J01CA09"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"az\", \"azl\", \"azlo\")"	""			12	"g"	"c(\"16422-8\", \"3368-8\")"
+"ATM"	"J01DF01"	5742832	"Aztreonam"	"Beta-lactams/penicillins"	"Other beta-lactam antibacterials"	"Monobactams"	"c(\"azt\", \"atm\", \"at\", \"azm\", \"aztr\")"	"c(\"Azactam\", \"Azetreonam\", \"Azthreonam\", \"Aztreonam\", \"Primbactam\")"			4	"g"	"c(\"16423-6\", \"25234-6\", \"3369-6\")"
+"AZA"			"Aztreonam/avibactam"	"Beta-lactams/penicillins"				""					
+"BAM"	"J01CA06"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Bacampicilina\", \"Bacampicillin\", \"Bacampicilline\", \"Bacampicillinum\", \"Penglobe\")"	1.2	"g"			
+"BAC"	"R02AB04"	78358334	"Bacitracin zinc"	"Other antibacterials"			"baci"	""					"87603-7"
+"BDQ"		5388906	"Bedaquiline"	"Other antibacterials"				"c(\"Bedaquiline\", \"Sirturo\")"					"80637-2"
+"BEK"		439318	"Bekanamycin"	"Aminoglycosides"				"c(\"Aminodeoxykanamycin\", \"Becanamicina\", \"Bekanamycin\", \"Bekanamycine\", \"Bekanamycinum\", \"Nebramycin V\")"					
+"BNB"	"J01CE08"		"Benzathine benzylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		""			3.6	"g"	
+"BNP"	"J01CE10"	64725	"Benzathine phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Bicillin V\", \"Biphecillin\")"	2	"g"			
+"BES"		10178705	"Besifloxacin"	"Quinolones"				"Besifloxacin"					
+"BIA"		71339	"Biapenem"	"Carbapenems"				"c(\"Biapenem\", \"Biapenern\", \"Bipenem\", \"Omegacin\")"					
+"BCZ"		65807	"Bicyclomycin (Bicozamycin)"	"Other antibacterials"				"c(\"Aizumycin\", \"Bacfeed\", \"Bacteron\", \"Bicozamicina\", \"Bicozamycin\", \"Bicozamycine\", \"Bicozamycinum\")"					
+"BDP"	"J01EA02"	68760	"Brodimoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"		"c(\"Brodimoprim\", \"Brodimoprima\", \"Brodimoprime\", \"Brodimoprimum\", \"Bromdimoprim\", \"Hyprim\", \"Unitrim\")"	0.2	"g"			
+"BUT"		47472	"Butoconazole"	"Antifungals/antimycotics"				"c(\"Butaconazole\", \"Butoconazol\", \"Butoconazole\", \"Butoconazolum\", \"Compositenstarke\", \"Dahlin\", \"Femstat\", \"Gynofort\", \"Polyfructosanum\")"					
+"CDZ"	"J01DD09"	44242317	"Cadazolid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		"Cadazolid"			2	"g"	
+"CLA"	"J04AA03"		"Calcium aminosalicylate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"		""					
+"CAP"	"J04AB30"	135565060	"Capreomycin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"		""			1	"g"	"16545-6"
+"CRB"	"J01CA03"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"cb\", \"bar\")"	"c(\"Anabactyl\", \"Carbenicilina\", \"Carbenicillin\", \"Carbenicillina\", \"Carbenicilline\", \"Carbenicillinum\", \"Geopen\", \"Pyopen\")"			12	"g"	"3434-8"
+"CRN"	"J01CA05"	93184	"Carindacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Carindacilina\", \"Carindacillin\", \"Carindacilline\", \"Carindacillinum\")"	4	"g"			
+"CAR"		6540466	"Carumonam"	"Other antibacterials"				"c(\"Carumonam\", \"Carumonamum\")"					
+"CAS"	"J02AX04"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp"	"c(\"Cancidas\", \"Capsofungin\", \"Caspofungin\")"			50	"mg"	"58419-3"
+"CAC"	"J01DB10"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Cefacetril\", \"Cefacetrile\", \"Cefacetrilo\", \"Cefacetrilum\", \"Celospor\", \"Celtol\", \"Cephacetrile\", \"Cristacef\", \"Vetrimast\")"					
+"CEC"	"J01DC04"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"ccl\", \"cec\", \"cfr\", \"fac\", \"cf\", \"cfac\", \"CFC\")"	"c(\"Alenfral\", \"Alfacet\", \"Ceclor\", \"Ceclor CD\", \"Cefaclor\", \"Cefaclor anhydrous\", \"Cefaclor monohydrate\", \"Cefacloro\", \"Cefaclorum\", \"Cefeaclor\", \"Cephaclor\", \"Dystaclor MR\", \"Keflor\", \"Kefral\", \"Raniclor\")"	1	"g"			"c(\"16564-7\", \"21149-0\")"
+"CFR"	"J01DB05"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfr\", \"fad\")"	"c(\"Cefadrops\", \"Cefadroxil\", \"Cefadroxil anhydrous\", \"Cefadroxilo\", \"Cefadroxilum\", \"Cefradroxil\", \"Cephadroxil\", \"Duricef\", \"Sumacef\", \"Ultracef\")"	2	"g"			"16565-4"
+"RID"	"J01DB02"	5773	"Cefaloridine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa"	"c(\"Aliporina\", \"Ampligram\", \"Cefaloridin\", \"Cefaloridina\", \"Cefaloridine\", \"Cefaloridinum\", \"Cefalorizin\", \"Ceflorin\", \"Cepaloridin\", \"Cepalorin\", \"Cephalomycine\", \"Cephaloridin\", \"Cephaloridine\", \"Cephaloridinum\", \"Ceporan\", \"Ceporin\", \"Ceporine\", \"Cilifor\", \"Deflorin\", \"Faredina\", \"Floridin\", \"Glaxoridin\", \"Intrasporin\", \"Keflodin\", \"Keflordin\", \"Kefloridin\", \"Kefspor\", \"Lloncefal\", \"Loridine\", \"Sasperin\", \"Sefacin\", \"Verolgin\", \"Vioviantine\")"			3	"g"	
+"MAN"	"J01DC03"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfam"	"c(\"Cefadole\", \"Cefamandol\", \"Cefamandole\", \"Cefamandolum\", \"Cephadole\", \"CEPHAMANDOLE\", \"Kefamandol\", \"Kefdole\", \"Mancef\")"			6	"g"	"3441-3"
+"CTZ"	"J01DB07"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Bricef\", \"Cefatrix\", \"Cefatrizine\", \"Cefatrizino\", \"Cefatrizinum\", \"Cepticol\", \"Cetrazil\", \"Latocef\", \"Orosporina\", \"Trizina\")"	1	"g"			
+"CZD"	"J01DB06"	71736	"Cefazedone"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Cefazedon\", \"Cefazedona\", \"Cefazedone\", \"Cefazedone acid\", \"Cefazedonum\", \"Refosporen\", \"Refosporene\", \"Refosporin\")"			3	"g"	
+"CZO"	"J01DB04"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfz\", \"cz\", \"faz\", \"kz\", \"czol\")"	"c(\"Atirin\", \"Cefamezin\", \"Cefamezine\", \"Cefazina\", \"Cefazolin\", \"Cefazolin acid\", \"Cefazolina\", \"Cefazoline\", \"Cefazolinum\", \"Cephamezine\", \"Cephazolidin\", \"Cephazolin\", \"Cephazoline\", \"Elzogram\", \"Firmacef\", \"Kefzol\", \"Liviclina\", \"Totacef\")"			3	"g"	"c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")"
+"CFB"		127527	"Cefbuperazone"	"Other antibacterials"				"c(\"Cefbuperazona\", \"Cefbuperazone\", \"Cefbuperazonum\", \"Cefbuperzaone\", \"Cerbuperazone\", \"Tomiporan\")"					
+"CCP"		6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"				"c(\"Cefcamate\", \"Cefcapene\")"					
+"CCX"		5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.)"				"c(\"Cefcamate pivoxil\", \"Cefcapene piroxil\")"					
+"CDR"	"J01DD15"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cdn\", \"cdr\", \"din\", \"cd\", \"cfd\")"	"c(\"Cefdinir\", \"Cefdinirum\", \"Cefdinyl\", \"Cefdirnir\", \"Ceftinex\", \"Cefzon\", \"Omnicef\")"	0.6	"g"			
+"DIT"	"J01DD16"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn"	"Cefditoren"	0.4	"g"			
+"DIX"		6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"				"c(\"Cefditoren\", \"Cefditoren PI voxil\", \"Cefditoren pivoxil\", \"Cefditoren Pivoxil\", \"Cefditorin\", \"CEFDITORIN PIVOXIL\", \"Meiact\", \"Spectracef\")"					
+"FEP"	"J01DE01"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"c(\"cpe\", \"fep\", \"pm\", \"cpm\", \"cfep\", \"xpm\")"	"c(\"Axepim\", \"Cefepima\", \"Cefepime\", \"Cefepimum\", \"Cepimax\", \"Cepimex\", \"Maxcef\", \"Maxipime\")"			2	"g"	"38363-8"
+"CPC"		9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.)"			"xpml"	""					
+"FPT"		9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"				""					
+"FPZ"			"Cefepime/zidebactam"	"Other antibacterials"				""					
+"CAT"	"J01DD10"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		"c(\"Cefetamet\", \"Cefetametum\", \"Cepime O\", \"Deacetoxycefotaxime\")"	1	"g"			
+"CPI"		5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.)"				"c(\"Cefetamet pivoxyl\", \"Globocef\")"					
+"CCL"		71719688	"Cefetecol (Cefcatacol)"	"Cephalosporins (4th gen.)"				""					
+"CZL"		193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"				"c(\"Cefetrizole\", \"Cefetrizolum\")"					
+"FDC"		77843966	"Cefiderocol"	"Other antibacterials"				"Cefiderocol"					
+"CFM"	"J01DD08"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfe\", \"dcfm\", \"fix\", \"ix\", \"cfix\")"	"c(\"Cefixim\", \"Cefixima\", \"Cefixime\", \"Cefixime Anhydrous\", \"Cefiximum\", \"Cefixoral\", \"Cefspan\", \"Cephoral\", \"Denvar\", \"Necopen\", \"Suprax\", \"Tricef\", \"Unixime\")"	0.4	"g"			"c(\"16567-0\", \"25236-1\")"
+"CMX"	"J01DD05"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		"c(\"Bestron\", \"Cefmax\", \"Cefmenoxima\", \"Cefmenoxime\", \"Cefmenoximum\")"			2	"g"	
+"CMZ"	"J01DC09"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"		"c(\"Cefmetazole\", \"Cefmetazolo\", \"Cefmetazolum\")"			4	"g"	
+"CNX"		71141	"Cefminox"	"Other antibacterials"				"c(\"Cefminox\", \"Cefminoxum\")"					
+"DIZ"	"J01DD09"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		"c(\"Cefodizima\", \"Cefodizime\", \"Cefodizime Acid\", \"Cefodizimum\", \"Cefodizme\", \"Diezime\", \"Modivid\", \"Neucef\", \"Timecef\")"			2	"g"	
+"CID"	"J01DC06"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"		"c(\"Cefonicid\", \"Cefonicido\", \"Cefonicidum\", \"Monocef\")"			1	"g"	"c(\"25237-9\", \"3444-7\")"
+"CFP"	"J01DD12"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfp\", \"cpz\", \"per\", \"fop\", \"cp\")"	"c(\"Bioperazone\", \"Cefobid\", \"Cefoperazine\", \"Cefoperazon\", \"Cefoperazone\", \"Cefoperazone acid\", \"Cefoperazono\", \"Cefoperazonum\", \"Cefozon\", \"Medocef\", \"Myticef\", \"Pathozone\", \"Peracef\")"			4	"g"	"3445-4"
+"CSL"	"J01DD62"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		""			4	"g"	
+"CND"	"J01DC11"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"		"c(\"Ceforanide\", \"Ceforanido\", \"Ceforanidum\", \"Precef\", \"Radacef\")"			4	"g"	
+"CSE"		9830519	"Cefoselis"	"Cephalosporins (4th gen.)"				"c(\"Cefoselis\", \"Cefoselis sulfate\", \"Winsef\")"					
+"CTX"	"J01DD01"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cft\", \"ctx\", \"tax\", \"fot\", \"ct\", \"cfot\", \"xct\")"	"c(\"Cefotaxim\", \"Cefotaxim Hikma\", \"Cefotaxima\", \"Cefotaxime\", \"Cefotaxime acid\", \"Cefotaximum\", \"Cephotaxime\", \"Claforan\", \"Omnatax\")"			4	"g"	"c(\"25238-7\", \"3446-2\", \"80961-6\")"
+"CTC"		9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.)"			"xctl"	""					
+"CTS"		9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"				""					
+"CTT"	"J01DC05"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"ctn\", \"ctt\", \"cte\", \"tans\", \"cn\")"	"c(\"Apacef\", \"Cefotetan\", \"Cefotetan free acid\", \"Cefotetanum\")"			4	"g"	"c(\"25239-5\", \"3447-0\")"
+"CTF"	"J01DC07"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"		"c(\"Cefotiam\", \"Cefotiam?\", \"Cefotiamum\", \"Ceradolan\", \"Ceradon\", \"Haloapor\")"	1.2	"g"	4	"g"	
+"CHE"		125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"				"c(\"Cefotiam cilexetil\", \"Pansporin T\")"					
+"FOV"		9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"				""					
+"FOX"	"J01DC01"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfx\", \"fox\", \"cx\", \"fx\", \"cfox\")"	"c(\"Cefoxitin\", \"Cefoxitina\", \"Cefoxitine\", \"Cefoxitinum\", \"Cefoxotin\", \"CEPHOXITIN\", \"Mefoxin\", \"Mefoxitin\", \"Rephoxitin\")"			6	"g"	"c(\"25240-3\", \"3448-8\")"
+"ZOP"		9571080	"Cefozopran"	"Cephalosporins (4th gen.)"				"Cefozopran"					
+"CFZ"		68597	"Cefpimizole"	"Cephalosporins (3rd gen.)"				"c(\"Cefpimizol\", \"Cefpimizole\", \"Cefpimizole sodium\", \"Cefpimizolum\")"					
+"CPM"	"J01DD11"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"		"c(\"Cefpiramide\", \"Cefpiramide acid\", \"Cefpiramido\", \"Cefpiramidum\")"			2	"g"	
+"CPO"	"J01DE02"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"		"c(\"Broact\", \"Cefpiroma\", \"Cefpirome\", \"Cefpiromum\", \"Cefrom\", \"Cerfpirome\", \"Keiten\")"			4	"g"	
+"CPD"	"J01DD13"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cpd\", \"pod\", \"px\", \"cfpo\")"	"c(\"Cefpodoxim acid\", \"Cefpodoxima\", \"Cefpodoxime\", \"Cefpodoxime acid\", \"Cefpodoximum\", \"Epoxim\")"	0.4	"g"			"25241-1"
+"CPX"		6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.)"				"c(\"Cefodox\", \"Cefoprox\", \"Cefpodoxime proxetil\", \"Cepodem\", \"Orelox\", \"Otreon\", \"Podomexef\", \"Simplicef\", \"Vantin\")"					
+"CDC"			"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.)"				""					
+"CPR"	"J01DC10"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cpz\", \"cpr\", \"fp\")"	"c(\"Arzimol\", \"Brisoral\", \"Cefprozil\", \"Cefprozil anhydrous\", \"Cefprozil hydrate\", \"Cefprozilo\", \"Cefprozilum\", \"Cefzil\", \"Cronocef\", \"Procef\", \"Serozil\")"	1	"g"			
+"CEQ"		5464355	"Cefquinome"	"Cephalosporins (4th gen.)"				"c(\"Cefquinoma\", \"Cefquinome\", \"Cefquinomum\", \"Cobactan\")"					
+"CRD"	"J01DB11"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Cefroxadine\", \"Cefroxadino\", \"Cefroxadinum\")"					
+"CFS"	"J01DD03"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfsu"	"c(\"Cefsulodin\", \"Cefsulodine\", \"Cefsulodino\", \"Cefsulodinum\")"			4	"g"	"c(\"131-3\", \"25242-9\")"
+"CSU"		68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"				"c(\"Cefsumide\", \"Cefsumido\", \"Cefsumidum\")"					
+"CPT"	"J01DI02"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"				"c(\"Teflaro\", \"Zinforo\")"					
+"CPA"			"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"				""					
+"CAZ"	"J01DD02"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"caz\", \"taz\", \"tz\", \"cfta\", \"xtz\", \"cefta\")"	"c(\"Ceftazidim\", \"Ceftazidima\", \"Ceftazidime\", \"CEFTAZIDIME\", \"Ceftazidimum\", \"Ceptaz\", \"Fortaz\", \"Fortum\", \"Pentacef\", \"Tazicef\", \"Tazidime\")"			4	"g"	"c(\"21151-6\", \"3449-6\", \"80960-8\")"
+"CZA"			"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"				""					
+"CCV"	"J01DD52"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"xtzl"	""					
+"CEM"		6537431	"Cefteram"	"Cephalosporins (3rd gen.)"				"c(\"Cefteram\", \"Cefterame\", \"Cefteramum\", \"Ceftetrame\")"					
+"CPL"		5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"				"c(\"Cefteram pivoxil\", \"Tomiron\")"					
+"CTL"	"J01DB12"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Ceftezol\", \"Ceftezole\", \"Ceftezolo\", \"Ceftezolum\", \"Demethylcefazolin\")"			3	"g"	
+"CTB"	"J01DD14"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"ctb\", \"tib\", \"cb\")"	"c(\"Ceftem\", \"Ceftibuten\", \"Ceftibuten hydrate\", \"Ceftibutene\", \"Ceftibuteno\", \"Ceftibutenum\", \"Cephem\", \"Ceprifran\", \"Isocef\", \"Keimax\")"	0.4	"g"			
+"TIO"		6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"				"c(\"Ceftiofur\", \"Ceftiofurum\", \"Excede\", \"Excenel\", \"Naxcel\")"					
+"CZX"	"J01DD07"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cz\", \"zox\", \"czx\", \"ctz\", \"tiz\")"	"c(\"Cefizox\", \"Ceftisomin\", \"Ceftix\", \"Ceftizoxima\", \"Ceftizoxime\", \"Ceftizoximum\", \"Epocelin\", \"Eposerin\")"			4	"g"	"c(\"25243-7\", \"3450-4\")"
+"CZP"		9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"				""					
+"BPR"	"J01DI01"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"				"Ceftobiprole"					
+"CFM1"	"J01DI01"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"		""					
+"CEI"	"J01DI54"		"Ceftolozane/enzyme inhibitor"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"		""					
+"CZT"			"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"				""					
+"CRO"	"J01DD04"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cax\", \"cro\", \"ctr\", \"frx\", \"axo\", \"tx\", \"cftr\")"	"c(\"Biotrakson\", \"Cefatriaxone\", \"Cefatriaxone hydrate\", \"Ceftriaxon\", \"Ceftriaxona\", \"Ceftriaxone\", \"CEFTRIAXONE SODIUM\", \"Ceftriaxonum\", \"Ceftriazone\", \"Cephtriaxone\", \"Longacef\", \"Rocefin\", \"Rocephalin\", \"Rocephin\", \"Rocephine\", \"Rophex\")"			2	"g"	"c(\"25244-5\", \"3451-2\", \"80957-4\")"
+"CXM"	"J01DC02"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"crm\", \"cxm\", \"cfx\", \"rox\", \"fur\", \"xm\", \"cfur\")"	"c(\"Biofuroksym\", \"Cefuril\", \"Cefuroxim\", \"Cefuroxime\", \"Cefuroximine\", \"Cefuroximo\", \"Cefuroximum\", \"Cephuroxime\", \"Kefurox\", \"Sharox\", \"Zinacef\", \"Zinacef Danmark\")"	0.5	"g"	3	"g"	"c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
+"CXA"		6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.)"				"c(\"Altacef\", \"Bioracef\", \"Cefaks\", \"Cefazine\", \"Ceftin\", \"Cefuroximaxetil\", \"Cefuroxime axetil\", \"Celocid\", \"Cepazine\", \"Cethixim\", \"Cetoxil\", \"Coliofossim\", \"Elobact\", \"Forcef\", \"Furoxime\", \"Kalcef\", \"Maxitil\", \"Medoxm\", \"Nivador\", \"Zinnat\")"					
+"CFM2"	"J01RA03"		"Cefuroxime/metronidazole"	"Other antibacterials"	"Combinations of antibacterials"	"Combinations of antibacterials"		""					
+"ZON"		6336505	"Cefuzonam"	"Other antibacterials"				"c(\"Cefuzonam\", \"Cefuzonam sodium\", \"Cefuzoname\", \"Cefuzonamum\")"					
+"LEX"	"J01DB01"	27447	"Cephalexin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Alcephin\", \"Alexin\", \"Alsporin\", \"Anhydrous cefalexin\", \"Anhydrous cephalexin\", \"Biocef\", \"Carnosporin\", \"Cefablan\", \"Cefadal\", \"Cefadin\", \"Cefadina\", \"Cefaleksin\", \"Cefalessina\", \"Cefalexin\", \"Cefalexin anhydrous\", \"Cefalexina\", \"Cefalexine\", \"Cefalexinum\", \"Cefalin\", \"Cefaloto\", \"Cefaseptin\", \"Ceflax\", \"Ceforal\", \"Cefovit\", \"Celexin\", \"Cepastar\", \"Cepexin\", \"Cephacillin\", \"Cephalexin\", \"Cephalexin anhydrous\", \"Cephalexine\", \"Cephalexinum\", \"Cephanasten\", \"Cephaxin\", \"Cephin\", \"Ceporex\", \"Ceporex Forte\", 
+\"Ceporexin\", \"Ceporexine\", \"Cerexin\", \"Cerexins\", \"Cophalexin\", \"Durantel\", \"Durantel DS\", \"Erocetin\", \"Factagard\", \"Felexin\", \"Ibilex\", \"Ibrexin\", \"Inphalex\", \"Kefalospes\", \"Keflet\", \"Keflex\", \"Kefolan\", \"Keforal\", \"Keftab\", \"Kekrinal\", \"Kidolex\", \"Lafarine\", \"Larixin\", \"Lenocef\", \"Lexibiotico\", \"Lonflex\", \"Lopilexin\", \"Madlexin\", \"Mamalexin\", \"Mamlexin\", \"Medoxine\", \"Neokef\", \"Neolexina\", \"Novolexin\", \"Optocef\", \"Oracef\", \"Oriphex\", \"Oroxin\", \"Ortisporina\", \"Ospexin\", \"Palitrex\", \"Panixine Disperdose\", 
+\"Pectril\", \"Pyassan\", \"Roceph\", \"Roceph Distab\", \"Sanaxin\", \"Sartosona\", \"Sencephalin\", \"Sepexin\", \"Servispor\", \"Sialexin\", \"Sinthecillin\", \"Sporicef\", \"Sporidex\", \"Syncle\", \"Synecl\", \"Tepaxin\", \"Tokiolexin\", \"Uphalexin\", \"Voxxim\", \"Winlex\", \"Zozarine\")"	2	"g"			"c(\"21175-5\", \"3453-8\")"
+"CEP"	"J01DB03"	6024	"Cephalothin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfal"	"c(\"Cefalothin\", \"Cefalotin\", \"Cefalotina\", \"Cefalotina fabra\", \"Cefalotine\", \"Cefalotinum\", \"Cemastin\", \"Cephalothinum\", \"Cephalotin\", \"Coaxin\", \"Keflin\", \"Seffin\")"			4	"g"	"c(\"25246-0\", \"3454-6\")"
+"HAP"	"J01DB08"	30699	"Cephapirin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"		"c(\"Ambrocef\", \"Cefadyl\", \"Cefapilin\", \"Cefapirin\", \"Cefapirina\", \"Cefapirine\", \"Cefapirinum\", \"Cefaprin\", \"Cefaprin sodium\", \"Cefatrex\", \"Cefatrexyl\", \"Cephapirine\", \"Metricure\")"			4	"g"	"10980-1"
+"CED"	"J01DB09"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfra"	"c(\"Anspor\", \"Cefradin\", \"Cefradina\", \"Cefradine\", \"Cefradinum\", \"Cekodin\", \"Cephradin\", \"Cephradine\", \"Eskacef\", \"Infexin\", \"Megace f\", \"Megacef\", \"Sefril\", \"Velocef\", \"Velosef\")"	2	"g"	2	"g"	
+"CTO"		71402	"Cetocycline"	"Tetracyclines"				"c(\"Cetocycline\", \"Cetocyline\", \"Cetotetrine\")"					
+"CHL"	"J01BA01"	5959	"Chloramphenicol"	"Amphenicols"	"Amphenicols"	"Amphenicols"	"c(\"c\", \"chl\", \"cl\", \"chlo\")"	"c(\"Alficetyn\", \"Ambofen\", \"Amphenicol\", \"Amphicol\", \"Amseclor\", \"Anacetin\", \"Aquamycetin\", \"Austracil\", \"Austracol\", \"Biocetin\", \"Biophenicol\", \"Catilan\", \"Ch loramex\", \"Chemiceticol\", \"Chemicetin\", \"Chemicetina\", \"Chlomin\", \"Chlomycol\", \"Chloramex\", \"Chloramfenikol\", \"Chloramficin\", \"Chloramfilin\", \"Chloramphenicol\", \"CHLORAMPHENICOL\", \"Chloramphenicole\", \"Chloramphenicolum\", \"Chloramsaar\", \"Chlorasol\", \"Chlorbiotic\", \"Chloricol\", \"Chlormycetin R\", \"Chlornitromycin\", \"Chloroamphenicol\", \"Chlorocaps\", 
+\"Chlorocid\", \"Chlorocid S\", \"Chlorocide\", \"Chlorocidin C\", \"Chlorocidin C tetran\", \"Chlorocin\", \"Chlorocol\", \"Chlorofair\", \"Chloroject L\", \"Chloromax\", \"Chloromycetin\", \"Chloromycetny\", \"Chloromyxin\", \"Chloronitrin\", \"Chloroptic\", \"CHLOROPTIC S.O.P\", \"Chloroptic S.O.P.\", \"Chlorovules\", \"Chlorsig\", \"Cidocetine\", \"Ciplamycetin\", \"Cloramfen\", \"Cloramfenicol\", \"Cloramfenicolo\", \"Cloramficin\", \"Cloramical\", \"Cloramicol\", \"Cloramidina\", \"Cloranfenicol\", \"Cloroamfenicolo\", \"Clorocyn\", \"Cloromisan\", \"Cloromissan\", 
+\"Clorosintex\", \"Comycetin\", \"Cylphenicol\", \"Desphen\", \"Detreomycin\", \"Detreomycine\", \"Dextromycetin\", \"Doctamicina\", \"Duphenicol\", \"Econochlor\", \"Embacetin\", \"Emetren\", \"Enicol\", \"Enteromycetin\", \"Erbaplast\", \"Ertilen\", \"F armicetina\", \"Farmicetina\", \"Fenicol\", \"Globenicol\", \"Glorous\", \"Halomycetin\", \"Hortfenicol\", \"Interomycetine\", \"Intramycetin\", \"Intramyctin\", \"Isicetin\", \"Ismicetina\", \"Isophenicol\", \"Isopto fenicol\", \"Juvamycetin\", \"Kamaver\", \"Kemicetina\", \"Kemicetine\", \"Kloramfenikol\", \"Klorita\", 
+\"Klorocid S\", \"Laevomycetinum\", \"Leukamycin\", \"Leukomyan\", \"Leukomycin\", \"Levocin\", \"Levomicetina\", \"Levomitsetin\", \"Levomycetin\", \"Levoplast\", \"Levosin\", \"Levovetin\", \"Loromicetina\", \"Loromisan\", \"Loromisin\", \"Mastiphen\", \"Mediamycetine\", \"Medichol\", \"Micloretin\", \"Micochlorine\", \"Micoclorina\", \"Microcetina\", \"Mychel\", \"Mycinol\", \"Myclocin\", \"Mycochlorin\", \"Myscel\", \"Normimycin V\", \"Novochlorocap\", \"Novomycetin\", \"Novophenicol\", \"Ocuphenicol\", \"Oftalent\", \"Oleomycetin\", \"Opclor\", \"Opelor\", \"Ophthochlor\", 
+\"Ophthocort\", \"Ophtochlor\", \"Optomycin\", \"Otachron\", \"Otophen\", \"Pantovernil\", \"Paraxin\", \"Pentamycetin\", \"Quemicetina\", \"Rivomycin\", \"Romphenil\", \"Ronfenil\", \"Ronphenil\", \"Septicol\", \"Sificetina\", \"Sintomicetina\", \"Sintomicetine R\", \"Sno Phenicol\", \"Soluthor\", \"Stanomycetin\", \"Synthomycetin\", \"Synthomycetine\", \"Synthomycine\", \"Syntomycin\", \"Tevcocin\", \"Tevcosin\", \"Tifomycin\", \"Tifomycine\", \"Tiromycetin\", \"Treomicetina\", \"Unimycetin\", \"Veticol\", \"Vice ton\", \"Viceton\")"	3	"g"	3	"g"	"c(\"15101-9\", \"16603-3\", \"16604-1\", \"25247-8\", \"29214-4\", \"29346-4\", \"29347-2\", \"3455-3\")"
+"CTE"	"J01AA03"	54675777	"Chlortetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Acronize\", \"Aueromycin\", \"Aureocina\", \"Aureomycin\", \"AUREOMYCIN\", \"Aureomykoin\", \"Biomitsin\", \"Biomycin\", \"Biomycin a\", \"Chlormax\", \"Chlorotetracycline\", \"Chlortetracycline\", \"Chlortetracyclinum\", \"Chrysomykine\", \"Clortetraciclina\", \"Duomycin\", \"Flamycin\", \"Uromycin\")"	1	"g"			"87600-3"
+"CIC"		19003	"Ciclacillin"	"Beta-lactams/penicillins"				"c(\"Bastcillin\", \"Calthor\", \"Ciclacilina\", \"Ciclacillin\", \"Ciclacilline\", \"Ciclacillinum\", \"Ciclacillum\", \"Citosarin\", \"Cyclacillin\", \"Cyclapen\", \"Noblicil\", \"Orfilina\", \"Peamezin\", \"Syngacillin\", \"Ultracillin\", \"Vastcillin\", \"Vipicil\", \"Wyvital\")"					
+"CIN"	"J01MB06"	2762	"Cinoxacin"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"cnox"	"c(\"Azolinic Acid\", \"Cinobac\", \"Cinobactin\", \"Cinoxacin\", \"Cinoxacine\", \"Cinoxacino\", \"Cinoxacinum\", \"Clinoxacin\", \"Noxigram\", \"Uronorm\")"	1	"g"			
+"CIP"	"J01MA02"	2764	"Ciprofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"cp\", \"cip\", \"ci\", \"cipr\")"	"c(\"Alcon Cilox\", \"AuriPro\", \"Bacquinor\", \"Baflox\", \"Baycip\", \"Bernoflox\", \"Cetraxal\", \"Ciflox\", \"Cifloxin\", \"Ciloxan\", \"Ciplus\", \"Ciprecu\", \"Ciprine\", \"Ciprinol\", \"Cipro I.V.\", \"Cipro IV\", \"Cipro XL\", \"Cipro XR\", \"Ciprobay\", \"Ciprobay Uro\", \"Ciprocinol\", \"Ciprodar\", \"Ciproflox\", \"Ciprofloxacin\", \"Ciprofloxacina\", \"Ciprofloxacine\", \"Ciprofloxacino\", \"Ciprofloxacinum\", \"Ciprogis\", \"Ciprolin\", \"Ciprolon\", \"Cipromycin\", \"Ciproquinol\", \"Ciprowin\", \"Ciproxan\", \"Ciproxin\", \"Ciproxina\", \"Ciproxine\", \"Ciriax\", 
+\"Citopcin\", \"Corsacin\", \"Cyprobay\", \"Fimoflox\", \"Flociprin\", \"Ipiflox\", \"Italnik\", \"Linhaliq\", \"Otiprio\", \"Probiox\", \"Proflaxin\", \"Quinolid\", \"Quintor\", \"Rancif\", \"Roxytal\", \"Septicide\", \"Sophixin Ofteno\", \"Spitacin\", \"Superocin\", \"Velmonit\", \"Velomonit\", \"Zumaflox\")"	1	"g"	0.5	"g"	"c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
+"CLR"	"J01FA09"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"cla\", \"clr\", \"clm\", \"ch\", \"clar\")"	"c(\"Abbotic\", \"Astromen\", \"Biaxin\", \"Biaxin filmtab\", \"Biaxin HP\", \"Biaxin XL\", \"Biaxin xl filmtab\", \"Bicrolid\", \"Clacee\", \"Clacid\", \"Clacine\", \"Clambiotic\", \"Clarem\", \"Claribid\", \"Claricide\", \"Claridar\", \"Claripen\", \"Clarith\", \"Clarithromycin\", \"Clarithromycine\", \"Clarithromycinum\", \"Claritromicina\", \"Clathromycin\", \"Crixan\", \"Cyllid\", \"Cyllind\", \"Fromilid\", \"Heliclar\", \"Klabax\", \"Klacid\", \"Klaciped\", \"Klaricid\", \"Klaricid H.P\", \"Klaricid H.P.\", \"Klaricid Pediatric\", \"Klaricid XL\", \"Klarid\", \"Klarin\", 
+\"Kofron\", \"Mabicrol\", \"Macladin\", \"Maclar\", \"Veclam\", \"Vikrol\", \"Zeclar\")"	0.5	"g"	1	"g"	"c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")"
+"CLA1"		5280980	"Clavulanic acid"	"Other antibacterials"				"c(\"Acide clavulanique\", \"Acido clavulanico\", \"Acidum clavulanicum\", \"Clavulanate\", \"Clavulanate acid\", \"CLAVULANATE LITHIUM\", \"Clavulanic acid\", \"Clavulansaeure\", \"Clavulansaure\", \"Clavulinic Acid\", \"Clavulox\", \"Sodium Clavulanate\")"					
+"CLX"		60063	"Clinafloxacin"	"Quinolones"				"Clinafloxacin"					
+"CLI"	"J01FF01"	446598	"Clindamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"c(\"cd\", \"cc\", \"cm\", \"cli\", \"da\", \"clin\")"	"c(\"Antirobe\", \"Chlolincocin\", \"ClindaDerm\", \"Clindamicina\", \"Clindamycin\", \"Clindamycine\", \"Clindamycinum\", \"Clinimycin\", \"Dalacin C\", \"Dalacine\", \"Klimicin\", \"Sobelin\")"	1.2	"g"	1.8	"g"	"c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")"
+"CLF"	"J04BA01"	2794	"Clofazimine"	"Antimycobacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"c(\"Chlofazimine\", \"Clofazimin\", \"Clofazimina\", \"Clofazimine\", \"Clofaziminum\", \"Lampren\", \"Lamprene\", \"Riminophenazine\")"	0.1	"g"			
+"CLF1"	"J01XX03"	2799	"Clofoctol"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"		"c(\"Clofoctol\", \"Clofoctolo\", \"Clofoctolum\", \"Gramplus\", \"Octofene\")"					
+"CLM"	"J01CE07"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Chlomethocillin\", \"Clometacillin\", \"Clometocilina\", \"Clometocillin\", \"Clometocilline\", \"Clometocillinum\", \"Rixapen\")"	1	"g"			
+"CLM1"	"J01AA11"	54680675	"Clomocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"CHLORMETHYLENCYCLINE\", \"Clomociclina\", \"Clomocyclin\", \"Clomocycline\", \"Clomocyclinum\", \"Megaclor\")"	1	"g"			
+"CTR"	"G01AF02"	2812	"Clotrimazole"	"Antifungals/antimycotics"			"clot"	"c(\"Canesten\", \"Canesten Cream\", \"Canesten Solution\", \"Canestene\", \"Canestine\", \"Canifug\", \"Chlotrimazole\", \"Cimitidine\", \"Clomatin\", \"Clotrimaderm\", \"Clotrimaderm Cream\", \"Clotrimazol\", \"Clotrimazole\", \"Clotrimazolum\", \"Cutistad\", \"Desamix F\", \"Diphenylmethane\", \"Empecid\", \"Esparol\", \"Fem Care\", \"FemCare\", \"Gyne lotrimin\", \"Jidesheng\", \"Kanesten\", \"Klotrimazole\", \"Lotrimax\", \"Lotrimin\", \"Lotrimin Af\", \"Lotrimin AF Cream\", \"Lotrimin AF Lotion\", \"Lotrimin AF Solution\", \"Lotrimin Cream\", \"Lotrimin Lotion\", 
+\"Lotrimin Solution\", \"Monobaycuten\", \"Mycelax\", \"Mycelex\", \"Mycelex Cream\", \"Mycelex G\", \"Mycelex OTC\", \"Mycelex Solution\", \"Mycelex Troches\", \"Mycelex Twin Pack\", \"Myclo Cream\", \"Myclo Solution\", \"Myclo Spray Solution\", \"Mycofug\", \"Mycosporin\", \"Mykosporin\", \"Nalbix\", \"Otomax\", \"Pedisafe\", \"Rimazole\", \"Stiemazol\", \"Tibatin\", \"Trimysten\", \"Veltrim\")"					
+"CLO"	"J01CF02"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"		"c(\"Chloroxacillin\", \"Clossacillina\", \"Cloxacilina\", \"Cloxacillin\", \"Cloxacillin sodium\", \"Cloxacilline\", \"CloxacillinNa\", \"Cloxacillinum\", \"Cloxapen\", \"Methocillin S\", \"Orbenin\", \"Syntarpen\", \"Tegopen\")"	2	"g"	2	"g"	"c(\"16628-0\", \"25250-2\")"
+"COL"	"J01XB01"	5311054	"Colistin"	"Polymyxins"	"Other antibacterials"	"Polymyxins"	"c(\"cl\", \"cs\", \"ct\", \"coli\")"	"c(\"Belcomycine\", \"Colimycin\", \"Colimycin sulphate\", \"Colisticin\", \"Colistimethate\", \"Colistimethate Sodium\", \"Colistin sulfate\", \"Colistin sulphate\", \"Colomycin\", \"Coly-Mycin\", \"Polymyxin E\", \"Polymyxin E. Sulfate\", \"Promixin\", \"Totazina\")"			3	"MU"	"c(\"16645-4\", \"29493-4\")"
+"COP"			"Colistin/polysorbate"	"Other antibacterials"				""					
+"CYC"	"J04AB01"	6234	"Cycloserine"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl"	"c(\"Cicloserina\", \"Closerin\", \"Closina\", \"Cyclorin\", \"Cycloserin\", \"Cycloserine\", \"CYCLOSERINE\", \"Cycloserinum\", \"Farmiserina\", \"Micoserina\", \"Miroserina\", \"Miroseryn\", \"Novoserin\", \"Oxamicina\", \"Oxamycin\", \"Seromycin\", \"Tebemicina\", \"Tisomycin\", \"Wasserina\")"	0.75	"g"			"c(\"16702-3\", \"25251-0\", \"3519-6\")"
+"DAL"	"J01XA04"	23724878	"Dalbavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb"	"c(\"Dalbavancin\", \"Dalvance\")"					
+"DAN"		71335	"Danofloxacin"	"Quinolones"				"c(\"Advocin\", \"Danofloxacin\", \"Danofloxacine\", \"Danofloxacino\", \"Danofloxacinum\")"					
+"DPS"	"J04BA02"	2955	"Dapsone"	"Other antibacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"		"c(\"Aczone\", \"Araldite HT\", \"Atrisone\", \"Avlosulfon\", \"Avlosulfone\", \"Avlosulphone\", \"Avsulfor\", \"Bis sulfone\", \"BIS SULFONE\", \"Bissulfone\", \"Bissulphone\", \"Croysulfone\", \"Croysulphone\", \"Dapson\", \"Dapsona\", \"Dapsone\", \"Dapsonum\", \"Di sulfone\", \"Diaphenyl sulfone\", \"Diaphenylsulfon\", \"Diaphenylsulfone\", \"Diaphenylsulphon\", \"Diaphenylsulphone\", \"Dimitone\", \"Diphenasone\", \"Diphone\", \"Disulfone\", \"Disulone\", \"Disulphone\", \"Dubronax\", \"Dubronaz\", \"Dumitone\", \"Eporal\", \"Metabolite C\", \"Novophone\", \"Protogen\", 
+\"Servidapson\", \"Slphadione\", \"Sulfadione\", \"Sulfona\", \"Sulfone ucb\", \"Sulfonyldianiline\", \"Sulphadione\", \"Sulphonyldianiline\", \"Sumicure S\", \"Tarimyl\", \"Udolac\", \"WLN: ZR DSWR DZ\")"	50	"mg"			"9747-7"
+"DAP"	"J01XX09"	16134395	"Daptomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"dap\", \"dapt\")"	"c(\"Cidecin\", \"Cubicin\", \"Dapcin\", \"Daptomicina\", \"Daptomycine\", \"Daptomycinum\")"			0.28	"g"	
+"DFX"		487101	"Delafloxacin"	"Quinolones"				"c(\"Baxdela\", \"Delafloxacin\", \"Delafloxacinum\")"					
+"DLM"	"J04AK06"	6480466	"Delamanid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"c(\"Delamanid\", \"Deltyba\")"					
+"DEM"	"J01AA01"	54680690	"Demeclocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Bioterciclin\", \"Clortetrin\", \"Deganol\", \"Demeclociclina\", \"Demeclocycline\", \"Demeclocyclinum\", \"Demeclor\", \"Demetraclin\", \"Diuciclin\", \"Elkamicina\", \"Ledermycin\", \"Mexocine\", \"Novotriclina\", \"Perciclina\", \"Sumaclina\")"	0.6	"g"			"c(\"10982-7\", \"29494-2\")"
+"DKB"	"J01GB09"	470999	"Dibekacin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"		"c(\"Debecacin\", \"Dibekacin\", \"Dibekacin sulfate\", \"Dibekacina\", \"Dibekacine\", \"Dibekacinum\", \"Dideoxykanamycin B\", \"Kappati\", \"Orbicin\", \"Panamicin\")"			0.14	"g"	
+"DIC"	"J01CF01"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"		"c(\"Dichloroxacillin\", \"Diclossacillina\", \"Dicloxaciclin\", \"Dicloxacilin\", \"Dicloxacilina\", \"Dicloxacillin\", \"Dicloxacillin sodium\", \"Dicloxacillina\", \"Dicloxacilline\", \"Dicloxacillinum\", \"Dicloxacycline\", \"Dycill\", \"Dynapen\", \"Maclicine\", \"NM|| Dicloxacillin\", \"Pathocil\")"	2	"g"	2	"g"	"c(\"10984-3\", \"16769-2\", \"25252-8\")"
+"DIF"		56206	"Difloxacin"	"Quinolones"				"Difloxacin"					
+"DIR"	"J01FA13"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Dirithromycin\", \"Dirithromycine\", \"Dirithromycinum\", \"Diritromicina\", \"Divitross\", \"Dynabac\", \"Noriclan\", \"Valodin\")"	0.5	"g"			
+"DOR"	"J01DH04"	73303	"Doripenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"c(\"Doribax\", \"Doripenem\", \"Doripenem hydrate\", \"Finibax\")"					
+"DOX"	"J01AA02"	54671203	"Doxycycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"dox\", \"doxy\")"	"c(\"Atridox\", \"Azudoxat\", \"Deoxymykoin\", \"Dossiciclina\", \"DOXCYCLINE ANHYDROUS\", \"Doxiciclina\", \"Doxitard\", \"Doxivetin\", \"Doxycen\", \"Doxychel\", \"Doxycin\", \"Doxycyclin\", \"Doxycycline\", \"DOXYCYCLINE CALCIUM\", \"Doxycycline hyclate\", \"Doxycyclinum\", \"Doxylin\", \"Doxysol\", \"Doxytec\", \"Doxytetracycline\", \"Hydramycin\", \"Investin\", \"Jenacyclin\", \"Liviatin\", \"Monodox\", \"Oracea\", \"Periostat\", \"Ronaxan\", \"Spanor\", \"Supracyclin\", \"Vibramycin\", \"Vibramycin Novum\", \"Vibramycine\", \"Vibravenos\", \"Zenavod\")"	0.1	"g"	0.1	"g"	"c(\"10986-8\", \"21250-6\", \"26902-7\")"
+"ECO"	"J01XDXX"	3198	"Econazole"	"Antifungals/antimycotics"			"econ"	"c(\"Econazol\", \"Econazole\", \"Econazolum\", \"Ecostatin\", \"Ecostatin cream\", \"Palavale\", \"Pevaryl\", \"Spectazole\", \"Spectazole cream\")"					
+"ENX"	"J01MA04"	3229	"Enoxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Almitil\", \"Bactidan\", \"Bactidron\", \"Comprecin\", \"Enofloxacine\", \"Enoksetin\", \"Enoram\", \"Enoxacin\", \"Enoxacina\", \"Enoxacine\", \"Enoxacino\", \"Enoxacinum\", \"Enoxen\", \"Enoxin\", \"Enoxor\", \"Flumark\", \"Penetrex\")"	0.8	"g"			"c(\"16816-1\", \"3590-7\")"
+"ENR"		71188	"Enrofloxacin"	"Quinolones"				"c(\"Baytril\", \"Enrofloxacin\", \"Enrofloxacine\", \"Enrofloxacino\", \"Enrofloxacinum\")"					
+"ENV"		135565326	"Enviomycin (Tuberactinomycin)"	"Antimycobacterials"				"c(\"Enviomicina\", \"ENVIOMYCIN\", \"Enviomycina\", \"Enviomycinum\")"					
+"EPE"			"Eperozolid"	"Other antibacterials"				""					
+"EPC"	"J01CA07"	71392	"Epicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Dexacillin\", \"Dihydroampicillin\", \"Epicilina\", \"Epicillin\", \"Epicilline\", \"Epicillinum\")"	2	"g"	2	"g"	
+"EPP"		68916	"Epiroprim"	"Other antibacterials"				"c(\"Epiroprim\", \"Epiroprima\", \"Epiroprime\", \"Epiroprimum\")"					
+"ERV"	"J01AA13"	54726192	"Eravacycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"erav"	"Eravacycline"					
+"ETP"	"J01DH03"	150610	"Ertapenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"etp"	"c(\"Ertapenem\", \"Invanz\")"			1	"g"	
+"ERY"	"J01FA01"	12560	"Erythromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"e\", \"ery\", \"em\", \"eryt\")"	"c(\"Abboticin\", \"Abomacetin\", \"Acneryne\", \"Acnesol\", \"Akne Cordes Losung\", \"Aknederm Ery Gel\", \"Aknemycin\", \"AustriaS\", \"Benzamycin\", \"Derimer\", \"Deripil\", \"Dotycin\", \"Dumotrycin\", \"Emuvin\", \"Emycin\", \"Endoeritrin\", \"Erecin\", \"Erisone\", \"Eritomicina\", \"Eritrocina\", \"Eritromicina\", \"Ermycin\", \"Eryacne\", \"Eryacnen\", \"Eryc Sprinkles\", \"Erycen\", \"Erycette\", \"Erycin\", \"Erycinum\", \"Eryderm\", \"Erydermer\", \"Erygel\", \"Eryhexal\", \"Erymax\", \"Erymed\", \"Erysafe\", \"Erytab\", \"Erythrocin\", \"Erythrocin stearate\", 
+\"Erythroderm\", \"Erythrogran\", \"Erythroguent\", \"Erythromid\", \"Erythromycin\", \"Erythromycin A\", \"Erythromycin base\", \"Erythromycin Lactate\", \"Erythromycine\", \"Erythromycines\", \"Erythromycinum\", \"Erytop\", \"Erytrociclin\", \"Ilocaps\", \"Ilosone\", \"Iloticina\", \"Ilotycin\", \"Ilotycin gluceptate\", \"Ilotycin T.S.\", \"Inderm\", \"Inderm Gel\", \"IndermRetcin\", \"Latotryd\", \"Lederpax\", \"Mephamycin\", \"Mercina\", \"Oftamolets\", \"Paediathrocin\", \"Pantoderm\", \"Pantodrin\", \"Pantomicina\", \"PCE Dispertab\", \"Pharyngocin\", \"Primacine\", 
+\"Propiocine\", \"Proterytrin\", \"Retcin\", \"Robimycin\", \"Romycin\", \"Sansac\", \"Skid Gel E\", \"Staticin\", \"Stiemicyn\", \"Stiemycin\", \"Theramycin Z\", \"Tiloryth\", \"Tiprocin\", \"Torlamicina\", \"Udima Ery Gel\", \"Wyamycin S\")"	2	"g"	1	"g"	"c(\"12298-6\", \"16829-4\", \"25275-9\", \"3597-2\")"
+"ETH"	"J04AK02"	14052	"Ethambutol"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha"	"c(\"Aethambutolum\", \"Ebutol\", \"Etambutol\", \"Etambutolo\", \"Etapiam\", \"Ethambutol\", \"Ethambutolum\", \"Myambutol\", \"Mycobutol\", \"Purderal\", \"Servambutol\")"	1.2	"g"	1.2	"g"	"c(\"25404-5\", \"3607-9\")"
+"ETI"	"J04AM03"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		""					
+"ETI1"	"J04AD03"	2761171	"Ethionamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"c(\"Aethionamidum\", \"Aetina\", \"Aetiva\", \"Amidazin\", \"Amidazine\", \"Ethatyl\", \"Ethimide\", \"Ethina\", \"Ethinamide\", \"Ethionamide\", \"Ethionamidum\", \"Ethioniamide\", \"Ethylisothiamide\", \"Ethyonomide\", \"Etimid\", \"Etiocidan\", \"Etionamid\", \"Etionamida\", \"Etionamide\", \"Etioniamid\", \"Etionid\", \"Etionizin\", \"Etionizina\", \"Etionizine\", \"Fatoliamid\", \"Iridocin\", \"Iridocin Bayer\", \"Iridozin\", \"Isothin\", \"Isotiamida\", \"Itiocide\", \"Nicotion\", \"Nisotin\", \"Nizotin\", \"Rigenicid\", \"Sertinon\", \"Teberus\", \"Thianid\", \"Thianide\", 
+\"Thioamide\", \"Thiodine\", \"Thiomid\", \"Thioniden\", \"Tianid\", \"Tiomid\", \"Trecator\", \"Trecator SC\", \"Trekator\", \"Trescatyl\", \"Trescazide\", \"Tubenamide\", \"Tubermin\", \"Tuberoid\", \"Tuberoson\")"	0.75	"g"			"16845-0"
+"ETO"		6034	"Ethopabate"	"Other antibacterials"				"c(\"Amprol Plus\", \"Ethopabat\", \"Ethopabate\", \"Ethyl Pabate\")"					
+"FAR"	"J01DI03"	65894	"Faropenem"	"Other antibacterials"				"c(\"Faropenem\", \"Faropenem sodium\", \"Fropenem\", \"Fropenum sodium\")"					
+"FDX"		10034073	"Fidaxomicin"	"Other antibacterials"				"c(\"Dificid\", \"Dificlir\", \"Difimicin\", \"Fidaxomicin\", \"Lipiarmycin\", \"Tiacumicin B\")"					
+"FIN"		11567473	"Finafloxacin"	"Quinolones"				"Finafloxacin"					
+"FLA"		46783781	"Flavomycin"	"Other antibacterials"				"Moenomycin complex"					
+"FLE"	"J01MA08"	3357	"Fleroxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Fleroxacin\", \"Fleroxacine\", \"Fleroxacino\", \"Fleroxacinum\", \"Fleroxicin\", \"Megalocin\", \"Megalone\", \"Megalosin\", \"Quinodis\")"	0.4	"g"	0.4	"g"	
+"FLO"		65864	"Flomoxef"	"Other antibacterials"				"c(\"Flomoxef\", \"Flomoxefo\", \"Flomoxefum\")"					
+"FLR"		114811	"Florfenicol"	"Other antibacterials"				"c(\"Aquafen\", \"Florfenicol\", \"Nuflor\", \"Nuflor gold\")"					"87599-7"
+"FLC"	"J01CF05"	21319	"Flucloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox"	"c(\"Floxacillin\", \"FLOXACILLIN\", \"Floxapen\", \"Floxapen sodium salt\", \"Fluclox\", \"Flucloxacilina\", \"Flucloxacillin\", \"Flucloxacilline\", \"Flucloxacillinum\", \"Fluorochloroxacillin\")"	2	"g"	2	"g"	
+"FLU"	"J02AC01"	3365	"Fluconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"fluz"	"c(\"Alflucoz\", \"Alfumet\", \"Biocanol\", \"Biozole\", \"Biozolene\", \"Canzol\", \"Cryptal\", \"Diflazon\", \"Diflucan\", \"Dimycon\", \"Elazor\", \"Flucazol\", \"Fluconazol\", \"Fluconazole\", \"Fluconazole capsules\", \"Fluconazolum\", \"Flucostat\", \"Flukezol\", \"Flunazol\", \"Flunizol\", \"Flusol\", \"Fluzon\", \"Fluzone\", \"Forcan\", \"Fuconal\", \"Fungata\", \"Loitin\", \"Oxifugol\", \"Pritenzol\", \"Syscan\", \"Trican\", \"Triconal\", \"Triflucan\", \"Zoltec\")"	0.2	"g"	0.2	"g"	"c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")"
+"FLM"	"J01MB07"	3374	"Flumequine"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"		"c(\"Apurone\", \"Fantacin\", \"Flumequine\", \"Flumequino\", \"Flumequinum\", \"Flumigal\", \"Flumiquil\", \"Flumisol\", \"Flumix\", \"Imequyl\")"	1.2	"g"			
+"FLR1"	"J01FA14"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Flurithromicina\", \"Flurithromycime\", \"Flurithromycin\", \"Flurithromycine\", \"Flurithromycinum\", \"Fluritromicina\", \"Fluritromycinum\", \"Flurizic\")"	0.75	"g"			
+"FFL"		214356	"Fosfluconazole"	"Antifungals/antimycotics"				"c(\"Fosfluconazole\", \"Phosfluconazole\", \"Procif\", \"Prodif\")"					
+"FOS"	"J01XX01"	446987	"Fosfomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"fos\", \"ff\", \"fo\", \"fm\", \"fosf\")"	"c(\"Fosfocina\", \"Fosfomicina\", \"Fosfomycin\", \"Fosfomycin sodium\", \"Fosfomycine\", \"Fosfomycinum\", \"Fosfonomycin\", \"Phosphonemycin\", \"Phosphonomycin\", \"Veramina\")"	3	"g"	8	"g"	
+"FMD"		572	"Fosmidomycin"	"Other antibacterials"				"c(\"Fosmidomycin\", \"Fosmidomycina\", \"Fosmidomycine\", \"Fosmidomycinum\")"					
+"FRM"		8378	"Framycetin"	"Aminoglycosides"				"c(\"Actilin\", \"Actiline\", \"Antibiotique\", \"Bycomycin\", \"Endomixin\", \"Enterfram\", \"Fradiomycin\", \"Fradiomycin B\", \"Fradiomycinum\", \"Framicetina\", \"Framycetin\", \"Framycetin sulfate\", \"Framycetine\", \"Framycetinum\", \"Framygen\", \"Fraquinol\", \"Jernadex\", \"Myacine\", \"Myacyne\", \"Mycerin\", \"Mycifradin\", \"Neobrettin\", \"Neolate\", \"Neomas\", \"Neomcin\", \"Neomicina\", \"Neomin\", \"Neomycin\", \"NEOMYCIN B\", \"Neomycin B sulfate\", \"Neomycin solution\", \"NEOMYCIN SULFATE\", \"Neomycin sulphate\", \"NEOMYCINB\", \"Neomycine\", \"Neomycinum\", 
+\"Nivemycin\", \"PIMAVECORT\", \"Soframycin\", \"Soframycine\", \"Tuttomycin\", \"VONAMYCIN\", \"Vonamycin powder V\")"					
+"FRZ"		5323714	"Furazolidone"	"Other antibacterials"				"c(\"Bifuron\", \"Corizium\", \"Coryzium\", \"Diafuron\", \"Enterotoxon\", \"Furall\", \"Furaxon\", \"Furaxone\", \"Furazol\", \"Furazolidine\", \"Furazolidon\", \"Furazolidona\", \"Furazolidone\", \"Furazolidonum\", \"Furazolum\", \"Furazon\", \"Furidon\", \"Furovag\", \"Furox Aerosol Powder\", \"Furoxal\", \"Furoxane\", \"Furoxon\", \"Furoxone\", \"Furoxone Liquid\", \"Furoxone Swine Mix\", \"Furozolidine\", \"Giardil\", \"Giarlam\", \"Medaron\", \"Neftin\", \"Nicolen\", \"Nifulidone\", \"Nifuran\", \"Nifurazolidone\", \"Nifurazolidonum\", \"Nitrofurazolidone\", \"Nitrofurazolidonum\", 
+\"Nitrofuroxon\", \"Optazol\", \"Ortazol\", \"Puradin\", \"Roptazol\", \"Sclaventerol\", \"Tikofuran\", \"Topazone\", \"Trichofuron\", \"Tricofuron\", \"Tricoron\", \"Trifurox\", \"Viofuragyn\")"					
+"FUS"	"J01XC01"	3000226	"Fusidic acid"	"Other antibacterials"	"Other antibacterials"	"Steroid antibacterials"	"fusi"	"c(\"Acide fusidique\", \"Acido fusidico\", \"Acidum fusidicum\", \"Flucidin\", \"Fucidate\", \"Fucidate Sodium\", \"Fucidic acid\", \"FUCIDIN\", \"Fucidin acid\", \"Fucithalmic\", \"Fusidate\", \"Fusidate Acid\", \"Fusidic acid\", \"Fusidine\", \"Fusidinic Acid\", \"Ramycin\")"	1.5	"g"	1.5	"g"	
+"GAM"		59364992	"Gamithromycin"	"Macrolides/lincosamides"				"Gamithromycin"					
+"GRN"		124093	"Garenoxacin"	"Quinolones"				"c(\"Ganefloxacin\", \"Garenfloxacin\", \"Garenoxacin\")"					
+"GAT"	"J01MA16"	5379	"Gatifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Gatiflo\", \"Gatifloxacin\", \"Gatifloxacine\", \"Gatifloxcin\", \"Gatilox\", \"Gatiquin\", \"Gatispan\", \"Tequin\", \"Tequin and Zymar\", \"Zymaxid\")"	0.4	"g"	0.4	"g"	
+"GEM"	"J01MA15"	9571107	"Gemifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Factiv\", \"Factive\", \"Gemifioxacin\", \"Gemifloxacin\", \"Gemifloxacine\", \"Gemifloxacino\", \"Gemifloxacinum\")"					
+"GEN"	"J01GB03"	3467	"Gentamicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"gm\", \"cn\", \"gen\", \"gent\")"	"c(\"Apogen\", \"Centicin\", \"Cidomycin\", \"Garasol\", \"Genoptic Liquifilm\", \"Genoptic S.O.P.\", \"Gentacycol\", \"Gentafair\", \"Gentak\", \"Gentamar\", \"Gentamcin Sulfate\", \"Gentamicin\", \"Gentamicina\", \"Gentamicine\", \"Gentamicins\", \"Gentamicinum\", \"GENTAMYCIN\", \"Gentamycins\", \"Gentamycinum\", \"Gentavet\", \"Gentocin\", \"Jenamicin\", \"Lyramycin\", \"Oksitselanim\", \"Refobacin\", \"Refobacin TM\", \"Septigen\", \"Uromycine\")"			0.24	"g"	"c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
+"GEH"			"Gentamicin-high"	"Aminoglycosides"			"c(\"gehl\", \"gentamicin high\", \"genta high\")"	""					
+"GEP"		25101874	"Gepotidacin"	"Other antibacterials"				"Gepotidacin"					
+"GRX"	"J01MA11"	72474	"Grepafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"Grepafloxacin"	0.4	"g"			
+"GRI"		441140	"Griseofulvin"	"Antifungals/antimycotics"				"c(\"Amudane\", \"Curling factor\", \"Delmofulvina\", \"Fulcin\", \"Fulcine\", \"Fulvican grisactin\", \"Fulvicin\", \"Fulvicin Bolus\", \"Fulvidex\", \"Fulvina\", \"Fulvinil\", \"Fulvistatin\", \"Fungivin\", \"Greosin\", \"Gresfeed\", \"Gricin\", \"Grifulin\", \"Grifulvin\", \"Grifulvin V\", \"Grisactin\", \"Grisactin Ultra\", \"Grisactin V\", \"Griscofulvin\", \"Grise ostatin\", \"Grisefuline\", \"Griseo\", \"Griseofulvin\", \"Griseofulvin forte\", \"Griseofulvina\", \"Griseofulvine\", \"Griseofulvinum\", \"Griseomix\", \"Griseostatin\", \"Grisetin\", \"Grisofulvin\", 
+\"Grisovin\", \"Grisovin FP\", \"Grizeofulvin\", \"Grysio\", \"Guservin\", \"Lamoryl\", \"Likuden\", \"Likunden\", \"Murfulvin\", \"Poncyl\", \"Spirofulvin\", \"Sporostatin xan\", \"Xuanjing\")"					"12402-4"
+"HAB"		175989	"Habekacin"	"Aminoglycosides"				"c(\"Arbekacin sulfate\", \"Habekacin\", \"Habekacin sulfate\", \"Habekacin xsulfate\")"					
+"HCH"	"J02AA02"	11979956	"Hachimycin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Antibiotics"		"c(\"Cabimicina\", \"Hachimicina\", \"Hachimycin\", \"Hachimycine\", \"Hachimycinum\", \"Trichomycinum\", \"Trichonat\")"					
+"HET"	"J01CA18"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Etacillina\", \"Hetacilina\", \"Hetacillin\", \"Hetacilline\", \"Hetacillinum\", \"Phenazacillin\", \"Versapen\")"	2	"g"			
+"HYG"		56928061	"Hygromycin"	"Aminoglycosides"				"c(\"Antihelmycin\", \"Hydromycin B\", \"Hygrovetine\")"					
+"ICL"		213043	"Iclaprim"	"Other antibacterials"				"c(\"Iclaprim\", \"Mersarex\")"					
+"IPM"	"J01DH51"	104838	"Imipenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"imip\", \"imi\", \"imp\")"	"c(\"Imipemide\", \"Imipenem\", \"Imipenem anhydrous\", \"imipenem/cilastatin\", \"Imipenemum\", \"Imipenen\", \"Primaxin\", \"Tienamycin\")"			2	"g"	"c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")"
+"IPE"			"Imipenem/EDTA"	"Carbapenems"				""					
+"IMR"			"Imipenem/relebactam"	"Carbapenems"				""					
+"ISV"		6918485	"Isavuconazole"	"Antifungals/antimycotics"				"Isavuconazole"					
+"ISE"	"J01GB11"	3037209	"Isepamicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"		"c(\"Isepacin\", \"Isepalline\", \"Isepamicin\", \"Isepamicina\", \"Isepamicine\", \"Isepamicinum\")"			0.4	"g"	
+"ISO"	"D01AC05"	3760	"Isoconazole"	"Antifungals/antimycotics"	"Antimycotics for topic use"	"Triazole derivatives"		"c(\"Isoconazol\", \"Isoconazole\", \"Isoconazolum\", \"Travogen\")"					
+"INH"	"J04AC01"	3767	"Isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh"	"c(\"Abdizide\", \"Andrazide\", \"Anidrasona\", \"Antimicina\", \"Antituberkulosum\", \"Armacide\", \"Armazid\", \"Armazide\", \"Atcotibine\", \"AZT + Isoniazid\", \"Azuren\", \"Bacillin\", \"Cemidon\", \"Chemiazid\", \"Chemidon\", \"Continazine\", \"Cortinazine\", \"Cotinazin\", \"Cotinizin\", \"Defonin\", \"Dibutin\", \"Diforin\", \"Dinacrin\", \"Ditubin\", \"Ebidene\", \"Eralon\", \"Ertuban\", \"Eutizon\", \"Evalon\", \"Fetefu\", \"Fimalene\", \"Hid rasonil\", \"Hidranizil\", \"Hidrasonil\", \"Hidrulta\", \"Hidrun\", \"Hycozid\", \"Hydrazid\", \"Hydrazide\", \"Hyozid\", \"I.A.I.\", 
+\"Idrazil\", \"Inizid\", \"Iscotin\", \"Isidrina\", \"Ismazide\", \"Isobicina\", \"Isocid\", \"Isocidene\", \"Isocotin\", \"Isohydrazide\", \"Isokin\", \"Isolyn\", \"Isonerit\", \"Isonex\", \"Isoniacid\", \"Isoniazid\", \"Isoniazid SA\", \"Isoniazida\", \"Isoniazide\", \"Isoniazidum\", \"Isonicazide\", \"Isonicid\", \"Isonico\", \"Isonicotan\", \"Isonicotil\", \"Isonicotinhydrazid\", \"Isonicotinohydrazide\", \"Isonide\", \"Isonidrin\", \"Isonikazid\", \"Isonilex\", \"Isonin\", \"Isonindon\", \"Isonirit\", \"Isoniton\", \"Isonizida\", \"Isonizide\", \"Isotamine\", \"Isotebe\", 
+\"Isotebezid\", \"Isotinyl\", \"Isozid\", \"Isozide\", \"Isozyd\", \"Laniazid\", \"Laniozid\", \"LANIZID\", \"Mayambutol\", \"Mybasan\", \"Neoteben\", \"Neoxin\", \"Neumandin\", \"Niadrin\", \"Nicazide\", \"Nicetal\", \"Nicizina\", \"Niconyl\", \"Nicotibina\", \"Nicotibine\", \"Nicotisan\", \"Nicozide\", \"Nidaton\", \"Nidrazid\", \"Nikozid\", \"Niplen\", \"Nitadon\", \"Niteban\", \"Nydrazid\", \"Nyscozid\", \"Pelazid\", \"Percin\", \"Phthisen\", \"Pycazide\", \"Pyreazid\", \"Pyricidin\", \"Pyridicin\", \"Pyrizidin\", \"Raumanon\", \"Razide\", \"Retozide\", \"Rifater\", \"Rimicid\", 
+\"Rimifon\", \"Rimiphone\", \"Rimitsid\", \"Robiselin\", \"Robisellin\", \"Roxifen\", \"Sanohidrazina\", \"Sauterazid\", \"Sauterzid\", \"Stanozide\", \"Tebecid\", \"Tebenic\", \"Tebexin\", \"Tebilon\", \"Teebaconin\", \"Tekazin\", \"Tibazide\", \"Tibemid\", \"Tibiazide\", \"Tibinide\", \"Tibison\", \"Tibivis\", \"Tibizide\", \"Tibusan\", \"Tisiodrazida\", \"Tizide\", \"Tubazid\", \"Tubazide\", \"Tubeco\", \"Tubecotubercid\", \"Tuberian\", \"Tubicon\", \"Tubilysin\", \"Tubizid\", \"Tubomel\", \"Unicocyde\", \"Unicozyde\", \"Vazadrine\", \"Vederon\", \"Zidafimia\", \"Zinadon\", 
+\"Zonazide\")"	0.3	"g"	0.3	"g"	"c(\"25451-6\", \"26756-7\", \"3697-0\", \"40371-7\")"
+"ITR"	"J02AC02"	3793	"Itraconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra"	"c(\"Itraconazol\", \"Itraconazole\", \"Itraconazolum\", \"Itraconzaole\", \"ITRAZOLE\", \"Oriconazole\", \"Sporanox\")"	0.2	"g"	0.2	"g"	"c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")"
+"JOS"	"J01FA07"	5282165	"Josamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Josacine\", \"Josamicina\", \"Josamycin\", \"Josamycine\", \"Josamycinum\")"	2	"g"			
+"KAN"	"J01GB04"	6032	"Kanamycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"k\", \"kan\", \"hlk\", \"km\", \"kana\")"	"c(\"Kanamicina\", \"Kanamycin\", \"KANAMYCIN A\", \"Kanamycin Base\", \"Kanamycine\", \"Kanamycinum\", \"Kantrex\", \"Kenamycin A\", \"Klebcil\", \"Liposomal Kanamycin\")"			1	"g"	"c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")"
+"KAH"			"Kanamycin-high"	"Aminoglycosides"				""					
+"KAC"			"Kanamycin/cephalexin"	"Aminoglycosides"				""					
+"KET"	"J02AB02"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Imidazole derivatives"	"keto"	"c(\"Extina\", \"Fungarest\", \"Fungoral\", \"Ketocanazole\", \"Ketoconazol\", \"Ketoconazole\", \"Ketoconazolum\", \"Ketoderm\", \"Nizoral\", \"Xolegel\")"	0.2	"g"			"c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")"
+"KIT"			"Kitasamycin (Leucomycin)"	"Macrolides/lincosamides"				""					
+"LAS"		5360807	"Lasalocid"	"Other antibacterials"				"c(\"Avatec\", \"Lasalocid\", \"Lasalocid A\", \"Lasalocide\", \"Lasalocide A\", \"Lasalocido\", \"Lasalocidum\")"					"87598-9"
+"LTM"	"J01DD06"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"MOX\", \"moxa\")"	"c(\"Disodium Moxalactam\", \"Festamoxin\", \"Lamoxactam\", \"Latamoxef\", \"Latamoxefum\", \"Shiomarin\")"			4	"g"	
+"LMU"		25185057	"Lefamulin"	"Other antibacterials"				"Lefamulin"					
+"LEN"		65646	"Lenampicillin"	"Beta-lactams/penicillins"				"c(\"Lenampicilina\", \"Lenampicillin\", \"Lenampicillin HCl\", \"Lenampicilline\", \"Lenampicillinum\")"					
+"LVX"	"J01MA12"	149096	"Levofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"lvx\", \"lev\", \"levo\", \"le\")"	"c(\"Aeroquin\", \"Cravit\", \"Cravit hydrate\", \"Cravit IV\", \"Cravit Ophthalmic\", \"Elequine\", \"Floxacin\", \"Floxel\", \"Iquix hydrate\", \"Leroxacin\", \"Lesacin\", \"Levaquin\", \"Levaquin hydrate\", \"Levo Floxacin\", \"Levofiexacin\", \"Levofloxacin\", \"Levofloxacin hydrate\", \"Levofloxacine\", \"Levofloxacino\", \"Levofloxacinum\", \"Levokacin\", \"Levoxacin\", \"Mosardal\", \"Nofaxin\", \"Oftaquix\", \"Quixin\", \"Reskuin\", \"Tavanic\", \"Unibiotic\", \"Venaxan\", \"Volequin\")"	0.5	"g"	0.5	"g"	"c(\"21368-6\", \"30532-6\", \"30533-4\")"
+"LND"		9850038	"Levonadifloxacin"	"Quinolones"				"Levonadifloxacin"					
+"LSP"			"Linco-spectin (lincomycin/spectinomycin)"	"Other antibacterials"				""					
+"LIN"	"J01FF02"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc"	"c(\"Cillimycin\", \"Jiemycin\", \"Lincolcina\", \"Lincolnensin\", \"Lincomicina\", \"Lincomycin\", \"Lincomycin A\", \"Lincomycine\", \"Lincomycinum\")"	1.8	"g"	1.8	"g"	"87597-1"
+"LNZ"	"J01XX08"	441401	"Linezolid"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"lzd\", \"lnz\", \"lz\", \"line\")"	"c(\"Linezlid\", \"Linezoid\", \"Linezolid\", \"LINEZOLIDE\", \"Linezolidum\", \"Zivoxid\", \"Zyvoxa\", \"Zyvoxam\", \"Zyvoxid\")"	1.2	"g"	1.2	"g"	"c(\"34202-2\", \"80609-1\")"
+"LFE"			"Linoprist-flopristin"	"Other antibacterials"				""					
+"LOM"	"J01MA07"	3948	"Lomefloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"lmf\", \"lom\", \"lome\")"	"c(\"Lomefloxacin\", \"Lomefloxacine\", \"Lomefloxacino\", \"Lomefloxacinum\", \"Maxaquin\")"					
+"LOR"	"J01DC08"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"		"c(\"Anhydrous loracarbef\", \"Lorabid\", \"Loracarbef\", \"Loracarbefum\", \"Lorbef\", \"Loribid\")"	0.6	"g"			
+"LYM"	"J01AA04"	54707177	"Lymecycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Biovetin\", \"Chlortetracyclin\", \"Ciclisin\", \"Ciclolysal\", \"Infaciclina\", \"Limeciclina\", \"Lisinbiotic\", \"Lymecyclin\", \"Lymecycline\", \"Lymecyclinum\", \"Mucomycin\", \"Ntetracycline\", \"Tetralisal\", \"Tetralysal\", \"Vebicyclysal\")"	0.6	"g"	0.6	"g"	
+"MNA"	"J01XX06"	1292	"Mandelic acid"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"		"c(\"Acido mandelico\", \"Almond acid\", \"Amygdalic acid\", \"Benzoglycolic acid\", \"Hydroxyacetic acid\", \"Kyselina mandlova\", \"Mandelic acid\", \"Mandelic Acid\", \"Paramandelic acid\", \"Phenylglycolic acid\", \"Uromaline\")"	12	"g"			
+"MAR"		60651	"Marbofloxacin"	"Quinolones"				"c(\"Marbocyl\", \"Marbofloxacin\", \"Marbofloxacine\", \"Marbofloxacino\", \"Marbofloxacinum\", \"Zeniquin\")"					
+"MEC"	"J01CA11"	36273	"Mecillinam (Amdinocillin)"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Amdinocillin\", \"AMDINOCILLIN\", \"Coactin\", \"Hexacillin\", \"Mecilinamo\", \"Mecillinam\", \"Mecillinamum\", \"MICILLINAM\", \"Penicillin HX\", \"Selexidin\")"			1.2	"g"	
+"MEL"		71306732	"Meleumycin"	"Macrolides/lincosamides"				""					
+"MEM"	"J01DH02"	441130	"Meropenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"mer\", \"mem\", \"mero\", \"mrp\", \"mp\")"	"c(\"Meronem\", \"MERONEM\", \"Meropen\", \"Meropenem\", \"Meropenem anhydrous\", \"Meropenem Hydrate\", \"Meropenem trihydrate\", \"Meropenemum\", \"Merrem\", \"Merrem I.V.\", \"Merrem IV\")"			2	"g"	"41406-0"
+"MNC"			"Meropenem/nacubactam"	"Carbapenems"				""					
+"MEV"	"J01DH52"		"Meropenem/vaborbactam"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"		""					
+"MES"		176886	"Mesulfamide"	"Other antibacterials"				"c(\"Mesulfamide\", \"Mesulfamido\", \"Mesulfamidum\")"					
+"MTC"	"J01AA05"	54675785	"Metacycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Bialatan\", \"Metaciclina\", \"Metacycline\", \"Metacyclinum\", \"Methacycline\", \"Methacycline base\", \"Methacyclinum\", \"Methylenecycline\", \"Physiomycine\", \"Rondomycin\")"	0.6	"g"			
+"MTM"	"J01CA14"	6713928	"Metampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Blomopen\", \"Bonopen\", \"Celinmicina\", \"Elatocilline\", \"Fedacilina kapseln\", \"Filorex\", \"Italcina kapseln\", \"Magnipen\", \"Metabacter ampullen\", \"Metambac\", \"Metampicilina\", \"Metampicillin\", \"METAMPICILLIN SODIUM\", \"Metampicillina\", \"Metampicilline\", \"Metampicillinum\", \"METHAMPICILLIN\", \"Metiskia ampullen\", \"Micinovo\", \"Micinovo ampullen\", \"Pangocilin\", \"Probiotic\", \"Rastomycin K\", \"Relyothenate\", \"Ruticina\", \"Rutizina\", \"Rutizina ampullen\", \"Sedomycin\", \"Suvipen\", \"Suvipen ampullen\", \"Tampilen ampullen\", 
+\"Teonicon Trofen\", \"Viderpen\", \"Viderpin\", \"Vioplex\")"	1.5	"g"	1.5	"g"	
+"MTH"	"J01XX05"	4101	"Methenamine"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"		"c(\"Aceto HMT\", \"Aminoform\", \"Aminoformaldehyde\", \"Ammoform\", \"Ammonioformaldehyde\", \"Antihydral\", \"Cystamin\", \"Cystex\", \"Cystogen\", \"Duirexol\", \"Ekagom H\", \"Esametilentetramina\", \"Formamine\", \"Formin\", \"H.M.T.\", \"Heksa K\", \"Herax UTS\", \"Heterin\", \"Hexa B\", \"Hexaform\", \"Hexaloids\", \"Hexamethylamine\", \"Hexamethylenamine\", \"Hexamethyleneamine\", \"Hexamethylentetramin\", \"Hexamine\", \"Hexamine Silver\", \"Hexamine Superfine\", \"Hexaminum\", \"Hexasan\", \"Hexilmethylenamine\", \"Metenamina\", \"Metenamine\", \"Methamin\", 
+\"Methenamin\", \"Methenamine\", \"Methenamine Silver\", \"Methenaminum\", \"Metramine\", \"Naphthamine\", \"Nocceler H\", \"Preparation AF\", \"Resotropin\", \"Sanceler H\", \"Sanceler HT\", \"Silver Methenamine\", \"Uramin\", \"Uratrine\", \"Urisol\", \"Uritone\", \"Urodeine\", \"Urotropin\", \"Urotropine\", \"Vesaloin\", \"Vesalvine\", \"Xametrin\")"	3	"g"			
+"MET"	"J01CF03"	6087	"Methicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"meti"	"c(\"Dimocillin\", \"Metacillin\", \"Methcilline\", \"Methicillin\", \"Methicillinum\", \"Methycillin\", \"Meticilina\", \"Meticillin\", \"Meticillina\", \"Meticilline\", \"Meticillinum\", \"Staphcillin\")"			4	"g"	"c(\"29492-6\", \"3788-7\")"
+"MTP"		68590	"Metioprim"	"Other antibacterials"				"c(\"Methioprim\", \"Metioprim\", \"Metioprima\", \"Metioprime\", \"Metioprimum\")"					
+"MXT"		3047729	"Metioxate"	"Quinolones"				"c(\"Metioxate\", \"Metioxato\", \"Metioxatum\")"					
+"MTR"	"J01XD01"	4173	"Metronidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"	"c(\"mnz\", \"metr\")"	"c(\"Acromona\", \"Anagiardil\", \"Arilin\", \"Atrivyl\", \"Danizol\", \"Deflamon\", \"Efloran\", \"Elyzol\", \"Entizol\", \"Flagemona\", \"Flagesol\", \"Flagil\", \"Flagyl\", \"Flagyl Er\", \"Flagyl I.V.\", \"Flagyl I.V. RTU\", \"Flazol\", \"Flegyl\", \"Florazole\", \"Fossyol\", \"Giatricol\", \"Ginefla vir\", \"Gineflavir\", \"HELIDAC\", \"Mepagyl\", \"Meronidal\", \"Methronidazole\", \"Metric\", \"Metro Cream\", \"Metro Gel\", \"METRO I.V\", \"Metro I.V.\", \"Metro IV\", \"MetroCream\", \"Metrodzhil\", \"MetroGel\", \"Metrogyl\", \"Metrolag\", \"MetroLotion\", \"Metrolyl\", 
+\"Metromidol\", \"Metronidaz\", \"Metronidazol\", \"Metronidazole\", \"METRONIDAZOLE USP\", \"Metronidazolo\", \"Metronidazolum\", \"Metrotop\", \"Metrozine\", \"Metryl\", \"Mexibol\", \"Mexibol 'silanes'\", \"Monagyl\", \"Monasin\", \"Nidagel\", \"Nidagyl\", \"Noritate\", \"Novonidazol\", \"Orvagil\", \"Polibiotic\", \"Protostat\", \"Rathimed\", \"Rosased\", \"Sanatrichom\", \"Satric\", \"Takimetol\", \"Trichazol\", \"Trichex\", \"Tricho cordes\", \"Trichobrol\", \"Trichocide\", \"Trichomol\", \"Trichopal\", \"Trichopol\", \"Tricocet\", \"Tricom\", \"Tricowas B\", \"Trikacide\", 
+\"Trikamon\", \"Trikhopol\", \"Trikojol\", \"Trikozol\", \"Trimeks\", \"Trivazol\", \"Vagilen\", \"Vagimid\", \"Vandazole\", \"Vertisal\", \"Wagitran\", \"Zadstat\", \"Zidoval\")"			1.5	"g"	"10991-8"
+"MEZ"	"J01CA10"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"mz\", \"mez\")"	"c(\"Mezlin\", \"Mezlocilina\", \"Mezlocillin\", \"Mezlocillin acid\", \"MEZLOCILLIN SODIUM\", \"Mezlocilline\", \"Mezlocillinum\", \"Multocillin\")"			6	"g"	"3820-8"
+"MSU"			"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"				""					
+"MIF"	"J02AX05"	477468	"Micafungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"		"c(\"Micafungin\", \"Mycamine\")"			0.1	"g"	"58418-5"
+"MCZ"	"J02AB01"	4189	"Miconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"c(\"Aflorix\", \"Albistat\", \"Andergin\", \"Brentan\", \"Conofite\", \"Dactarin\", \"Daktarin\", \"Daktarin IV\", \"Florid\", \"Lotrimin AF\", \"Micantin\", \"Miconasil Nitrate\", \"Miconazol\", \"Miconazole\", \"Miconazole Base\", \"Miconazolo\", \"Miconazolum\", \"Micozole\", \"Minostate\", \"Monista\", \"Monistat\", \"Monistat IV\", \"Oravig\", \"Vusion\", \"Zimybase\", \"Zimycan\")"			1	"g"	"17278-3"
+"MCR"		3037206	"Micronomicin"	"Aminoglycosides"				"c(\"Gentamicin C\", \"Micromycin\", \"Micronomicin\", \"Micronomicina\", \"Micronomicine\", \"Micronomicinum\", \"Sagamicin\", \"Santemycin\")"					
+"MID"	"J01FA03"	5282169	"Midecamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Aboren\", \"Espinomycin A\", \"Macropen\", \"Madecacine\", \"Medemycin\", \"Midecamicina\", \"Midecamycin\", \"Midecamycin A\", \"Midecamycine\", \"Midecamycinum\", \"Midecin\", \"Momicine\", \"Mydecamycin\", \"Myoxam\", \"Normicina\", \"Rubimycin\", \"Turimycin P\")"			1	"g"	
+"MIL"		37614	"Miloxacin"	"Quinolones"				"c(\"Miloxacin\", \"Miloxacine\", \"Miloxacino\", \"Miloxacinum\")"					
+"MNO"	"J01AA08"	54675783	"Minocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"min\", \"mi\", \"mn\", \"mno\", \"mc\", \"mh\", \"mino\")"	"c(\"Akamin\", \"Aknemin\", \"Borymycin\", \"Dynacin\", \"Klinomycin\", \"Minociclina\", \"Minocin\", \"Minocline\", \"Minocyclin\", \"Minocycline\", \"Minocyclinum\", \"Minocyn\", \"Minoderm\", \"Minomycin\", \"Sebomin\", \"Solodyn\", \"Vectrin\")"	0.2	"g"	0.2	"g"	"c(\"34606-4\", \"3822-4\", \"49757-8\")"
+"MCM"	"J01FA11"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Acecamycin\", \"Macroral\", \"Midecamycin acetate\", \"Miocamen\", \"Miocamycine\", \"Miokamycin\", \"Myocamicin\", \"Ponsinomycin\")"	1.2	"g"			
+"MON"		23667299	"Monensin sodium"	"Other antibacterials"				"c(\"Monensin sodium\", \"Sodium monensin\")"					
+"MRN"	"J04AK04"	70374	"Morinamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"		"c(\"Morfazinamide\", \"Morfazinammide\", \"Morfgazinamide\", \"Morinamida\", \"Morinamide\", \"Morinamidum\", \"Morphazinamid\", \"Morphazinamide\", \"Piazofolina\", \"Piazolin\", \"Piazolina\")"					
+"MFX"	"J01MA14"	152946	"Moxifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"mox\", \"mxf\", \"moxi\")"	"c(\"Actira\", \"Avelox\", \"Avelox I.V.\", \"Avelox IV\", \"Avolex\", \"Izilox\", \"Moxeza\", \"Moxifloxacin\", \"Moxifloxacine\", \"Vigamox\")"	0.4	"g"	0.4	"g"	"c(\"43751-7\", \"45223-5\", \"80540-8\")"
+"MUP"	"R01AX06"	446596	"Mupirocin"	"Other antibacterials"			"c(\"mup\", \"mupi\")"	"c(\"Bactoderm\", \"Bactroban\", \"Bactroban Nasal\", \"Bactroban Ointment\", \"Centany\", \"Mupirocin\", \"Mupirocina\", \"Mupirocine\", \"Mupirocinum\", \"Plasimine\", \"Pseudomonic acid\", \"Pseudomonic acid A\", \"Turixin\")"					
+"NAC"		73386748	"Nacubactam"	"Beta-lactams/penicillins"				"Nacubactam"					
+"NAD"		4410	"Nadifloxacin"	"Quinolones"				"c(\"Acuatim\", \"Nadifloxacin\", \"Nadifloxacine\", \"Nadifloxacino\", \"Nadifloxacinum\", \"Nadixa\", \"Nadoxin\")"					
+"NAF"		8982	"Nafcillin"	"Beta-lactams/penicillins"				"c(\"Nafcilina\", \"Nafcillin\", \"NAFCILLIN SODIUM\", \"Nafcilline\", \"Nafcillinum\", \"Nallpen\", \"Naphcillin\", \"Unipen\")"					"c(\"10993-4\", \"25232-0\")"
+"ZWK"		117587595	"Nafithromycin"	"Macrolides/lincosamides"				"Nafithromycin"					
+"NAL"	"J01MB02"	4421	"Nalidixic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"c(\"na\", \"nal\", \"nali\")"	"c(\"Acide nalidixico\", \"Acide nalidixique\", \"Acido nalidissico\", \"Acido nalidixico\", \"Acidum nalidixicum\", \"Betaxina\", \"Dixiben\", \"Dixinal\", \"Eucisten\", \"Eucistin\", \"Innoxalomn\", \"Innoxalon\", \"Jicsron\", \"Kusnarin\", \"Naldixic acid\", \"Nalidic acid\", \"Nalidicron\", \"Nalidixan\", \"Nalidixane\", \"Nalidixate\", \"NALIDIXATE SODIUM\", \"Nalidixic\", \"Nalidixic acid\", \"Nalidixin\", \"Nalidixinic acid\", \"Nalidixinsaure\", \"Nalitucsan\", \"Nalurin\", \"Narigix\", \"Naxuril\", \"NegGram\", \"Negram\", \"Nevigramon\", \"Nicelate\", \"Nogram\", 
+\"Poleon\", \"Sicmylon\", \"Specifen\", \"Specifin\", \"Unaserus\", \"Uralgin\", \"Uriben\", \"Uriclar\", \"Urisal\", \"Urodixin\", \"Uroman\", \"Uroneg\", \"Uronidix\", \"Uropan\", \"Wintomylon\", \"Wintron\")"	4	"g"			
+"NAR"		65452	"Narasin"	"Other antibacterials"				"c(\"Monteban\", \"Narasin\", \"Narasin A\", \"Narasine\", \"Narasino\", \"Narasinum\", \"Narasul\")"					"87570-8"
+"NEO"	"J01GB05"	8378	"Neomycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom"	"c(\"Actilin\", \"Actiline\", \"Antibiotique\", \"Bycomycin\", \"Endomixin\", \"Enterfram\", \"Fradiomycin\", \"Fradiomycin B\", \"Fradiomycinum\", \"Framicetina\", \"Framycetin\", \"Framycetin sulfate\", \"Framycetine\", \"Framycetinum\", \"Framygen\", \"Fraquinol\", \"Jernadex\", \"Myacine\", \"Myacyne\", \"Mycerin\", \"Mycifradin\", \"Neobrettin\", \"Neolate\", \"Neomas\", \"Neomcin\", \"Neomicina\", \"Neomin\", \"Neomycin\", \"NEOMYCIN B\", \"Neomycin B sulfate\", \"Neomycin solution\", \"NEOMYCIN SULFATE\", \"Neomycin sulphate\", \"NEOMYCINB\", \"Neomycine\", \"Neomycinum\", 
+\"Nivemycin\", \"PIMAVECORT\", \"Soframycin\", \"Soframycine\", \"Tuttomycin\", \"VONAMYCIN\", \"Vonamycin powder V\")"	1	"g"			"c(\"10995-9\", \"25262-7\")"
+"NET"	"J01GB07"	441306	"Netilmicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti"	"c(\"Netillin\", \"Netilmicin\", \"NETILMICIN SULFATE\", \"Netilmicina\", \"Netilmicine\", \"Netilmicinum\", \"Netilyn\", \"Netira\", \"Vectacin\")"	0.35	"g"	0.35	"g"	"c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")"
+"NIC"		9507	"Nicarbazin"	"Other antibacterials"				"c(\"Nicarb\", \"Nicarbasin\", \"Nicarbazin\", \"Nicarbazine\", \"Nicoxin\", \"Nicrazin\", \"Nicrazine\", \"Nirazin\")"					
+"NIF"		71946	"Nifuroquine"	"Quinolones"				"c(\"Nifuroquina\", \"Nifuroquine\", \"Nifuroquinum\", \"Quinaldofur\")"					
+"NFR"	"J01XE02"	9571062	"Nifurtoinol"	"Other antibacterials"	"Other antibacterials"	"Nitrofuran derivatives"		"c(\"Levantin\", \"Nifurtoinol\", \"Nifurtoinolo\", \"Nifurtoinolum\", \"Urfadin\", \"Urfadine\", \"Urfadyn\")"	0.16	"g"			
+"NTZ"		41684	"Nitazoxanide"	"Other antibacterials"				"c(\"Adrovet\", \"Alinia\", \"AZT + Nitazoxanide\", \"Colufase\", \"Cryptaz\", \"Dexidex\", \"Heliton\", \"Kidonax\", \"Nitaxozanid\", \"Nitaxozanide\", \"Nitazox\", \"Nitazoxamide\", \"Nitazoxanid\", \"Nitazoxanida\", \"Nitazoxanide\", \"Nitazoxanidum\", \"Omniparax\", \"Pacovanton\", \"Paramix\", \"Taenitaz\")"					
+"NIT"	"J01XE01"	6604200	"Nitrofurantoin"	"Other antibacterials"	"Other antibacterials"	"Nitrofuran derivatives"	"c(\"fd\", \"f/m\", \"ft\", \"nit\", \"ni\", \"f\", \"nitr\")"	"c(\"Alfuran\", \"Benkfuran\", \"Berkfuran\", \"Berkfurin\", \"Ceduran\", \"Chemiofuran\", \"Cistofuran\", \"Cyantin\", \"Cystit\", \"Dantafur\", \"Fua Med\", \"Fuamed\", \"Furabid\", \"Furachel\", \"Furadantin\", \"Furadantin Retard\", \"Furadantina MC\", \"Furadantine\", \"Furadantine mc\", \"Furadantoin\", \"Furadoin\", \"Furadoine\", \"Furadonin\", \"Furadonine\", \"Furadoninum\", \"Furadontin\", \"Furadoxyl\", \"Furalan\", \"Furaloid\", \"Furantoin\", \"Furantoina\", \"Furatoin\", \"Furedan\", \"Furina\", \"Furobactina\", \"Furodantin\", \"Furophen T\", \"Gerofuran\", 
+\"Io>>uss>>a<<IxOo\", \"Ituran\", \"Ivadantin\", \"Macpac\", \"Macrobid\", \"Macrodantin\", \"Macrodantina\", \"Macrofuran\", \"Macrofurin\", \"Nierofu\", \"Nifurantin\", \"Nifuretten\", \"Nitoin\", \"Nitrex\", \"Nitrofuradantin\", \"NITROFURANTION\", \"Nitrofurantoin\", \"Nitrofurantoin Macro\", \"Nitrofurantoina\", \"Nitrofurantoine\", \"Nitrofurantoinum\", \"Novofuran\", \"Orafuran\", \"Parfuran\", \"Phenurin\", \"PiyEloseptyl\", \"Siraliden\", \"Trantoin\", \"Uerineks\", \"Urantoin\", \"Urizept\", \"Urodin\", \"Urofuran\", \"Urofurin\", \"Urolisa\", \"Urolong\", 
+\"Uvamin\", \"Welfurin\", \"Zoofurin\")"	0.2	"g"			"3860-4"
+"NIZ"		5447130	"Nitrofurazone"	"Other antibacterials"				"c(\"Acutol\", \"Aldomycin\", \"Alfucin\", \"Amifur\", \"Babrocid\", \"Becafurazone\", \"Biofuracina\", \"Biofurea\", \"Chemofuran\", \"Chixin\", \"Cocafurin\", \"Coxistat\", \"Dermofural\", \"Dymazone\", \"Dynazone\", \"Eldezol\", \"Fedacin\", \"Flavazone\", \"Fracine\", \"Furacilin\", \"Furacilinum\", \"Furacillin\", \"Furacin\", \"Furacine\", \"Furacinetten\", \"Furacoccid\", \"Furacort\", \"Furacycline\", \"Furaderm\", \"Furagent\", \"Furalcyn\", \"Furaldon\", \"Furalone\", \"Furametral\", \"Furaplast\", \"Furaseptyl\", \"Furaskin\", \"Furatsilin\", \"Furaziline\", \"Furazin\", 
+\"Furazina\", \"Furazol W\", \"Furazone\", \"Furazyme\", \"Furesol\", \"Furfurin\", \"Furosem\", \"Fuvacillin\", \"Hemofuran\", \"Ibiofural\", \"Mammex\", \"Mastofuran\", \"Monafuracin\", \"Monafuracis\", \"Monofuracin\", \"Nfz mix\", \"Nifucin\", \"Nifurid\", \"Nifuzon\", \"Nitrofural\", \"Nitrofuralum\", \"Nitrofuran\", \"Nitrofurane\", \"Nitrofurazan\", \"Nitrofurazone\", \"Nitrofurazonum\", \"Nitrofurol\", \"Nitrozone\", \"Otofural\", \"Otofuran\", \"Rivafurazon\", \"Sanfuran\", \"Vabrocid\", \"Vadrocid\", \"Yatrocin\")"					
+"NTR"	"J01XX07"	19910	"Nitroxoline"	"Quinolones"	"Other antibacterials"	"Other antibacterials"		"c(\"Galinok\", \"Isinok\", \"Nibiol\", \"Nicene Forte\", \"Nitroxolin\", \"Nitroxolina\", \"Nitroxoline\", \"Nitroxolinum\", \"Notroxoline\", \"Noxibiol\")"	1	"g"			
+"NOR"	"J01MA06"	4539	"Norfloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"nxn\", \"nor\", \"nx\", \"norf\")"	"c(\"Baccidal\", \"Barazan\", \"Chibroxin\", \"Chibroxine\", \"Chibroxol\", \"Fulgram\", \"Gonorcin\", \"Lexinor\", \"Nolicin\", \"Noracin\", \"Noraxin\", \"Norflo\", \"Norfloxacin\", \"Norfloxacine\", \"Norfloxacino\", \"Norfloxacinum\", \"Norocin\", \"Noroxin\", \"Noroxine\", \"Norxacin\", \"Sebercim\", \"Uroxacin\", \"Utinor\", \"Zoroxin\")"	0.8	"g"			"3867-9"
+"NVA"		10419027	"Norvancomycin"	"Glycopeptides"				"Norvancomycin"					
+"NOV"	"QJ01XX95"	54675769	"Novobiocin"	"Other antibacterials"			"novo"	"c(\"Albamix\", \"Albamycin\", \"Cardelmycin\", \"Cathocin\", \"Cathomycin\", \"Crystallinic acid\", \"Inamycin\", \"Novobiocin\", \"Novobiocina\", \"Novobiocine\", \"Novobiocinum\", \"Robiocina\", \"Sirbiocina\", \"Spheromycin\", \"Stilbiocina\", \"Streptonivicin\")"					"17378-1"
+"NYS"	"G01AA01"	6433272	"Nystatin"	"Antifungals/antimycotics"			"nyst"	"c(\"Biofanal\", \"Candex Lotion\", \"Comycin\", \"Diastatin\", \"Herniocid\", \"Moronal\", \"Myconystatin\", \"Mycostatin\", \"Mycostatin Pastilles\", \"Mykinac\", \"Mykostatyna\", \"Nilstat\", \"Nistatin\", \"Nistatina\", \"Nyamyc\", \"Nyotran\", \"Nyotrantrade mark\", \"Nystaform\", \"Nystan\", \"Nystatin\", \"Nystatin A\", \"Nystatin G\", \"Nystatin LF\", \"Nystatine\", \"Nystatinum\", \"Nystatyna\", \"Nystavescent\", \"Nystex\", \"Nystop\", \"Stamycin\", \"Terrastatin\", \"Zydin E\")"					
+"OFX"	"J01MA01"	4583	"Ofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"ofl\", \"ofx\", \"of\", \"oflo\")"	"c(\"Bactocin\", \"Danoflox\", \"Effexin\", \"Exocin\", \"Exocine\", \"Flobacin\", \"Flodemex\", \"Flotavid\", \"Flovid\", \"Floxal\", \"Floxil\", \"Floxin\", \"Floxin otic\", \"Floxstat\", \"Fugacin\", \"Inoflox\", \"Kinflocin\", \"Kinoxacin\", \"LEVOFLOXACIN HCL\", \"Liflox\", \"Loxinter\", \"Marfloxacin\", \"Medofloxine\", \"Mergexin\", \"Monoflocet\", \"Novecin\", \"Nufafloqo\", \"Occidal\", \"Ocuflox\", \"Oflocee\", \"Oflocet\", \"Oflocin\", \"Oflodal\", \"Oflodex\", \"Oflodura\", \"Ofloxacin\", \"Ofloxacin Otic\", \"Ofloxacina\", \"Ofloxacine\", \"Ofloxacino\", \"Ofloxacinum\", 
+\"Ofloxin\", \"Onexacin\", \"Operan\", \"Orocin\", \"Otonil\", \"Oxaldin\", \"Pharflox\", \"Praxin\", \"Puiritol\", \"Qinolon\", \"Quinolon\", \"Quotavil\", \"Sinflo\", \"Tabrin\", \"Taravid\", \"Tariflox\", \"Tarivid\", \"Telbit\", \"Tructum\", \"Uro Tarivid\", \"Viotisone\", \"Visiren\", \"Zanocin\")"	0.4	"g"	0.4	"g"	"c(\"25264-3\", \"3877-8\")"
+"OLE"	"J01FA05"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Amimycin\", \"Landomycin\", \"Matromycin\", \"Oleandomycin A\", \"Romicil\")"	1	"g"			
+"OMC"		54697325	"Omadacycline"	"Tetracyclines"				"c(\"Amadacycline\", \"Omadacycline\")"					
+"OPT"		87880	"Optochin"	"Other antibacterials"				"c(\"Numoquin\", \"Optochin\", \"Optoquine\")"					
+"ORB"		60605	"Orbifloxacin"	"Quinolones"				"Orbifloxacin"					
+"ORI"	"J01XA05"	16136912	"Oritavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit"	"Oritavancin"					
+"ORS"			"Ormetroprim/sulfamethoxazole"	"Other antibacterials"				""					
+"ORN"	"J01XD03"	28061	"Ornidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"		"c(\"Madelen\", \"Ornidal\", \"Ornidazol\", \"Ornidazole\", \"Ornidazolum\", \"Tiberal\")"			1	"g"	
+"OXA"	"J01CF04"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"ox\", \"oxs\", \"oxa\", \"oxac\")"	"c(\"Bactocill\", \"Ossacillina\", \"Oxacilina\", \"Oxacillin\", \"OXACILLIN SODIUM\", \"Oxacilline\", \"Oxacillinum\", \"Oxazocillin\", \"Oxazocilline\", \"Prostaphlin\", \"Prostaphlyn\", \"Sodium oxacillin\")"	2	"g"	2	"g"	"c(\"25265-0\", \"3882-8\")"
+"OXO"	"J01MB05"	4628	"Oxolinic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"		"c(\"Acide oxolinique\", \"Acido ossolico\", \"Acido oxolinico\", \"Acidum oxolinicum\", \"Aqualinic\", \"Cistopax\", \"Dioxacin\", \"Emyrenil\", \"Gramurin\", \"Inoxyl\", \"Nidantin\", \"Oksaren\", \"Orthurine\", \"Ossian\", \"Oxoboi\", \"Oxolinic\", \"Oxolinic acid\", \"Pietil\", \"Prodoxal\", \"Prodoxol\", \"Starner\", \"Tiurasin\", \"Ultibid\", \"Urinox\", \"Uritrate\", \"Urotrate\", \"Uroxol\", \"Utibid\")"	1	"g"			
+"OXY"	"J01AA06"	54675779	"Oxytetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Adamycin\", \"Berkmycen\", \"Biostat\", \"Biostat PA\", \"Dabicycline\", \"Dalimycin\", \"Embryostat\", \"Fanterrin\", \"Galsenomycin\", \"Geomycin\", \"Geotilin\", \"Hydroxytetracyclinum\", \"Imperacin\", \"Lenocycline\", \"Macocyn\", \"Medamycin\", \"Mepatar\", \"Oksisyklin\", \"Ossitetraciclina\", \"Oxacycline\", \"Oxitetraciclina\", \"Oxitetracyclin\", \"Oxitetracycline\", \"Oxitetracyclinum\", \"Oxydon\", \"Oxymycin\", \"Oxymykoin\", \"Oxypam\", \"Oxysteclin\", \"Oxyterracin\", \"Oxyterracine\", \"Oxyterracyne\", \"Oxytetracid\", \"Oxytetracyclin\", \"Oxytetracycline\", 
+\"Oxytetracycline base\", \"Oxytetracyclinum\", \"Proteroxyna\", \"Riomitsin\", \"Ryomycin\", \"Solkaciclina\", \"Stecsolin\", \"Stevacin\", \"Tarocyn\", \"Tarosin\", \"Teravit\", \"Terrafungine\", \"Terramitsin\", \"Terramycin\", \"Terramycin im\", \"Tetran\", \"Unimycin\", \"Ursocyclin\", \"Ursocycline\", \"Vendarcin\")"	1	"g"	1	"g"	"c(\"17396-3\", \"25266-8\", \"87595-5\")"
+"PAS"		4649	"P-aminosalicylic acid"	"Antimycobacterials"				"c(\"Aminopar\", \"Aminosalicylic\", \"Aminosalicylic acid\", \"Aminosalicylic Acid\", \"Aminosalyl\", \"Aminox\", \"Apacil\", \"Deapasil\", \"Entepas\", \"Ferrosan\", \"Gabbropas\", \"Helipidyl\", \"Hellipidyl\", \"Neopasalate\", \"Osacyl\", \"Pamacyl\", \"Pamisyl\", \"Paramycin\", \"Parasal\", \"Parasalicil\", \"Parasalindon\", \"Pasalon\", \"Pasara\", \"Pascorbic\", \"Pasdium\", \"Paser Granules\", \"PASKALIUM\", \"Pasmed\", \"Pasnodia\", \"Pasolac\", \"Propasa\", \"Rezipas\", \"TEEBACIN\", \"WLN: ZR CQ DVQ\")"					
+"PAN"		72015	"Panipenem"	"Carbapenems"				"c(\"Panipenem\", \"Panipenemum\", \"Penipanem\")"					
+"PAR"		165580	"Paromomycin"	"Other antibacterials"				"c(\"Aminosidin\", \"AMINOSIDINE\", \"Aminosidine I\", \"Aminosidine sulfate\", \"Amminosidin\", \"Crestomycin\", \"Estomycin\", \"Gabbromicina\", \"Gabbromycin\", \"Gabromycin\", \"Humatin\", \"Humycin\", \"Hydroxymycin\", \"Hydroxymycin sulfate\", \"Monomycin\", \"Monomycin A\", \"Neomycin E\", \"Paramomycin\", \"Paramomycin Sulfate\", \"Paromomicina\", \"Paromomycin\", \"Paromomycin I\", \"Paromomycine\", \"Paromomycinum\", \"Paucimycin\", \"Paucimycinum\", \"Quintomycin C\")"					
+"PAZ"	"J01MA18"	65957	"Pazufloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Pazufloxacin\", \"Pazufloxacine\", \"Pazufloxacino\", \"Pazufloxacinum\")"			1	"g"	
+"PEF"	"J01MA03"	51081	"Pefloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Abactal\", \"Labocton\", \"Pefloxacin\", \"Pefloxacine\", \"Pefloxacino\", \"Pefloxacinum\", \"PERFLOXACIN\", \"Silver Pefloxacin\")"	0.8	"g"	0.8	"g"	"3906-5"
+"PNM"	"J01CE06"	10250769	"Penamecillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Hydroxymethyl\", \"Penamecilina\", \"Penamecillin\", \"Penamecillina\", \"Penamecilline\", \"Penamecillinum\")"	1.05	"g"			
+"PEN"	"J01CE01"	5904	"Penicillin G"	"Beta-lactams/penicillins"	"Combinations of antibacterials"	"Combinations of antibacterials"	"c(\"p\", \"pen\", \"pv\", \"peni\")"	"c(\"Abbocillin\", \"Ayercillin\", \"Bencilpenicilina\", \"Benzopenicillin\", \"Benzyl penicillin\", \"Benzylpenicillin\", \"Benzylpenicillin G\", \"Benzylpenicilline\", \"Benzylpenicillinum\", \"Bicillin\", \"Cillora\", \"Cilloral\", \"Cilopen\", \"Compocillin G\", \"Cosmopen\", \"Dropcillin\", \"Free penicillin G\", \"Free penicillin II\", \"Galofak\", \"Gelacillin\", \"Liquacillin\", \"Megacillin\", \"Pencillin G\", \"Penicillin\", \"PenicillinG\", \"Pentids\", \"Permapen\", \"Pfizerpen\", \"Pfizerpen G\", \"Pharmacillin\", \"Pradupen\", \"Specilline G\", \"Ursopen\"
+)"					"3913-1"
+"PNV"	"J01CE01"	6869	"Penicillin V"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"c(\"p\", \"pen\", \"pv\", \"bepe\")"	"c(\"Acipen V\", \"Apocillin\", \"Apopen\", \"Beromycin\", \"Calcipen\", \"Compocillin V\", \"Crystapen V\", \"Distaquaine V\", \"Eskacillian V\", \"Eskacillin V\", \"Fenacilin\", \"Fenospen\", \"Meropenin\", \"Oracillin\", \"Oratren\", \"Penicillin V\", \"Phenocillin\", \"Phenomycilline\", \"Phenopenicillin\", \"Robicillin\", \"Rocilin\", \"Stabicillin\", \"Vebecillin\", \"Veetids\", \"Vegacillin\")"			3.6	"g"	"3914-9"
+"PNO"			"Penicillin/novobiocin"	"Beta-lactams/penicillins"				""					
+"PSU"			"Penicillin/sulbactam"	"Beta-lactams/penicillins"				""					
+"PNM1"	"J01AA10"	54686187	"Penimepicycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Duamine\", \"Hydrocycline\", \"Penetracyne\", \"Penimepiciclina\", \"Penimepicycline\", \"Penimepicyclinum\")"					
+"PIM"		65453	"Pentisomicin"	"Aminoglycosides"				"c(\"Pentisomicin\", \"Pentisomicina\", \"Pentisomicine\", \"Pentisomicinum\")"					
+"PTZ"		55250256	"Pentizidone"	"Other antibacterials"				""					
+"PEX"		16132253	"Pexiganan"	"Other antibacterials"				"Pexiganan"					
+"PHE"	"J01CE05"	272833	"Phenethicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Feneticilina\", \"Feneticillina\", \"Feneticilline\", \"K Phenethicillin\", \"Phenethicilin\", \"Phenethicillinum\", \"Pheneticillin\", \"Pheneticilline\", \"Pheneticillinum\", \"Phenoxy PC\", \"Potassium penicillin\")"	1	"g"			"41471-4"
+"PHN"	"J01CE02"	6869	"Phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Acipen V\", \"Apocillin\", \"Apopen\", \"Beromycin\", \"Calcipen\", \"Compocillin V\", \"Crystapen V\", \"Distaquaine V\", \"Eskacillian V\", \"Eskacillin V\", \"Fenacilin\", \"Fenospen\", \"Meropenin\", \"Oracillin\", \"Oratren\", \"Penicillin V\", \"Phenocillin\", \"Phenomycilline\", \"Phenopenicillin\", \"Robicillin\", \"Rocilin\", \"Stabicillin\", \"Vebecillin\", \"Veetids\", \"Vegacillin\")"	2	"g"			
+"PMR"		5284447	"Pimaricin (Natamycin)"	"Antifungals/antimycotics"				"c(\"Delvocid\", \"Mycophyt\", \"Myprozine\", \"Natacyn\", \"Natamicina\", \"Natamycin\", \"Natamycine\", \"Natamycinum\", \"Pimafucin\", \"Pimaracin\", \"Pimarizin\", \"Synogil\", \"Tennecetin\")"					
+"PPA"	"J01MB04"	4831	"Pipemidic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"pizu"	"c(\"Acide pipemidique\", \"Acido pipemidico\", \"Acidum pipemidicum\", \"Deblaston\", \"Dolcol\", \"Pipedac\", \"Pipemid\", \"Pipemidic\", \"Pipemidic acid\", \"Pipemidicacid\", \"Pipram\", \"Uromidin\")"	0.8	"g"			
+"PIP"	"J01CA12"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"pi\", \"pip\", \"pp\", \"pipe\")"	"c(\"Isipen\", \"Pentcillin\", \"Peperacillin\", \"Peracin\", \"Piperacilina\", \"Piperacillin\", \"PIPERACILLIN NA\", \"PIPERACILLIN SODIUM\", \"Piperacilline\", \"Piperacillinum\", \"Pipercillin\", \"Pipracil\", \"Pipril\")"			14	"g"	"c(\"25268-4\", \"3972-7\")"
+"PIS"			"Piperacillin/sulbactam"	"Beta-lactams/penicillins"				""					
+"TZP"	"J01CR05"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"pt\", \"tzp\", \"ptz\", \"p/t\", \"ptc\", \"pita\")"	"c(\"\", \"Tazocel\", \"tazocillin\", \"Tazocin\", \"Zosyn\")"			14	"g"	
+"PRC"		71978	"Piridicillin"	"Beta-lactams/penicillins"				"Piridicillin"					
+"PRL"		157385	"Pirlimycin"	"Other antibacterials"				"c(\"Pirlimycin\", \"Pirlimycina\", \"Pirlimycine\", \"Pirlimycinum\", \"Pirsue\")"					
+"PIR"	"J01MB03"	4855	"Piromidic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"		"c(\"Acide piromidique\", \"Acido piromidico\", \"Acidum piromidicum\", \"Actrun C\", \"Bactramyl\", \"Enterol\", \"Gastrurol\", \"Panacid\", \"Pirodal\", \"Piromidic acid\", \"Pyrido\", \"Reelon\", \"Septural\", \"Urisept\", \"Uropir\", \"Zaomeal\")"	2	"g"			
+"PVM"	"J01CA02"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Berocillin\", \"Pivaloylampicillin\", \"Pivampicilina\", \"Pivampicillin\", \"Pivampicilline\", \"Pivampicillinum\", \"Pondocillin\")"	1.05	"g"			
+"PME"	"J01CA08"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Amdinocillin pivoxil\", \"Amdinocillin Pivoxil\", \"Coactabs\", \"Hydroxymethyl\", \"Pivmecilinamo\", \"Pivmecillinam\", \"Pivmecillinam HCl\", \"Pivmecillinamum\")"	0.6	"g"			
+"PLZ"		42613186	"Plazomicin"	"Aminoglycosides"				"Plazomicin"					"92024-9"
+"PLB"	"J01XB02"	49800004	"Polymyxin B"	"Polymyxins"	"Other antibacterials"	"Polymyxins"	"c(\"pb\", \"poly\", \"POL\", \"Polymixin\", \"Polymixin B\")"	"c(\"Polimixina B\", \"POLUMYXIN B\", \"Polymixin B\", \"Polymyxine B\")"			0.15	"g"	"c(\"17473-0\", \"25269-2\")"
+"POP"			"Polymyxin B/polysorbate 80"	"Polymyxins"				""					
+"POS"	"J02AC04"	468595	"Posaconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa"	"c(\"Noxafil\", \"Posaconazole\", \"Posaconazole SP\", \"Posconazole\")"	0.3	"g"	0.3	"g"	"c(\"53731-6\", \"80545-7\")"
+"PRA"		9802884	"Pradofloxacin"	"Quinolones"				"Pradofloxacin"					
+"PRX"		71455	"Premafloxacin"	"Quinolones"				"Premafloxacin"					
+"PRM"		6446787	"Primycin"	"Macrolides/lincosamides"				""					
+"PRI"	"J01FG01"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"		"c(\"Eskalin V\", \"Mikamycin\", \"Mikamycine\", \"Mikamycinum\", \"Ostreogrycinum\", \"Pristinamycine\", \"Pristinamycinum\", \"Stafac\", \"Stafytracine\", \"Staphylomycin\", \"Starfac\", \"Streptogramin\", \"Vernamycin\", \"Virgimycin\", \"Virgimycine\", \"Virginiamycina\", \"Virginiamycine\", \"Virginiamycinum\")"	2	"g"			
+"PRB"	"J01CE09"	5903	"Procaine benzylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Depocillin\", \"Duphapen\", \"Hostacillin\", \"Hydracillin\", \"Jenacillin O\", \"Nopcaine\", \"Penicillin procaine\", \"Retardillin\", \"Vetspen\", \"Vitablend\")"			0.6	"g"	
+"PRP"	"J01CE03"	92879	"Propicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"		"c(\"Propicilina\", \"Propicillin\", \"Propicilline\", \"Propicillinum\")"	0.9	"g"			
+"PKA"		9872451	"Propikacin"	"Aminoglycosides"				"c(\"Propikacin\", \"Propikacina\", \"Propikacine\", \"Propikacinum\")"					
+"PTH"	"J04AD01"	666418	"Prothionamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"prot"	"c(\"Ektebin\", \"Peteha\", \"Prothionamide\", \"Prothionamidum\", \"Protion\", \"Protionamid\", \"Protionamida\", \"Protionamide\", \"Protionamidum\", \"Protionizina\", \"Tebeform\", \"Trevintix\", \"Tuberex\")"	0.75	"g"			
+"PRU"	"J01MA17"	65947	"Prulifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Prulifloxacin\", \"Pruvel\", \"Pufloxacin dioxolil\", \"Quisnon\")"	0.6	"g"			
+"PZA"	"J04AK01"	1046	"Pyrazinamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"c(\"Aldinamid\", \"Aldinamide\", \"Braccopiral\", \"Corsazinmid\", \"Dipimide\", \"Eprazin\", \"Farmizina\", \"Isopas\", \"Lynamide\", \"Novamid\", \"P ezetamid\", \"Pezetamid\", \"Pharozinamide\", \"Piraldina\", \"Pirazimida\", \"Pirazinamid\", \"Pirazinamida\", \"Pirazinamide\", \"Prazina\", \"Pyrafat\", \"Pyramide\", \"Pyrazide\", \"Pyrazinamdie\", \"Pyrazinamid\", \"Pyrazinamide\", \"Pyrazinamidum\", \"Pyrazine carboxamide\", \"Pyrazineamide\", \"Pyrizinamide\", \"Rifafour\", \"Rozide\", \"Tebrazid\", \"Tebrazio\", \"Tisamid\", \"Unipyranamide\", \"Zinamide\", \"Zinastat\"
+)"	1.5	"g"			"c(\"11001-5\", \"25270-0\")"
+"QDA"	"J01FG02"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"c(\"syn\", \"q/d\", \"qda\", \"rp\", \"qida\")"	""			1.5	"g"	
+"RAC"		56052	"Ractopamine"	"Other antibacterials"				"c(\"Ractopamina\", \"Ractopamine\", \"Ractopaminum\")"					
+"RAM"		16132338	"Ramoplanin"	"Glycopeptides"				"Ramoplanin"					
+"RZM"		10993211	"Razupenem"	"Carbapenems"				"Razupenem"					
+"RTP"	"A07AA11"	6918462	"Retapamulin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"		"c(\"Altabax\", \"Altargo\", \"Retapamulin\")"	0.6	"g"			
+"RBC"	"J02AC05"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"c(\"Kisqali\", \"Ribociclib\")"					
+"RST"	"J01GB10"	33042	"Ribostamycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"		"c(\"Dekamycin IV\", \"Hetangmycin\", \"Ribastamin\", \"Ribostamicina\", \"Ribostamycin\", \"Ribostamycine\", \"Ribostamycinum\", \"Vistamycin\", \"Xylostatin\")"			1	"g"	
+"RID1"		16659285	"Ridinilazole"	"Other antibacterials"				"Ridinilazole"					
+"RIB"	"J04AB04"	135398743	"Rifabutin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifb"	"c(\"Alfacid\", \"Ansamicin\", \"Ansamycin\", \"Ansatipin\", \"Ansatipine\", \"Mycobutin\", \"Rifabutin\", \"Rifabutina\", \"Rifabutine\", \"Rifabutinum\")"	0.15	"g"			"24032-5"
+"RIF"	"J04AB02"	135398735	"Rifampicin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa"	"c(\"Abrifam\", \"Archidyn\", \"Arficin\", \"Arzide\", \"AZT + Rifampin\", \"Benemicin\", \"Benemycin\", \"Dipicin\", \"Doloresum\", \"Eremfat\", \"Famcin\", \"Fenampicin\", \"Rifadin\", \"Rifadin I.V\", \"Rifadin I.V.\", \"Rifadine\", \"Rifagen\", \"Rifaldazin\", \"Rifaldazine\", \"Rifaldin\", \"Rifamate\", \"Rifamicin AMP\", \"Rifamor\", \"Rifampicin\", \"Rifampicin SV\", \"Rifampicina\", \"Rifampicine\", \"Rifampicinum\", \"Rifampin\", \"Rifamsolin\", \"Rifamycin AMP\", \"Rifaprodin\", \"Rifcin\", \"Rifobac\", \"Rifoldin\", \"Rifoldine\", \"Riforal\", \"Rimactan\", \"Rimactane\", 
+\"Rimactizid\", \"Rimazid\", \"Rimycin\", \"Sinerdol\", \"Tubocin\")"	0.6	"g"	0.6	"g"	
+"RFI"	"J04AM02"		"Rifampicin/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		"c(\"Rifinah\", \"Rimactazid\")"					
+"RPEI"	"J04AM06"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		""					
+"RPI"	"J04AM05"		"Rifampicin/pyrazinamide/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		""					
+"RFM"	"J04AB03"	6324616	"Rifamycin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"		"c(\"Aemcolo\", \"Rifacin\", \"Rifamicina\", \"Rifamicine SV\", \"Rifamycin\", \"RIFAMYCIN\", \"Rifamycine\", \"Rifamycinum\", \"Rifocin\", \"Rifocyn\", \"RIFOMYCIN\", \"Rifomycin SV\", \"Tuborin\")"			0.6	"g"	
+"RFP"	"J04AB05"	135403821	"Rifapentine"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp"	"c(\"Cyclopentyl rifampin\", \"Priftin\", \"Rifapentin\", \"Rifapentina\", \"Rifapentine\", \"Rifapentinum\")"	0.11	"g"			
+"RFX"	"A07AA11"	6436173	"Rifaximin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"		"c(\"Fatroximin\", \"Flonorm\", \"Lormyx\", \"Lumenax\", \"Normix\", \"RedActiv\", \"Rifacol\", \"Rifamixin\", \"Rifaxidin\", \"Rifaximin\", \"Rifaximina\", \"Rifaximine\", \"Rifaximinum\", \"Rifaxin\", \"Ritacol\", \"Spiraxin\", \"Xifaxan\", \"Xifaxsan\")"	0.6	"g"			
+"RIT"		65633	"Ritipenem"	"Carbapenems"				"Ritipenem"					
+"RIA"		163692	"Ritipenem acoxil"	"Carbapenems"				"Ritipenem Acoxil"					
+"ROK"	"J01FA12"	5282211	"Rokitamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Propionylleucomycin\", \"Ricamycin\", \"Rokicid\", \"Rokital\", \"Rokitamicina\", \"Rokitamycin\", \"Rokitamycine\", \"Rokitamycinum\")"	0.8	"g"			
+"RLT"	"J01AA09"	54682938	"Rolitetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"		"c(\"Bristacin\", \"Kinteto\", \"Reverin\", \"Rolitetraciclina\", \"Rolitetracycline\", \"Rolitetracyclinum\", \"Solvocillin\", \"Superciclin\", \"Synotodecin\", \"Synterin\", \"Syntetrex\", \"Syntetrin\", \"Velacicline\", \"Velacycline\")"			0.35	"g"	
+"ROS"	"J01MB01"	287180	"Rosoxacin"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"		"c(\"Acrosoxacin\", \"Eracine\", \"Eradacil\", \"Eradacin\", \"Rosoxacin\", \"Rosoxacine\", \"Rosoxacino\", \"Rosoxacinum\", \"Roxadyl\", \"Winuron\")"	0.3	"g"			
+"RXT"	"J01FA06"		"Roxithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi"	""	0.3	"g"			
+"RFL"	"J01MA10"	58258	"Rufloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Rufloxacin\", \"RUFLOXACIN HCl\", \"Rufloxacine\", \"Rufloxacino\", \"Rufloxacinum\")"	0.2	"g"			
+"SAL"		3085092	"Salinomycin"	"Other antibacterials"				"c(\"Coxistac\", \"Procoxacin\", \"Salinomicina\", \"Salinomycin\", \"Salinomycine\", \"Salinomycinum\")"					"87593-0"
+"SAR"		56208	"Sarafloxacin"	"Quinolones"				"c(\"Difloxacine\", \"Difloxacino\", \"Difloxacinum\", \"Saraflox\", \"Sarafloxacin\", \"Sarafloxacine\", \"Sarafloxacino\", \"Sarafloxacinum\")"					
+"SRX"		9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"				"Sarmoxicillin"					
+"SEC"		71815	"Secnidazole"	"Other antibacterials"				"c(\"Flagentyl\", \"Secnidal\", \"Secnidazol\", \"Secnidazole\", \"Secnidazolum\", \"Secnil\", \"Sindose\", \"Solosec\")"					
+"SMF"	"J04AK05"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	""					
+"SIS"	"J01GB08"	36119	"Sisomicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso"	"c(\"Rickamicin\", \"Salvamina\", \"Siseptin sulfate\", \"Sisomicin\", \"Sisomicin sulfate\", \"Sisomicina\", \"Sisomicine\", \"Sisomicinum\", \"Sisomin\", \"Sisomycin\", \"Sissomicin\", \"Sizomycin\")"			0.24	"g"	
+"SIT"		461399	"Sitafloxacin"	"Quinolones"				"c(\"Gracevit\", \"SITAFLOXACINISOMER\")"					
+"SDA"	"J04AA02"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"		"c(\"Bactylan\", \"Decapasil\", \"Lepasen\", \"Monopas\", \"Nippas\", \"P.A.S. SODIUM\", \"Pamisyl sodium\", \"Parasal sodium\", \"PAS Sodium\", \"Pasade\", \"Pasnal\", \"Passodico\", \"Salvis\", \"Sanipirol\", \"Sodiopas\", \"SODIUM P.A.S\", \"Sodium PAS\", \"TEEBACIN\", \"Tubersan\")"	14	"g"	14	"g"	
+"SOL"		25242512	"Solithromycin"	"Macrolides/lincosamides"				""					
+"SPX"	"J01MA09"	60464	"Sparfloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Esparfloxacino\", \"Sparfloxacin\", \"Sparfloxacine\", \"Sparfloxacinum\")"	0.2	"g"			
+"SPT"	"J01XX04"	15541	"Spectinomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"spt\", \"spe\", \"sc\", \"spec\")"	"c(\"Actinospectacina\", \"Adspec\", \"Espectinomicina\", \"Prospec\", \"Specitinomycin\", \"Spectam\", \"Spectinomicina\", \"Spectinomycin\", \"Spectinomycin Di HCl\", \"Spectinomycine\", \"Spectinomycinum\", \"Stanilo\", \"Togamycin\", \"Trobicin\")"			3	"g"	
+"SPI"	"J01FA02"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"Espiramicin\", \"Provamycin\", \"Rovamycin\", \"Rovamycine\", \"Sequamycin\", \"Spiramycine\", \"Spiramycinum\")"	3	"g"			
+"SPM"	"J01RA04"		"Spiramycin/metronidazole"	"Other antibacterials"	"Combinations of antibacterials"	"Combinations of antibacterials"		""					
+"STR"	"J01GA02"		"Streptoduocin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Streptomycins"		""			1	"g"	
+"STR1"	"J01GA01"	19649	"Streptomycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Streptomycins"	"c(\"s\", \"str\", \"stre\")"	"c(\"Agrept\", \"Agrimycin\", \"Chemform\", \"Estreptomicina\", \"Neodiestreptopab\", \"Strepcen\", \"Streptomicina\", \"Streptomycin\", \"Streptomycin A\", \"Streptomycin SPX\", \"Streptomycin sulfate\", \"Streptomycine\", \"Streptomyzin\", \"Vetstrep\")"			1	"g"	"4039-4"
+"STH"			"Streptomycin-high"	"Aminoglycosides"			"c(\"sthl\", \"streptomycin high\", \"strepto high\")"	""					
+"STI"	"J04AM01"		"Streptomycin/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		""					
+"SUL"	"J01CG01"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"		"c(\"Betamaze\", \"Sulbactam\", \"Sulbactam acid\", \"Sulbactam free acid\", \"Sulbactamum\")"			1	"g"	
+"SBC"	"J01CA16"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Kedacillina\", \"Sulbenicilina\", \"Sulbenicilline\", \"Sulbenicillinum\")"			15	"g"	
+"SUC"		5318	"Sulconazole"	"Antifungals/antimycotics"				"c(\"Sulconazol\", \"Sulconazole\", \"Sulconazolum\")"					
+"SUP"		6634	"Sulfachlorpyridazine"	"Other antibacterials"				"c(\"Cluricol\", \"Cosulid\", \"Cosumix\", \"Durasulf\", \"Nefrosul\", \"Nsulfanilamide\", \"Prinzone vet\", \"Prinzone vet.\", \"Solfaclorpiridazina\", \"Sonilyn\", \"Sulfachlorpyridazine\", \"Sulfacloropiridazina\", \"Vetisulid\")"					
+"SDI"	"J01EC02"	5215	"Sulfadiazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"		"c(\"Adiazin\", \"Adiazine\", \"CocoDiazine\", \"Codiazine\", \"Cremodiazine\", \"Cremotres\", \"Debenal\", \"Deltazina\", \"Diazin\", \"Diazolone\", \"Diazovit\", \"Diazyl\", \"Eskadiazine\", \"Honey diazine\", \"Liquadiazine\", \"Microsulfon\", \"Neazine\", \"Neotrizine\", \"Nsulfanilamide\", \"Palatrize\", \"Piridisir\", \"Pirimal\", \"Pyrimal\", \"Quadetts\", \"Quadramoid\", \"Sanodiazine\", \"Sildaflo\", \"Silvadene\", \"Solfadiazina\", \"Spofadrizine\", \"Sterazine\", \"Sulfacombin\", \"Sulfadiazene\", \"Sulfadiazin\", \"Sulfadiazina\", \"Sulfadiazine\", \"SULFADIAZINE\", 
+\"Sulfadiazinum\", \"Sulfapirimidin\", \"Sulfapyrimidin\", \"Sulfapyrimidine\", \"Sulfatryl\", \"Sulfazine\", \"Sulfolex\", \"Sulfonamides Duplex\", \"Sulfonsol\", \"Sulfose\", \"Sulphadiazine\", \"Sulphadiazine E\", \"Terfonyl\", \"Theradiazine\", \"Thermazene\", \"Trifonamide\", \"Triple sulfa\", \"Triple Sulfas\", \"Trisem\", \"Truozine\", \"Zinc Sulfadiazine\")"	0.6	"g"			"c(\"27216-1\", \"59742-7\", \"6907-0\")"
+"SLT"	"J01EE06"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		""					
+"SLT1"	"J01EE02"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		"c(\"Antastmon\", \"CoTrimazine\", \"Diaziprim forte\", \"Ditrim\", \"Ditrivet\", \"Sultrisan\", \"Triglobe\", \"Trimin\", \"Tucoprim\", \"Uniprim\")"					
+"SUD"	"J01ED01"	5323	"Sulfadimethoxine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Agribon\", \"Arnosulfan\", \"Bactrovet\", \"Deposul\", \"Diasulfa\", \"Diasulfyl\", \"Dimetazina\", \"Dinosol\", \"Dorisul\", \"Lasibon\", \"Madribon\", \"Madrigid\", \"Madriqid\", \"Madroxin\", \"Madroxine\", \"Maxulvet\", \"Mecozine\", \"Memcozine\", \"Metoxidon\", \"Neostrepal\", \"Neostreptal\", \"Nsulfanilamide\", \"Omnibon\", \"Persulfen\", \"Primor\", \"Radonin\", \"Redifal\", \"Rofenaid\", \"Roscosulf\", \"Scandisil\", \"Solfadimetossina\", \"Sudine\", \"Suldixine\", \"Sulfabon\", \"Sulfadimethoxin\", \"Sulfadimethoxine\", \"Sulfadimethoxinum\", \"Sulfadimetossina\", 
+\"Sulfadimetoxin\", \"Sulfadimetoxina\", \"Sulfadimetoxine\", \"Sulfastop\", \"Sulfdimethoxine\", \"Sulfoplan\", \"Sulphadimethoxine\", \"Sulxin\", \"Sumbio\", \"Symbio\", \"Theracanzan\", \"Ultrasulfon\")"	0.5	"g"			
+"SDM"	"J01EB03"	5327	"Sulfadimidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Azolmetazin\", \"BENZENE SULFONAMIDE\", \"Calfspan\", \"Calfspan Tablets\", \"Cremomethazine\", \"Diazil\", \"Diazilsulfadine\", \"Dimezathine\", \"Intradine\", \"Kelametazine\", \"Mermeth\", \"Metazin\", \"Neasina\", \"Neazina\", \"Nsulfanilamide\", \"Panazin\", \"Pirmazin\", \"Primazin\", \"Sa III\", \"Solfadimidina\", \"Spanbolet\", \"Sulfadimerazine\", \"Sulfadimesin\", \"Sulfadimesine\", \"Sulfadimethyldiazine\", \"Sulfadimezin\", \"Sulfadimezine\", \"Sulfadimezinum\", \"Sulfadimidin\", \"Sulfadimidina\", \"Sulfadimidine\", \"Sulfadimidinum\", \"Sulfadine\", 
+\"Sulfametazina\", \"Sulfametazyny\", \"Sulfamethazine\", \"SULFAMETHAZINE\", \"Sulfamethiazine\", \"Sulfamezathine\", \"Sulfamidine\", \"SulfaSURE SR Bolus\", \"Sulfodimesin\", \"Sulfodimezine\", \"Sulka k boluses\", \"Sulka S Boluses\", \"Sulmet\", \"Sulphadimidine\", \"Sulphamethasine\", \"Sulphamethazine\", \"Sulphamezathine\", \"Sulphamidine\", \"Sulphodimezine\", \"Superseptil\", \"Superseptyl\", \"Vertolan\")"	4	"g"			
+"SLT2"	"J01EE05"		"Sulfadimidine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		""					
+"SLF"	"J01EB05"	5344	"Sulfafurazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Accuzole\", \"Alphazole\", \"Amidoxal\", \"Astrazolo\", \"Azo Gantrisin\", \"Azosulfizin\", \"Bactesulf\", \"Barazae\", \"Chemouag\", \"Cosoxazole\", \"Dorsulfan\", \"Dorsulfan warthausen\", \"Entusil\", \"Entusul\", \"ERYZOLE\", \"Gantrisin\", \"Gantrisine\", \"Gantrisona\", \"Gantrizin\", \"Gantrosan\", \"Isoxamin\", \"Neazolin\", \"Neoxazoi\", \"Neoxazol\", \"Novazolo\", \"Novosaxazole\", \"Nsulfanilamide\", \"Nsulphanilamide\", \"Pancid\", \"Pediazole\", \"Renosulfan\", \"Resoxol\", \"Roxosul\", \"Roxosul tablets\", \"Roxoxol\", \"Saxosozine\", \"Sodizole\", \"Solfafurazolo\", 
+\"Soxamide\", \"Soxazole\", \"Soxisol\", \"Soxitabs\", \"Soxomide\", \"Stansin\", \"Sulbio\", \"Sulfafuraz ole\", \"Sulfafurazol\", \"Sulfafurazole\", \"Sulfafurazolum\", \"Sulfagan\", \"Sulfagen\", \"Sulfaisoxazole\", \"Sulfalar\", \"Sulfapolar\", \"Sulfasol\", \"Sulfasoxazole\", \"Sulfasoxizole\", \"Sulfazin\", \"Sulfisin\", \"Sulfisonazole\", \"Sulfisoxasole\", \"Sulfisoxazol\", \"Sulfisoxazole\", \"Sulfisoxazolum\", \"Sulfizin\", \"Sulfizol\", \"Sulfizole\", \"Sulfofurazole\", \"Sulfoxol\", \"Suloxsol\", \"Sulphafuraz\", \"Sulphafurazol\", \"Sulphafurazole\", \"Sulphafurazolum\", 
+\"Sulphaisoxazole\", \"Sulphisoxazol\", \"Sulphisoxazole\", \"Sulphofurazole\", \"Sulsoxin\", \"Thiasin\", \"Unisulf\", \"Urisoxin\", \"Uritrisin\", \"Urogan\", \"Vagilia\")"	4	"g"	4	"g"	
+"SLF1"	"J01EB01"	5343	"Sulfaisodimidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Aristamid\", \"Aristamide\", \"Aristogyn\", \"Domain\", \"Domian\", \"Elcosin\", \"Elcosine\", \"Elkosil\", \"Elkosin\", \"Elkosine\", \"Erycon\", \"Isosulf\", \"Mefenal\", \"Nsulfanilamide\", \"Solfisomidina\", \"Sulfadimetine\", \"Sulfaisodimerazine\", \"Sulfaisodimidine\", \"Sulfaisodimidinum\", \"Sulfaisomidine\", \"Sulfamethin\", \"Sulfasomidine\", \"Sulfisomidina\", \"Sulfisomidine\", \"Sulfisomidine sodium\", \"Sulfisomidinum\", \"Sulphasomidine\")"	4	"g"	4	"g"	
+"SLF2"	"J01ED02"	9047	"Sulfalene"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Dalysep\", \"Kelfizin\", \"Kelfizina\", \"Kelfizine\", \"Kelfizine W\", \"Longum\", \"Nsulfanilamide\", \"Policydal\", \"Polycidal\", \"Solfametopirazina\", \"Sulfalen\", \"Sulfalene\", \"Sulfaleno\", \"Sulfalenum\", \"Sulfamethopyrazine\", \"Sulfamethoxypyrazine\", \"Sulfametopyrazine\", \"Sulfametoxypyridazin\", \"Sulphalene\", \"Sulphametopyrazine\", \"Vetkelfizina\")"	0.1	"g"			
+"SZO"	"J01ED09"	187764	"Sulfamazone"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Sulfamazon\", \"Sulfamazona\", \"Sulfamazone\", \"Sulfamazonum\")"	1.5	"g"			
+"SLF3"	"J01ED07"	5325	"Sulfamerazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Cremomerazine\", \"Kelamerazine\", \"Mebacid\", \"Mesulfa\", \"Methylpyrimal\", \"Methylsulfazin\", \"Methylsulfazine\", \"Metilsulfadiazin\", \"Metilsulfazin\", \"Nsulfanilamide\", \"Percoccide\", \"Pyralcid\", \"Pyrimal M\", \"Romezin\", \"Septacil\", \"Septosyl\", \"Solfamerazina\", \"Solumedin\", \"Sulfameradine\", \"Sulfamerazin\", \"Sulfamerazina\", \"Sulfamerazine\", \"SULFAMERAZINE\", \"Sulfamerazinum\", \"Sulfamethyldiazine\", \"Sulphamerazine\", \"Sumedine\", \"Susfamerazine\")"	3	"g"			
+"SLT3"	"J01EE07"		"Sulfamerazine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		""					
+"SUM"		5327	"Sulfamethazine"	"Other antibacterials"				"c(\"Azolmetazin\", \"BENZENE SULFONAMIDE\", \"Calfspan\", \"Calfspan Tablets\", \"Cremomethazine\", \"Diazil\", \"Diazilsulfadine\", \"Dimezathine\", \"Intradine\", \"Kelametazine\", \"Mermeth\", \"Metazin\", \"Neasina\", \"Neazina\", \"Nsulfanilamide\", \"Panazin\", \"Pirmazin\", \"Primazin\", \"Sa III\", \"Solfadimidina\", \"Spanbolet\", \"Sulfadimerazine\", \"Sulfadimesin\", \"Sulfadimesine\", \"Sulfadimethyldiazine\", \"Sulfadimezin\", \"Sulfadimezine\", \"Sulfadimezinum\", \"Sulfadimidin\", \"Sulfadimidina\", \"Sulfadimidine\", \"Sulfadimidinum\", \"Sulfadine\", 
+\"Sulfametazina\", \"Sulfametazyny\", \"Sulfamethazine\", \"SULFAMETHAZINE\", \"Sulfamethiazine\", \"Sulfamezathine\", \"Sulfamidine\", \"SulfaSURE SR Bolus\", \"Sulfodimesin\", \"Sulfodimezine\", \"Sulka k boluses\", \"Sulka S Boluses\", \"Sulmet\", \"Sulphadimidine\", \"Sulphamethasine\", \"Sulphamethazine\", \"Sulphamezathine\", \"Sulphamidine\", \"Sulphodimezine\", \"Superseptil\", \"Superseptyl\", \"Vertolan\")"					"87592-2"
+"SLF4"	"J01EB02"	5328	"Sulfamethizole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Ayerlucil\", \"Lucosil\", \"Methazol\", \"Microsul\", \"Nsulfanilamide\", \"Proklar\", \"Renasul\", \"Salimol\", \"Solfametizolo\", \"Sulamethizole\", \"Sulfa gram\", \"Sulfamethizol\", \"Sulfamethizole\", \"Sulfamethizolum\", \"Sulfametizol\", \"Sulfapyelon\", \"Sulfstat\", \"Sulfurine\", \"Sulphamethizole\", \"Tetracid\", \"Thidicur\", \"Thiosulfil\", \"Thiosulfil Forte\", \"Ultrasul\", \"Urocydal\", \"Urodiaton\", \"Urolucosil\", \"Urosulfin\")"	4	"g"			"c(\"60175-7\", \"60176-5\", \"60177-3\")"
+"SMX"	"J01EC01"	5329	"Sulfamethoxazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sulf"	"c(\"Azo gantanol\", \"Eusaprim\", \"Gamazole\", \"Gantanol\", \"Gantanol DS\", \"Metoxal\", \"Nsulfanilamide\", \"Nsulphanilamide\", \"Radonil\", \"Septran\", \"Septrin\", \"Simsinomin\", \"Sinomin\", \"Solfametossazolo\", \"Sulfamethalazole\", \"Sulfamethoxazol\", \"Sulfamethoxazole\", \"SULFAMETHOXAZOLE\", \"Sulfamethoxazolum\", \"Sulfamethoxizole\", \"Sulfamethylisoxazole\", \"Sulfametoxazol\", \"Sulfisomezole\", \"Sulphamethalazole\", \"Sulphamethoxazol\", \"Sulphamethoxazole\", \"Sulphisomezole\", \"Urobak\")"	2	"g"			"c(\"10342-4\", \"25271-8\", \"39772-9\", \"59971-2\", \"59972-0\", \"60333-2\", \"72674-5\", \"80549-9\", \"80974-9\")"
+"SLF5"	"J01ED05"	5330	"Sulfamethoxypyridazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Altezol\", \"Davosin\", \"Depovernil\", \"Kineks\", \"Lederkyn\", \"Lentac\", \"Lisulfen\", \"Longin\", \"Medicel\", \"Midicel\", \"Midikel\", \"Myasul\", \"Nsulfanilamide\", \"Opinsul\", \"Paramid\", \"Paramid Supra\", \"Petrisul\", \"Piridolo\", \"Quinoseptyl\", \"Retamid\", \"Retasulfin\", \"Retasulphine\", \"Slosul\", \"Spofadazine\", \"Sulfalex\", \"Sulfapyridazine\", \"Sulfdurazin\", \"Sulfozona\", \"Sultirene\", \"Vinces\")"	0.5	"g"			
+"SLF6"	"J01ED03"	19596	"Sulfametomidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Duroprocin\", \"Methofadin\", \"Methofazine\", \"Nsulfanilamide\", \"Solfametomidina\", \"SULFAMETHOMIDINE\", \"Sulfametomidin\", \"Sulfametomidina\", \"Sulfametomidine\", \"Sulfametomidinum\")"					
+"SLF7"	"J01ED04"	5326	"Sulfametoxydiazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Bayrena\", \"Berlicid\", \"Dairena\", \"Durenat\", \"Juvoxin\", \"Kinecid\", \"Kirocid\", \"Longasulf\", \"Methoxypyrimal\", \"Nsulfanilamide\", \"Solfametossidiazina\", \"Sulfameter\", \"Sulfamethorine\", \"Sulfamethoxine\", \"Sulfamethoxydiazin\", \"Sulfamethoxydiazine\", \"Sulfamethoxydin\", \"Sulfamethoxydine\", \"Sulfametin\", \"Sulfametinum\", \"Sulfametorin\", \"Sulfametorine\", \"Sulfametorinum\", \"Sulfametoxidiazina\", \"Sulfametoxidine\", \"Sulfametoxydiazine\", \"Sulfametoxydiazinum\", \"Sulphameter\", \"Sulphamethoxydiazine\", \"Supramid\", 
+\"Ultrax\")"	0.5	"g"			
+"SLT4"	"J01EE03"		"Sulfametrole/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		""					
+"SLF8"	"J01EC03"	12894	"Sulfamoxole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"		"c(\"Justamil\", \"Nsulfanilamide\", \"Oxasulfa\", \"Solfamossolo\", \"Sulfadimethyloxazole\", \"Sulfamoxol\", \"Sulfamoxole\", \"Sulfamoxolum\", \"Sulfano\", \"Sulfavigor\", \"Sulfmidil\", \"Sulfono\", \"Sulfune\", \"Sulfuno\", \"Sulphamoxole\", \"Tardamid\", \"Tardamide\")"	1	"g"	1	"g"	
+"SLT5"	"J01EE04"		"Sulfamoxole/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"		""					
+"SLF9"	"J01EB06"	5333	"Sulfanilamide"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Albexan\", \"Albosal\", \"Ambeside\", \"Antistrept\", \"Astreptine\", \"Astrocid\", \"Bacteramid\", \"Bactesid\", \"Collomide\", \"Colsulanyde\", \"Copticide\", \"Deseptyl\", \"Desseptyl\", \"Dipron\", \"Ergaseptine\", \"Erysipan\", \"Estreptocida\", \"Exoseptoplix\", \"Gerison\", \"Gombardol\", \"Infepan\", \"Lysococcine\", \"Neococcyl\", \"Orgaseptine\", \"Prontalbin\", \"Prontosil Album\", \"Prontosil I\", \"Prontosil White\", \"Prontylin\", \"Pronzin Album\", \"Proseptal\", \"Proseptine\", \"Proseptol\", \"Pysococcine\", \"Rubiazol A\", \"Sanamid\", \"Septamide Album\", 
+\"Septanilam\", \"Septinal\", \"Septolix\", \"Septoplex\", \"Septoplix\", \"Solfanilamide\", \"Stopton Album\", \"Stramid\", \"Strepamide\", \"Strepsan\", \"Streptagol\", \"Streptamid\", \"Streptamin\", \"Streptasol\", \"Streptocid\", \"Streptocid album\", \"Streptocide\", \"Streptocide White\", \"Streptocidum\", \"Streptoclase\", \"Streptocom\", \"Streptol\", \"Strepton\", \"Streptopan\", \"Streptosil\", \"Streptozol\", \"Streptozone\", \"Streptrocide\", \"Sulfamidyl\", \"Sulfamine\", \"Sulfana\", \"Sulfanalone\", \"Sulfanidyl\", \"Sulfanil\", \"Sulfanilamida\", \"Sulfanilamide\", 
+\"Sulfanilamidum\", \"Sulfanilimidic acid\", \"Sulfanimide\", \"Sulfocidin\", \"Sulfocidine\", \"Sulfonamide\", \"Sulfonamide P\", \"Sulfonylamide\", \"Sulphanilamide\", \"Sulphanilamide Gr\", \"Sulphonamide\", \"Therapol\", \"Tolder\", \"White streptocide\", \"WLN: ZSWR DZ\")"					
+"SLF10"	"J01ED06"	68933	"Sulfaperin"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Anastaf\", \"Archisulfa\", \"Avissul\", \"Chemiopen\", \"Demosulfan\", \"Durisan saft\", \"Ipersulfidin sirup\", \"Isosulfamerazine\", \"Methylsulfadiazin\", \"Novosul\", \"Nsulfanilamide\", \"Orosulfan\", \"Pallidin\", \"Retardon\", \"Risulfasens\", \"Sulfaperin\", \"Sulfaperina\", \"Sulfaperine\", \"Sulfaperinum\", \"Sulfatreis\", \"Sulfopirimidine\", \"Sulpenta\", \"Ultrasulfon sirup\")"	0.5	"g"			
+"SLF11"	"J01ED08"	5335	"Sulfaphenazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"		"c(\"Depocid\", \"Depotsulfonamide\", \"Eftolon\", \"Firmazolo\", \"Inamil\", \"Isarol\", \"Isarol V\", \"Merian\", \"Microtan pirazolo\", \"Nsulfanilamide\", \"Orisul\", \"Orisulf\", \"Paidazolo\", \"Phenylsulfapyrazole\", \"Plisulfan\", \"Raziosulfa\", \"Solfafenazolo\", \"Sulfabid\", \"Sulfafenazol\", \"Sulfafenazolo\", \"Sulfaphenazol\", \"Sulfaphenazole\", \"Sulfaphenazolum\", \"Sulfaphenazon\", \"Sulfaphenylpipazol\", \"Sulfaphenylpyrazol\", \"Sulfaphenylpyrazole\", \"Sulfonylpyrazol\", \"Sulphaphenazole\", \"Sulphenazole\")"	1	"g"			
+"SLF12"	"J01EB04"	5336	"Sulfapyridine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Adiplon\", \"Coccoclase\", \"Dagenan\", \"Eubasin\", \"Eubasinum\", \"Haptocil\", \"Piridazol\", \"Plurazol\", \"Pyriamid\", \"Pyridazol\", \"Relbapiridina\", \"Septipulmon\", \"Solfapiridina\", \"Streptosilpyridine\", \"Sulfapiridina\", \"Sulfapyridin\", \"Sulfapyridine\", \"Sulfapyridinum\", \"Sulfidin\", \"Sulfidine\", \"Sulphapyridin\", \"Sulphapyridine\", \"Thioseptal\", \"Trianon\")"	1	"g"			"c(\"14075-6\", \"55580-5\")"
+"SNA"		60582	"Sulfasuccinamide"	"Other antibacterials"				"c(\"Ambesid\", \"Derganil\", \"Sulfasuccinamid\", \"Sulfasuccinamida\", \"Sulfasuccinamide\", \"Sulfasuccinamidum\")"					
+"SUT"	"J01EB07"	5340	"Sulfathiazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Azoquimiol\", \"Azoseptale\", \"Cerazol\", \"Cerazole\", \"Chemosept\", \"Cibazol\", \"Duatok\", \"Dulana\", \"Eleudron\", \"Enterobiocine\", \"Estafilol\", \"Formosulfathiazole\", \"Neostrepsan\", \"Norsulfasol\", \"Norsulfazol\", \"Norsulfazole\", \"Norsulfazolum\", \"Nsulfanilamide\", \"Planomide\", \"Poliseptil\", \"Sanotiazol\", \"Septozol\", \"Solfatiazolo\", \"Streptosilthiazole\", \"Sulfamul\", \"Sulfathiazol\", \"Sulfathiazole\", \"SULFATHIAZOLE\", \"Sulfathiazolum\", \"Sulfatiazol\", \"Sulfavitina\", \"Sulfocerol\", \"Sulphathiazole\", \"Sulzol\", \"Thiacoccine\", 
+\"Thiasulfol\", \"Thiazamide\", \"Thiozamide\", \"Wintrazole\")"					"87591-4"
+"SLF13"	"J01EB08"	3000579	"Sulfathiourea"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"		"c(\"Badional\", \"Baldinol\", \"Fontamide\", \"Salvoseptyl\", \"Solfatiourea\", \"Solufontamide\", \"Sulfanilthiourea\", \"Sulfathiocarbamid\", \"Sulfathiocarbamide\", \"Sulfathiocarbamidum\", \"Sulfathiourea\", \"Sulfathiouree\", \"Sulfatiourea\", \"Sulphathiourea\")"	6	"g"			
+"SOX"		5344	"Sulfisoxazole"	"Other antibacterials"				"c(\"Accuzole\", \"Alphazole\", \"Amidoxal\", \"Astrazolo\", \"Azo Gantrisin\", \"Azosulfizin\", \"Bactesulf\", \"Barazae\", \"Chemouag\", \"Cosoxazole\", \"Dorsulfan\", \"Dorsulfan warthausen\", \"Entusil\", \"Entusul\", \"ERYZOLE\", \"Gantrisin\", \"Gantrisine\", \"Gantrisona\", \"Gantrizin\", \"Gantrosan\", \"Isoxamin\", \"Neazolin\", \"Neoxazoi\", \"Neoxazol\", \"Novazolo\", \"Novosaxazole\", \"Nsulfanilamide\", \"Nsulphanilamide\", \"Pancid\", \"Pediazole\", \"Renosulfan\", \"Resoxol\", \"Roxosul\", \"Roxosul tablets\", \"Roxoxol\", \"Saxosozine\", \"Sodizole\", \"Solfafurazolo\", 
+\"Soxamide\", \"Soxazole\", \"Soxisol\", \"Soxitabs\", \"Soxomide\", \"Stansin\", \"Sulbio\", \"Sulfafuraz ole\", \"Sulfafurazol\", \"Sulfafurazole\", \"Sulfafurazolum\", \"Sulfagan\", \"Sulfagen\", \"Sulfaisoxazole\", \"Sulfalar\", \"Sulfapolar\", \"Sulfasol\", \"Sulfasoxazole\", \"Sulfasoxizole\", \"Sulfazin\", \"Sulfisin\", \"Sulfisonazole\", \"Sulfisoxasole\", \"Sulfisoxazol\", \"Sulfisoxazole\", \"Sulfisoxazolum\", \"Sulfizin\", \"Sulfizol\", \"Sulfizole\", \"Sulfofurazole\", \"Sulfoxol\", \"Suloxsol\", \"Sulphafuraz\", \"Sulphafurazol\", \"Sulphafurazole\", \"Sulphafurazolum\", 
+\"Sulphaisoxazole\", \"Sulphisoxazol\", \"Sulphisoxazole\", \"Sulphofurazole\", \"Sulsoxin\", \"Thiasin\", \"Unisulf\", \"Urisoxin\", \"Uritrisin\", \"Urogan\", \"Vagilia\")"					"9701-4"
+"SSS"		86225	"Sulfonamides"	"Other antibacterials"				""					
+"SLP"		9950244	"Sulopenem"	"Other antibacterials"				"Sulopenem"					
+"SLT6"	"J01CR04"	444022	"Sultamicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"		"c(\"Sultamicilina\", \"Sultamicillin\", \"Sultamicillinum\")"	1.5	"g"			
+"SUR"		46700778	"Surotomycin"	"Other antibacterials"				"Surotomycin"					
+"TAL"	"J01CA15"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Talampicilina\", \"Talampicillin\", \"Talampicilline\", \"Talampicillinum\")"	2	"g"			
+"TLP"		163307	"Talmetoprim"	"Other antibacterials"				"Talmetoprim"					
+"TAZ"	"J01CG02"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo"	"c(\"Tazobactam\", \"Tazobactam acid\", \"Tazobactamum\", \"Tazobactum\")"					
+"TBP"		9800194	"Tebipenem"	"Carbapenems"				""					
+"TZD"	"J01XX11"	11234049	"Tedizolid"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"tedi"	"c(\"Tedizolid\", \"Torezolid\")"					
+"TEC"	"J01XA02"	16131923	"Teicoplanin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"tei\", \"tec\", \"tpn\", \"tp\", \"tpl\", \"teic\")"	"c(\"Targocid\", \"Tecoplanina\", \"Tecoplanine\", \"Tecoplaninum\", \"Teichomycin\", \"Teicoplanina\", \"Teicoplanine\", \"Teicoplaninum\")"			0.4	"g"	"c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
+"TCM"			"Teicoplanin-macromethod"	"Glycopeptides"				""					
+"TLV"	"J01XA03"	3081362	"Telavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela"	"c(\"Telavancin\", \"Vibativ\")"					
+"TLT"	"J01FA15"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"Levviax"	0.8	"g"			
+"TMX"	"J01MA05"	60021	"Temafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Omniflox\", \"Temafloxacin\", \"Temafloxacina\", \"Temafloxacine\", \"Temafloxacinum\")"	0.8	"g"			
+"TEM"	"J01CA17"	171758	"Temocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"		"c(\"Temocilina\", \"Temocillin\", \"Temocillina\", \"Temocilline\", \"Temocillinum\")"			2	"g"	
+"TRB"	"D01BA02"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"Antifungals for systemic use"	"Antifungals for systemic use"		"c(\"Corbinal\", \"Lamasil\", \"Lamisil\", \"Lamisil AT\", \"Lamisil Tablet\", \"Terbinafina\", \"Terbinafine\", \"Terbinafinum\", \"Terbinex\")"	0.25	"g"			
+"TRC"		441383	"Terconazole"	"Antifungals/antimycotics"				"c(\"Fungistat\", \"Panlomyc\", \"Terazol\", \"Terconazol\", \"Terconazole\", \"Terconazolum\", \"Tercospor\", \"Triaconazole\", \"Zazole\")"					
+"TRZ"	"J04AK03"	65720	"Terizidone"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"		"c(\"Terivalidin\", \"Terizidon\", \"Terizidona\", \"Terizidone\", \"Terizidonum\")"					
+"TCY"	"J01AA07"	54675776	"Tetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"te\", \"tet\", \"tc\", \"tetr\")"	"c(\"Abramycin\", \"Abricycline\", \"Achromycin\", \"Achromycin V\", \"Actisite\", \"Agromicina\", \"Ambramicina\", \"Ambramycin\", \"Amycin\", \"Biocycline\", \"Bristaciclin\", \"Bristaciclina\", \"Bristacycline\", \"Cefracycline\", \"Centet\", \"Ciclibion\", \"Copharlan\", \"Criseociclina\", \"Cyclomycin\", \"Cyclopar\", \"Cytome\", \"Democracin\", \"Deschlorobiomycin\", \"Dumocyclin\", \"Enterocycline\", \"Hostacyclin\", \"Lexacycline\", \"Limecycline\", \"Liquamycin\", \"Medocycline\", \"Mericycline\", \"Micycline\", \"Neocycline\", \"Oletetrin\", \"Omegamycin\", 
+\"Orlycycline\", \"Panmycin\", \"Piracaps\", \"Polycycline\", \"Polyotic\", \"Purocyclina\", \"Resteclin\", \"Robitet\", \"Roviciclina\", \"Sigmamycin\", \"Solvocin\", \"Sumycin\", \"Sumycin syrup\", \"Tetrabon\", \"Tetrachel\", \"Tetraciclina\", \"Tetracycl\", \"Tetracyclin\", \"Tetracycline\", \"Tetracycline base\", \"Tetracycline I\", \"Tetracycline II\", \"Tetracyclinum\", \"Tetracyn\", \"Tetradecin\", \"Tetrafil\", \"Tetramed\", \"TetraSURE\", \"Tetraverine\", \"Tetrazyklin\", \"Tetrex\", \"Topicycline\", \"Tsiklomistsin\", \"Tsiklomitsin\", \"Veracin\", \"Vetacyclinum\"
+)"	1	"g"	1	"g"	"c(\"25272-6\", \"4045-1\", \"87590-6\")"
+"TET"		65450	"Tetroxoprim"	"Other antibacterials"				"c(\"Tetroxoprim\", \"Tetroxoprima\", \"Tetroxoprime\", \"Tetroxoprimum\")"					
+"THA"		9568512	"Thiacetazone"	"Antimycobacterials"				"c(\"Aktivan\", \"Ambathizon\", \"AMITHIOZONE\", \"Amithizone\", \"Amitiozon\", \"Benthiozone\", \"Benzothiozane\", \"Benzothiozon\", \"Berculon A\", \"Berkazon\", \"Citazone\", \"Conteben\", \"Diasan\", \"Diazan\", \"Domakol\", \"Ilbion\", \"Livazone\", \"Mirizone neustab\", \"Mivizon\", \"Myvizone\", \"Neotibil\", \"Neustab\", \"Novakol\", \"Nuclon argentinian\", \"Panrone\", \"Parazone\", \"Seroden\", \"Siocarbazone\", \"Tebalon\", \"Tebecure\", \"Tebemar\", \"Tebesone I\", \"Tebethion\", \"Tebethione\", \"Tebezon\", \"Thiacetazone\", \"Thiacetone\", \"Thiacetozone\", 
+\"Thibon\", \"Thibone\", \"Thioacetazon\", \"Thioacetazone\", \"Thioacetazonum\", \"Thioazetazone\", \"Thiocarbazil\", \"Thiomicid\", \"Thionicid\", \"Thioparamizon\", \"Thioparamizone\", \"Thiosemicarbarzone\", \"Thiosemicarbazone\", \"Thiotebesin\", \"Thiotebezin\", \"Thiotebicina\", \"Thizone\", \"Tiacetazon\", \"Tibicur\", \"Tibion\", \"Tibione\", \"Tibizan\", \"Tibone\", \"Tioacetazon\", \"Tioacetazona\", \"Tioatsetazon\", \"Tiobicina\", \"Tiocarone\", \"Tiosecolo\", \"Tubercazon\", \"Tubigal\")"					
+"THI"	"J01BA02"	27200	"Thiamphenicol"	"Amphenicols"	"Amphenicols"	"Amphenicols"		"c(\"Descocin\", \"Dexawin\", \"Dextrosulfenidol\", \"Dextrosulphenidol\", \"Efnicol\", \"Hyrazin\", \"Igralin\", \"Macphenicol\", \"Masatirin\", \"Neomyson\", \"Racefenicol\", \"Racefenicolo\", \"Racefenicolum\", \"Raceophenidol\", \"Racephenicol\", \"RACEPHENICOL\", \"Rincrol\", \"Thiamcol\", \"Thiamphenicol\", \"Thiamphenicolum\", \"Thiocymetin\", \"Thiomycetin\", \"Thiophenicol\", \"Tiamfenicol\", \"Tiamfenicolo\", \"Urfamicina\", \"Urfamycine\", \"Vicemycetin\")"	1.5	"g"	1.5	"g"	
+"THI1"	"J04AM04"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"		""					
+"TIA"		656958	"Tiamulin"	"Other antibacterials"				"c(\"Denagard\", \"Tiamulin\", \"Tiamulin pamoate\", \"Tiamulina\", \"Tiamuline\", \"Tiamulinum\")"					"87589-8"
+"TIC"	"J01CA13"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"ti\", \"tic\", \"tc\", \"tica\")"	"c(\"Ticarcilina\", \"Ticarcillin\", \"Ticarcilline\", \"Ticarcillinum\", \"Ticillin\")"			15	"g"	"c(\"25254-4\", \"4054-3\", \"4055-0\")"
+"TCC"	"J01CR03"	6437075	"Ticarcillin/clavulanic acid"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"tim\", \"t/c\", \"tcc\", \"tlc\", \"ticl\")"	"Timentin"			15	"g"	
+"TGC"	"J01AA12"	54686904	"Tigecycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"tgc\", \"tige\")"	"c(\"Haizheng Li Xing\", \"Tigeciclina\", \"Tigecyclin\", \"Tigecycline\", \"Tigecycline hydrate\", \"Tigecyclinum\", \"Tigilcycline\", \"Tygacil\")"			0.1	"g"	
+"TBQ"		65592	"Tilbroquinol"	"Quinolones"				"c(\"Tilbroquinol\", \"Tilbroquinolum\")"					
+"TIP"		24860548	"Tildipirosin"	"Macrolides/lincosamides"				"c(\"Tildipirosin\", \"Zuprevo\")"					
+"TIL"		5282521	"Tilmicosin"	"Macrolides/lincosamides"				"c(\"Micotil\", \"Pulmotil\", \"Tilmicosin\", \"Tilmicosina\", \"Tilmicosine\", \"Tilmicosinum\")"					"87588-0"
+"TIN"	"J01XD02"	5479	"Tinidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"		"c(\"Amtiba\", \"Bioshik\", \"Ethyl sulfone\", \"Fasigin\", \"Fasigyn\", \"Fasigyntrade mark\", \"Fasygin\", \"Glongyn\", \"Haisigyn\", \"Pletil\", \"Simplotan\", \"Simplotantrade mark\", \"Sorquetan\", \"Tindamax\", \"Tindamaxtrade mark\", \"Tinidazol\", \"Tinidazole\", \"Tinidazolum\", \"Tricolam\", \"Trimonase\")"			1.5	"g"	
+"TCR"	"J04AD02"	3001386	"Tiocarlide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"		"c(\"Amixyl\", \"Datanil\", \"Disocarban\", \"Disoxyl\", \"Thiocarlide\", \"Tiocarlid\", \"Tiocarlida\", \"Tiocarlide\", \"Tiocarlidum\")"	7	"g"			
+"TDC"		10247721	"Tiodonium chloride"	"Other antibacterials"				"c(\"Cloruro de tiodonio\", \"Tiodonii chloridum\", \"Tiodonium chloride\")"					
+"TXC"		65788	"Tioxacin"	"Quinolones"				"c(\"Tioxacin\", \"Tioxacine\", \"Tioxacino\", \"Tioxacinum\", \"Tioxic acid\")"					
+"TIZ"		394397	"Tizoxanide"	"Other antibacterials"				"NTZdes"					
+"TOB"	"J01GB01"	36294	"Tobramycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"to\", \"nn\", \"tm\", \"tob\", \"tobr\")"	"c(\"Bethkis\", \"Brulamycin\", \"Deoxykanamycin B\", \"Distobram\", \"Gernebcin\", \"Gotabiotic\", \"Kitabis Pak\", \"Nebcin\", \"Nebicin\", \"NEBRAMYCIN\", \"Nebramycin VI\", \"Obramycin\", \"Sybryx\", \"Tenebrimycin\", \"Tenemycin\", \"Tobacin\", \"Tobi Podhaler\", \"Tobracin\", \"Tobradex\", \"Tobradistin\", \"Tobralex\", \"Tobramaxin\", \"Tobramicin\", \"Tobramicina\", \"Tobramitsetin\", \"Tobramycetin\", \"Tobramycin\", \"Tobramycin Base\", \"TOBRAMYCIN SULFATE\", \"Tobramycine\", \"Tobramycinum\", \"Tobrased\", \"Tobrasone\", \"Tobrex\")"			0.24	"g"	"c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")"
+"TFX"		5517	"Tosufloxacin"	"Quinolones"				"Tosufloxacin"					
+"TMP"	"J01EA01"	5578	"Trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"c(\"t\", \"tmp\", \"tr\", \"w\", \"trim\")"	"c(\"Abaprim\", \"Alprim\", \"Anitrim\", \"Antrima\", \"Antrimox\", \"Bacdan\", \"Bacidal\", \"Bacide\", \"Bacterial\", \"Bacticel\", \"Bactifor\", \"Bactin\", \"Bactoprim\", \"Bactramin\", \"Bactrim\", \"Bencole\", \"Bethaprim\", \"Biosulten\", \"Briscotrim\", \"Chemotrin\", \"Colizole\", \"Colizole DS\", \"Conprim\", \"Cotrimel\", \"CoTrimoxizole\", \"Deprim\", \"Dosulfin\", \"Duocide\", \"Esbesul\", \"Espectrin\", \"Euctrim\", \"Exbesul\", \"Fermagex\", \"Fortrim\", \"Idotrim\", \"Ikaprim\", \"Instalac\", \"Kombinax\", \"Lagatrim\", \"Lagatrim Forte\", \"Lastrim\", \"Lescot\", 
+\"Methoprim\", \"Metoprim\", \"Monoprim\", \"Monotrim\", \"Monotrimin\", \"Novotrimel\", \"Omstat\", \"Oraprim\", \"Pancidim\", \"Polytrim\", \"Priloprim\", \"Primosept\", \"Primsol\", \"Proloprim\", \"Protrin\", \"Purbal\", \"Resprim\", \"Resprim Forte\", \"Roubac\", \"Roubal\", \"Salvatrim\", \"Septrin DS\", \"Septrin Forte\", \"Septrin S\", \"Setprin\", \"Sinotrim\", \"Stopan\", \"Streptoplus\", \"Sugaprim\", \"Sulfamar\", \"Sulfamethoprim\", \"Sulfoxaprim\", \"Sulthrim\", \"Sultrex\", \"Syraprim\", \"Tiempe\", \"Tmp Smx\", \"Toprim\", \"Trimanyl\", \"Trimethioprim\", \"Trimethopim\", 
+\"Trimethoprim\", \"TRIMETHOPRIM\", \"Trimethoprime\", \"Trimethoprimum\", \"Trimethopriom\", \"Trimetoprim\", \"Trimetoprima\", \"Trimexazole\", \"Trimexol\", \"Trimezol\", \"Trimogal\", \"Trimono\", \"Trimopan\", \"Trimpex\", \"Triprim\", \"Trisul\", \"Trisulcom\", \"Trisulfam\", \"Trisural\", \"Uretrim\", \"Urobactrim\", \"Utetrin\", \"Velaten\", \"Wellcoprim\", \"Wellcoprin\", \"Xeroprim\", \"Zamboprim\")"	0.4	"g"	0.4	"g"	"c(\"11005-6\", \"17747-7\", \"25273-4\", \"32342-8\", \"4079-0\", \"4080-8\", \"4081-6\", \"55584-7\", \"80552-3\", \"80973-1\")"
+"SXT"	"J01EE01"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"c(\"t/s\", \"sxt\", \"ts\", \"cot\", \"trsu\")"	"c(\"Bactrim\", \"Bactrimel\", \"Belcomycine\", \"Colimycin\", \"Colimycin sulphate\", \"Colisticin\", \"Colistimethate\", \"Colistimethate Sodium\", \"Colistin sulfate\", \"Colistin sulphate\", \"Colomycin\", \"Coly-Mycin\", \"Cotrimazole\", \"Cotrimoxazole\", \"Polymyxin E\", \"Polymyxin E. Sulfate\", \"Promixin\", \"Septra\", \"Totazina\")"					
+"TRL"	"J01FA08"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"		"c(\"ACETYLOLEANDOMYCIN\", \"Aovine\", \"Cyclamycin\", \"Evramicina\", \"Matromicina\", \"Matromycin T\", \"Oleandocetine\", \"T.A.O.\", \"Treolmicina\", \"Tribiocillina\", \"Triocetin\", \"Triolan\", \"Troleandomicina\", \"Troleandomycin\", \"Troleandomycine\", \"Troleandomycinum\", \"Viamicina\", \"Wytrion\")"	1	"g"			
+"TRO"		55886	"Trospectomycin"	"Other antibacterials"				"c(\"Trospectinomycin\", \"Trospectomicina\", \"Trospectomycin\", \"Trospectomycine\", \"Trospectomycinum\")"					
+"TVA"	"J01MA13"	62959	"Trovafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"		"c(\"Trovafloxacin\", \"Trovan\")"	0.2	"g"	0.2	"g"	
+"TUL"		9832301	"Tulathromycin"	"Macrolides/lincosamides"				"c(\"Draxxin\", \"Tulathrmycin A\", \"Tulathromycin\", \"Tulathromycin A\")"					
+"TYL"		5280440	"Tylosin"	"Macrolides/lincosamides"				"c(\"Fradizine\", \"Tilosina\", \"Tylocine\", \"Tylosin\", \"Tylosin A\", \"Tylosine\", \"Tylosinum\")"					"87587-2"
+"TYL1"	"A07AA11"	6441094	"Tylvalosin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"		""	0.6	"g"			"87586-4"
+"PRU1"		124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"				"Ulifloxacin"					
+"VAN"	"J01XA01"	14969	"Vancomycin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"va\", \"van\", \"vanc\")"	"c(\"Vancocin\", \"Vancocin HCL\", \"Vancoled\", \"Vancomicina\", \"Vancomycin\", \"Vancomycin HCL\", \"Vancomycine\", \"Vancomycinum\", \"VANCOR\", \"Viomycin derivative\")"			2	"g"	"c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
+"VAM"			"Vancomycin-macromethod"	"Glycopeptides"				""					
+"VIO"		135398671	"Viomycin"	"Antimycobacterials"				"c(\"Celiomycin\", \"Florimycin\", \"Floromycin\", \"Viomicina\", \"Viomycin\", \"Viomycine\", \"Viomycinum\")"					
+"VIR"		11979535	"Virginiamycine"	"Other antibacterials"				"c(\"Eskalin V\", \"Mikamycin\", \"Mikamycine\", \"Mikamycinum\", \"Ostreogrycinum\", \"Pristinamycine\", \"Pristinamycinum\", \"Stafac\", \"Stafytracine\", \"Staphylomycin\", \"Starfac\", \"Streptogramin\", \"Vernamycin\", \"Virgimycin\", \"Virgimycine\", \"Virginiamycina\", \"Virginiamycine\", \"Virginiamycinum\")"					
+"VOR"	"J02AC03"	71616	"Voriconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori"	"c(\"Pfizer\", \"VFEND I.V.\", \"Voriconazol\", \"Voriconazole\", \"Voriconazolum\", \"Vorikonazole\")"	0.4	"g"	0.4	"g"	"c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")"
+"XBR"	"J01XX02"	72144	"Xibornol"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"		"c(\"Bactacine\", \"Bracen\", \"Nanbacine\", \"Xibornol\", \"Xibornolo\", \"Xibornolum\")"					
+"ZID"		77846445	"Zidebactam"	"Other antibacterials"				"Zidebactam"					

data-raw/antivirals.txt

@@ -0,0 +1,103 @@
+"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"		
+"J05AR14"		"darunavir and cobicistat"	"Antivirals for treatment of HIV infections, combinations"	""				
+"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"	""				
+"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"	""				
+"J05AR18"		"emtricitabine, tenofovir alafenamide, elvitegravir and cobicistat"	"Antivirals for treatment of HIV infections, combinations"	""				
+"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"
+"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"		
+"J05AR02"		"lamivudine and abacavir"	"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"		
+"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"				
+"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"		
+"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"
+"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"	""				

data-raw/country_analysis.R

@@ -0,0 +1,185 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+# Read and format data ----------------------------------------------------
+
+library(tidyverse)
+library(maps)
+library(httr)
+
+GET_df <- function(ip) {
+  ip <- paste0("https://ipinfo.io/", ip, "?token=", ipinfo_token)
+  result <- ip %>% GET()
+  stop_for_status(result)
+  result %>%
+    content(type = "text", encoding = "UTF-8") %>%
+    jsonlite::fromJSON(flatten = TRUE) %>% 
+    as_tibble()
+}
+
+# get website analytics
+source("data-raw/country_analysis_url_token.R")
+url_json <- paste0(country_analysis_url, 
+                   "/index.php?&module=API&token_auth=", 
+                   country_analysis_token,
+                   "&method=Live.getLastVisitsDetails&idSite=3&language=en&expanded=1&date=2018-01-01,2028-01-01&period=range&filter_limit=-1&format=JSON&segment=&translateColumnNames=1")
+data_json <- jsonlite::read_json(url_json)
+data <- tibble(
+  timestamp_server = as.POSIXct(sapply(data_json, function(x) x$serverTimestamp), origin = "1970-01-01"),
+  ipaddress = sapply(data_json, function(x) x$visitIp))
+rm(data_json)
+
+# add country data based on IP address and ipinfo.io API
+unique_ip <- unique(data$ipaddress)
+ip_tbl <- GET_df(unique_ip[1])
+p <- progress_estimated(n = length(unique_ip) - 1, min_time = 0)
+for (i in 2:length(unique_ip)) {
+  p$tick()$print()
+  ip_tbl <- ip_tbl %>% 
+    bind_rows(GET_df(unique_ip[i]))
+}
+
+ip_tbl.bak <- ip_tbl
+
+# add long and lat
+ip_tbl <- ip_tbl %>% 
+  separate(loc, into = c("y", "x"), sep = ",", remove = FALSE, convert = TRUE)
+
+# Plot world map ----------------------------------------------------------
+
+countries_geometry <- sf::st_as_sf(map('world', plot = FALSE, fill = TRUE)) %>% 
+  mutate(countries_code = countrycode::countrycode(ID, 
+                                                   origin = 'country.name', 
+                                                   destination = 'iso2c', 
+                                                   custom_match = c("Ascension Island" = "GB", # Great Britain
+                                                                    "Azores" = "PT", # Portugal
+                                                                    "Barbuda" = "GB", # Great Britain
+                                                                    "Bonaire" = "BQ", # Bonaire, Saint Eustatius and Saba
+                                                                    "Canary Islands" = "ES", # Spain
+                                                                    "Chagos Archipelago" = "MU", # Mauritius
+                                                                    "Grenadines" = "VC", # Saint Vincent and the Grenadines
+                                                                    "Heard Island" = "AU", # Australia
+                                                                    "Kosovo" = "XK",
+                                                                    "Madeira Islands" = "PT", # Portugal
+                                                                    "Micronesia" = "FM",
+                                                                    "Saba" = "BQ", # Bonaire, Saint Eustatius and Saba
+                                                                    "Saint Martin" = "MF",
+                                                                    "Siachen Glacier" = "IN", # India
+                                                                    "Sint Eustatius" = "BQ" # Bonaire, Saint Eustatius and Saba
+                                                   )),
+         included = as.integer(countries_code %in% ip_tbl$country),
+         not_antarctica = as.integer(ID != "Antarctica"),
+         countries_name = ifelse(included == 1, as.character(ID), NA))
+
+# how many?
+countries_geometry %>% filter(included == 1) %>% nrow()
+
+countries_plot <- ggplot(countries_geometry) +
+    geom_sf(aes(fill = included, colour = not_antarctica),
+            size = 0.25, 
+            show.legend = FALSE) +
+    theme_minimal() +
+    theme(panel.grid = element_blank(),
+          axis.title = element_blank(),
+          axis.text = element_blank()) +
+    scale_fill_gradient(low = "white", high = "#CAD6EA", ) +
+    # this makes the border Antarctica turn white (invisible):
+    scale_colour_gradient(low = "white", high = "#81899B")
+
+countries_plot_mini <- countries_plot
+countries_plot_mini$data <- countries_plot_mini$data %>% filter(ID != "Antarctica")
+countries_plot_mini <- countries_plot_mini + scale_colour_gradient(low = "#81899B", high = "#81899B")
+countries_plot_big <- countries_plot +
+  labs(title = tools::toTitleCase("Countries where the AMR package for R was downloaded from"),
+       subtitle = paste0("Between March 2018 (first release) and ", format(Sys.Date(), "%B %Y"), "." #,
+                         #"The dots denote visitors on our website https://gitlab.io/msberends/AMR."
+                         )) +
+  theme(plot.title = element_text(size = 16, hjust = 0.5),
+        plot.subtitle = element_text(size = 12, hjust = 0.5)) +
+  geom_text(aes(x = -170,
+                y = -75,
+                label = stringr::str_wrap(paste0("Countries (n = ", 
+                                                 length(countries_name[!is.na(countries_name)]), "): ", 
+                                                 paste(sort(countries_name[!is.na(countries_name)]), collapse = ", ")),
+                                          200)),
+            hjust = 0,
+             size = 4) # +
+  # # points of visitors
+  # geom_point(data = ip_tbl,
+  #            aes(x = x, y = y), 
+  #            size = 1,
+  #            colour = "#81899B")
+
+# main website page
+ggsave("pkgdown/logos/countries.png",
+       width = 6, 
+       height = 2.5, 
+       units = "in", 
+       dpi = 100, 
+       plot = countries_plot_mini, 
+       scale = 1)
+# when clicked - a high res enlargement
+ggsave("pkgdown/logos/countries_large.png",
+       width = 11,
+       height = 6, 
+       units = "in", 
+       dpi = 300, 
+       plot = countries_plot_big,
+       scale = 1.5)
+
+
+# Gibberish ---------------------------------------------------------------
+
+data %>%
+  left_join(ip_tbl, by = c("ipaddress" = "ip")) %>% 
+  group_by(country = countrycode::countrycode(country, 
+                                              origin = 'iso2c', 
+                                              destination = 'country.name')) %>%
+  summarise(first = min(timestamp_server)) %>%
+  arrange(desc(first))
+# 
+# p1 <- data %>%
+#   group_by(country) %>%
+#   summarise(first = min(timestamp_server)) %>%
+#   arrange(first) %>%
+#   mutate(n = row_number()) %>%
+#   ggplot(aes(x = first, y = n)) + 
+#   geom_line() +
+#   geom_point(aes(x = max(first), y = max(n)), size = 3) + 
+#   scale_x_datetime(date_breaks = "2 months", date_labels = "%B %Y") +
+#   labs(x = NULL, y = "Number of countries")
+# 
+# package_releases <- read_html("https://cran.r-project.org/src/contrib/Archive/AMR/") %>%
+#   rvest::html_table() %>%
+#   .[[1]] %>%
+#   as_tibble(.name_repair = "unique") %>%
+#   filter(`Last modified` != "") %>%
+#   transmute(version = gsub("[^0-9.]", "", 
+#                            gsub(".tar.gz", "", Name)), 
+#             datetime = as.POSIXct(`Last modified`)) %>% 
+#   # add current
+#   bind_rows(tibble(version = as.character(packageVersion("AMR")),
+#                    datetime = as.POSIXct(packageDate("AMR")))) %>% 
+#   # remove the ones not plottable
+#   filter(datetime > min(p1$data$first))
+# 
+# p1 + geom_linerange(data = package_releases, aes(x = datetime, ymin = 0, ymax = 80), colour = "red", inherit.aes = FALSE)
+# 

data-raw/eucast_rules.tsv

@@ -5,7 +5,7 @@
 # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
 # The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
 # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
-# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J (2005, PMID 16217180).
+# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
 # -------------------------------------------------------------------------------------------------------------------------------
 if_mo_property	like.is.one_of	this_value	and_these_antibiotics	have_these_values	then_change_these_antibiotics	to_value	reference.rule	reference.rule_group
@@ -37,7 +37,6 @@ genus	is	Staphylococcus	ERY	S	AZM, CLR, RXT	S	Staphylococcus	Breakpoints
 genus	is	Staphylococcus	ERY	I	AZM, CLR, RXT	I	Staphylococcus	Breakpoints
 genus	is	Staphylococcus	ERY	R	AZM, CLR, RXT	R	Staphylococcus	Breakpoints
 genus	is	Staphylococcus	TCY	S	DOX, MNO	S	Staphylococcus	Breakpoints
-genus_species	is	Enterococcus faecium	AMP	R	all_betalactams	R	Enterococcus	Breakpoints
 genus	is	Enterococcus	AMP	S	AMX, AMC, PIP, TZP	S	Enterococcus	Breakpoints
 genus	is	Enterococcus	AMP	I	AMX, AMC, PIP, TZP	I	Enterococcus	Breakpoints
 genus	is	Enterococcus	AMP	R	AMX, AMC, PIP, TZP	R	Enterococcus	Breakpoints
@@ -47,7 +46,8 @@ genus	is	Enterococcus	NOR	R	CIP, LVX	R	Enterococcus	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	PEN	S	aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC	S	Streptococcus groups A, B, C, G	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	PEN	I	aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC	I	Streptococcus groups A, B, C, G	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	PEN	R	aminopenicillins, ureidopenicillins, cephalosporins_except_CAZ, carbapenems, FLC, AMC	R	Streptococcus groups A, B, C, G	Breakpoints
-genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	NOR	S	LVX, MFX	S	Streptococcus groups A, B, C, G	Breakpoints
+genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	NOR	S	MFX	S	Streptococcus groups A, B, C, G	Breakpoints
+genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	NOR	S	LVX	I	Streptococcus groups A, B, C, G	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	ERY	S	AZM, CLR, RXT	S	Streptococcus groups A, B, C, G	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	ERY	I	AZM, CLR, RXT	I	Streptococcus groups A, B, C, G	Breakpoints
 genus_species	like	^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$	ERY	R	AZM, CLR, RXT	R	Streptococcus groups A, B, C, G	Breakpoints
@@ -56,7 +56,8 @@ genus_species	is	Streptococcus pneumoniae	PEN	S	AMP, AMX, AMC, PIP, TZP	S	Strept
 genus_species	is	Streptococcus pneumoniae	AMP	S	AMX, AMC, PIP, TZP	S	Streptococcus pneumoniae	Breakpoints
 genus_species	is	Streptococcus pneumoniae	AMP	I	AMX, AMC, PIP, TZP	I	Streptococcus pneumoniae	Breakpoints
 genus_species	is	Streptococcus pneumoniae	AMP	R	AMX, AMC, PIP, TZP	R	Streptococcus pneumoniae	Breakpoints
-genus_species	is	Streptococcus pneumoniae	NOR	S	LVX, MFX	S	Streptococcus pneumoniae	Breakpoints
+genus_species	is	Streptococcus pneumoniae	NOR	S	MFX	S	Streptococcus pneumoniae	Breakpoints
+genus_species	is	Streptococcus pneumoniae	NOR	S	LVX	I	Streptococcus pneumoniae	Breakpoints
 genus_species	is	Streptococcus pneumoniae	ERY	S	AZM, CLR, RXT	S	Streptococcus pneumoniae	Breakpoints
 genus_species	is	Streptococcus pneumoniae	ERY	I	AZM, CLR, RXT	I	Streptococcus pneumoniae	Breakpoints
 genus_species	is	Streptococcus pneumoniae	ERY	R	AZM, CLR, RXT	R	Streptococcus pneumoniae	Breakpoints
@@ -122,6 +123,11 @@ genus_species	is	Kingella kingae	ERY	S	AZM, CLR	S	Kingella kingae	Breakpoints
 genus_species	is	Kingella kingae	ERY	I	AZM, CLR	I	Kingella kingae	Breakpoints
 genus_species	is	Kingella kingae	ERY	R	AZM, CLR	R	Kingella kingae	Breakpoints
 genus_species	is	Kingella kingae	TCY	S	DOX	S	Kingella kingae	Breakpoints
+genus_species	is	Kingella kingae	TCY	I	DOX	I	Kingella kingae	Breakpoints
+genus_species	is	Kingella kingae	TCY	R	DOX	R	Kingella kingae	Breakpoints
+genus_species	is	Burkholderia pseudomallei	TCY	S	DOX	S	Burkholderia pseudomallei	Breakpoints
+genus_species	is	Burkholderia pseudomallei	TCY	I	DOX	I	Burkholderia pseudomallei	Breakpoints
+genus_species	is	Burkholderia pseudomallei	TCY	R	DOX	R	Burkholderia pseudomallei	Breakpoints
 order	is	Enterobacterales			PEN, glycopeptides, FUS, macrolides, LIN, streptogramins, RIF, DAP, LNZ	R	Table 01: Intrinsic resistance in Enterobacteriaceae	Expert Rules
 fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			aminopenicillins, TIC	R	Table 01: Intrinsic resistance in Enterobacteriaceae	Expert Rules
 fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, CZO, FOX	R	Table 01: Intrinsic resistance in Enterobacteriaceae	Expert Rules
@@ -146,7 +152,7 @@ genus_species	is	Acinetobacter pittii			aminopenicillins, AMC, CZO, CTX, CRO, AT
 genus_species	is	Acinetobacter nosocomialis			aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
 genus_species	is	Acinetobacter calcoaceticus			aminopenicillins, AMC, CZO, CTX, CRO, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
 genus_species	is	Achromobacter xylosoxidans			aminopenicillins, CZO, CTX, CRO, ETP	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
-fullname	like	^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)			aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
+fullname	like	^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis)			aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
 genus_species	is	Elizabethkingia meningoseptica			aminopenicillins, AMC, TIC, CZO, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
 genus_species	is	Ochrobactrum anthropi			aminopenicillins, AMC, TIC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules
 genus_species	is	Pseudomonas aeruginosa			aminopenicillins, AMC, CZO, CTX, CRO, ETP, CHL, KAN, NEO, TMP, SXT, tetracyclines, TGC	R	Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria	Expert Rules

data-raw/internals.R

@@ -1,5 +1,27 @@
-# Run this file to update the package -------------------------------------
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+# Run this file to update the package using: -------------------------------
 # source("data-raw/internals.R")
+# --------------------------------------------------------------------------
 
 # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
 eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
@@ -9,7 +31,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
                             header = TRUE,
                             strip.white = TRUE,
                             na = c(NA, "", NULL))
-# take the order of the reference.rule_group column in the orginal data file
+# take the order of the reference.rule_group column in the original data file
 eucast_rules_file$reference.rule_group <- factor(eucast_rules_file$reference.rule_group,
                                                  levels = unique(eucast_rules_file$reference.rule_group),
                                                  ordered = TRUE)
@@ -47,15 +69,16 @@ rm(eucast_rules_file)
 rm(translations_file)
 rm(microorganisms.translation)
 
-# Clean mo history ----
-usethis::ui_done(paste0("Resetting {usethis::ui_value('mo_history.csv')}"))
-tryCatch(
-  write.csv(x = data.frame(x = character(0),
-                           mo = character(0),
-                           uncertainty_level = integer(0),
-                           package_version = character(0),
-                           stringsAsFactors = FALSE),
-            row.names = FALSE,
-            file = "inst/mo_history/mo_history.csv"),
-  warning = function(w) cat("Warning:", w$message, "\n"),
-  error = function(e) cat("Error:", e$message, "\n"))
+# Save to raw data to repository ----
+library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
+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(rsi_translation %>% mutate(ab = ab_name(ab), mo = mo_name(mo)),
+            "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
+write.table(microorganisms %>% mutate_if(~!is.numeric(.), as.character),
+            "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
+write.table(antibiotics %>% mutate_if(~!is.numeric(.), as.character),
+            "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
+write.table(antivirals %>% mutate_all(as.character),
+            "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)

data-raw/loinc.R

@@ -0,0 +1,52 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+# last updated: 20 January 2020 - Loinc_2.67
+
+# Steps to reproduce:
+# 1. Create a fake account at https://loinc.org (sad you have to create one...)
+# 2. Download the CSV from https://loinc.org/download/loinc-table-file-csv/ (Loinc_2.67_Text_2.67.zip)
+# 3. Read Loinc.csv that's in this zip file
+loinc_df <- read.csv("data-raw/Loinc.csv",
+                     row.names = NULL,
+                     stringsAsFactors = FALSE)
+
+# 4. Clean and add
+library(dplyr)
+library(cleaner)
+library(AMR)
+loinc_df %>% freq(CLASS) # to find the drugs
+loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
+ab_names <- antibiotics %>% pull(name) %>% paste0(collapse = "|") %>% paste0("(", ., ")")
+
+antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
+for (i in seq_len(nrow(antibiotics))) {
+  loinc_ab <- loinc_df %>%
+    filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
+    pull(LOINC_NUM)
+  if (length(loinc_ab) > 0) {
+    antibiotics$loinc[i] <- list(loinc_ab)
+  }
+}
+
+dim(antibiotics) # for R/data.R
+usethis::use_data(antibiotics, overwrite = TRUE)
+rm(antibiotics)

data-raw/read_EUCAST.R

@@ -0,0 +1,208 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+library(openxlsx)
+library(dplyr)
+library(cleaner)
+library(AMR)
+
+# USE THIS FUNCTION TO READ THE EUCAST EXCEL FILE THAT CONTAINS THE BREAKPOINT TABLES
+
+read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") { 
+  
+  message("Getting sheet ", sheet)
+  sheet.bak <- sheet
+  
+  raw_data <- read.xlsx(xlsxFile = file,
+                        sheet = sheet,
+                        colNames = FALSE,
+                        skipEmptyRows = FALSE,
+                        skipEmptyCols = FALSE, 
+                        fillMergedCells = TRUE,
+                        na.strings = c("", "-", "NA", "IE", "IP"))
+  
+  # in the info header in the Excel file, EUCAST mentions which genera are targeted
+  if (sheet %like% "anaerob.*Gram.*posi") {
+    sheet <- paste0(c("Actinomyces", "Bifidobacterium", "Clostridioides", 
+                      "Clostridium", "Cutibacterium", "Eggerthella", 
+                      "Eubacterium", "Lactobacillus", "Propionibacterium", 
+                      "Staphylococcus saccharolyticus"), 
+                    collapse = "_")
+  } else if (sheet %like% "anaerob.*Gram.*nega") {
+    sheet <- paste0(c("Bacteroides",
+                      "Bilophila",
+                      "Fusobacterium",
+                      "Mobiluncus",
+                      "Parabacteroides",
+                      "Porphyromonas",
+                      "Prevotella"), 
+                    collapse = "_")
+  } else if (sheet == "Streptococcus A,B,C,G") {
+    sheet <- paste0(microorganisms %>%
+                      filter(genus == "Streptococcus") %>%
+                      mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
+                      filter(lancefield %like% "^Streptococcus group") %>% 
+                      pull(fullname), 
+                    collapse = "_")
+  } else if (sheet %like% "PK.*PD") {
+    sheet <- "UNKNOWN"
+  }
+  mo_sheet <- paste0(as.mo(unlist(strsplit(sheet, "_"))), collapse = "|")
+  
+  set_columns_names <- function(x, cols) {
+    colnames(x) <- cols[1:length(colnames(x))]
+    x
+  }
+  
+  get_mo <- function(x) {
+    for (i in seq_len(length(x))) {
+      y <- trimws(unlist(strsplit(x[i], "(,|and)")))
+      y <- trimws(gsub("[(].*[)]", "", y))
+      y <- suppressWarnings(as.mo(y, allow_uncertain = FALSE))
+      y <- y[!is.na(y) & y != "UNKNOWN"]
+      x[i] <- paste(y, collapse = "|")
+    }
+    x
+  }
+  
+  MICs_with_trailing_superscript <- c(0.0011:0.0019, 11:19, 21:29, 0.51:0.59, 41:49,
+                                      81:89, 0.031:0.039, 0.061:0.069, 0.251:0.259,
+                                      0.1251:0.1259, 161:169, 321:329)
+  
+  has_zone_diameters <- rep(any(unlist(raw_data) %like% "zone diameter"), nrow(raw_data))
+
+  cleaned <- raw_data %>% 
+    as_tibble() %>% 
+    set_columns_names(LETTERS) %>% 
+    transmute(drug = A,
+              MIC_S = B,
+              MIC_R = C,
+              disk_dose = ifelse(has_zone_diameters, E, NA_character_),
+              disk_S = ifelse(has_zone_diameters, `F`, NA_character_),
+              disk_R = ifelse(has_zone_diameters, G, NA_character_)) %>% 
+    filter(!is.na(drug),
+           !(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
+           !MIC_S %like% "(MIC|S ≤|note)",
+           drug != MIC_S) %>% 
+    mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
+                                      drug %like% "[( ]iv"   ~ "iv",
+                                      TRUE ~ NA_character_),
+           uti = ifelse(drug %like% "(UTI|urinary|urine)", TRUE, FALSE),
+           systemic = ifelse(drug %like% "(systemic|septic)", TRUE, FALSE),
+           mo = ifelse(drug %like% "([.]|spp)", get_mo(drug), mo_sheet)) %>% 
+    # clean disk doses
+    mutate(disk_dose = clean_character(disk_dose, remove = "[^0-9.-]")) %>% 
+    # clean MIC and disk values
+    mutate(MIC_S = gsub(".,.", "", MIC_S), # remove superscript notes with comma, like 0.5^2,3
+           MIC_R = gsub(".,.", "", MIC_R),
+           disk_S = gsub(".,.", "", disk_S),
+           disk_R = gsub(".,.", "", disk_R),
+           MIC_S = clean_double(MIC_S), # make them valid numeric values
+           MIC_R = clean_double(MIC_R),
+           disk_S = clean_integer(disk_S),
+           disk_R = clean_integer(disk_R),
+           # invalid MIC values have a superscript text, delete those
+           MIC_S = ifelse(MIC_S %in% MICs_with_trailing_superscript,
+                          substr(MIC_S, 1, nchar(MIC_S) - 1),
+                          MIC_S),
+           MIC_R = ifelse(MIC_R %in% MICs_with_trailing_superscript,
+                          substr(MIC_R, 1, nchar(MIC_R) - 1),
+                          MIC_R)
+    ) %>% 
+    # clean drug names
+    mutate(drug = gsub(" ?[(, ].*$", "", drug),
+           drug = gsub("[1-9]+$", "", drug),
+           ab = as.ab(drug)) %>% 
+    select(ab, mo, everything(), -drug)
+  
+  # new row for every different MO mentioned
+  for (i in 1:nrow(cleaned)) {
+    mo <- cleaned[i, "mo", drop = TRUE]
+    if (grepl(pattern = "|", mo, fixed = TRUE)) {
+      mo_vect <- unlist(strsplit(mo, "|", fixed = TRUE))
+      cleaned[i, "mo"] <- mo_vect[1]
+      for (j in seq_len(length(mo_vect))) {
+        cleaned <- bind_rows(cleaned, cleaned[i ,])
+        cleaned[nrow(cleaned), "mo"] <- mo_vect[j]
+      }
+    }
+  }
+  
+  cleaned <- cleaned %>% 
+    distinct(ab, mo, administration, uti, systemic, .keep_all = TRUE) %>% 
+    arrange(ab, mo) %>% 
+    mutate_at(c("MIC_S", "MIC_R", "disk_S", "disk_R"), as.double) %>%
+    pivot_longer(c("MIC_S", "MIC_R", "disk_S", "disk_R"), "type") %>% 
+    mutate(method = ifelse(type %like% "MIC", "MIC", "DISK"), 
+           type = gsub("^.*_", "breakpoint_", type)) %>%
+    pivot_wider(names_from = type, values_from = value) %>% 
+    mutate(guideline = "EUCAST 2020",
+           disk_dose = ifelse(method == "DISK", disk_dose, NA_character_),
+           mo = ifelse(mo == "", mo_sheet, mo)) %>% 
+    filter(!(is.na(breakpoint_S) & is.na(breakpoint_R))) %>% 
+    # comply with rsi_translation for now
+    transmute(guideline,
+              method, 
+              site = case_when(uti ~ "UTI",
+                               systemic ~ "Systemic",
+                               TRUE ~ administration),
+              mo, ab, 
+              ref_tbl = sheet.bak, 
+              disk_dose = ifelse(!is.na(disk_dose), paste0(disk_dose, "ug"), NA_character_),
+              breakpoint_S, 
+              breakpoint_R)
+  
+  cleaned
+}
+
+sheets_to_analyse <- c("Enterobacterales",
+                       "Pseudomonas",
+                       "S.maltophilia",
+                       "Acinetobacter",
+                       "Staphylococcus",
+                       "Enterococcus",
+                       "Streptococcus A,B,C,G",
+                       "S.pneumoniae",
+                       "Viridans group streptococci",
+                       "H.influenzae",
+                       "M.catarrhalis",
+                       "N.gonorrhoeae",
+                       "N.meningitidis",
+                       "Anaerobes, Grampositive",
+                       "C.difficile",
+                       "Anaerobes, Gramnegative",
+                       "H.pylori",
+                       "L.monocytogenes",
+                       "P.multocida",
+                       "C.jejuni_C.coli",
+                       "Corynebacterium",
+                       "A.sanguinicola_A.urinae",
+                       "K.kingae",
+                       "Aeromonas",
+                       "B.pseudomallei",
+                       "M.tuberculosis",
+                       "PK PD breakpoints")
+
+new_EUCAST <- read_EUCAST(sheets_to_analyse[1]) # takes the longest time
+for (i in 2:length(sheets_to_analyse)) {
+  new_EUCAST <<- new_EUCAST %>% bind_rows(read_EUCAST(sheets_to_analyse[i]))
+}
+

data-raw/reproduction_of_antibiotics.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
@@ -327,8 +327,23 @@ antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(anti
 # High level Gentamcin and Streptomycin
 antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
 antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
-# add imi to imipenem
+# add imi and "imipenem/cilastatine" to imipenem
 antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))
+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"))))
+
 
 ## new ATC codes
 # ceftaroline
@@ -386,6 +401,8 @@ antibiotics <- antibiotics %>%
 antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
 class(antibiotics$ab) <- "ab"
 
+# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
+
 dim(antibiotics) # for R/data.R
 usethis::use_data(antibiotics, overwrite = TRUE)
 rm(antibiotics)

data-raw/reproduction_of_antivirals.R

@@ -6,16 +6,16 @@
 # https://gitlab.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
 #                                                                      #
 # 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.                                        #
 #                                                                      #
-# This R package was created for academic research and was publicly    #
-# released in the hope that it will be useful, but it comes WITHOUT    #
-# ANY WARRANTY OR LIABILITY.                                           #
+# 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.              #
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 

data-raw/reproduction_of_microorganisms.R

@@ -1,3 +1,24 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
 # Reproduction of the `microorganisms` data set
 
 # Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
@@ -831,7 +852,7 @@ saveRDS(microorganisms.codes, "microorganisms.codes.rds")
 ### for same server
 microorganisms <- MOs
 microorganisms.old <- MOs.old
-microorganisms.translation <- old_new %>% select(mo_old, mo_new)
+microorganisms.translation <- old_new %>% select(mo_old, mo_new) %>% as.data.frame()
 class(microorganisms.translation$mo_old) <- "mo"
 class(microorganisms.translation$mo_new) <- "mo"
 

data-raw/reproduction_of_microorganisms_new.R

@@ -1,3 +1,24 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
 # ---------------------------------------------------------------------------------
 # Reproduction of the `microorganisms` data set
 # ---------------------------------------------------------------------------------

data-raw/reproduction_of_rsi_translation.R

@@ -3,10 +3,12 @@ library(dplyr)
 # Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
 #    opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
 #    and exported table 'DRGLST1' to MS Excel
-DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx")
+DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
 rsi_translation <- DRGLST1 %>%
   # only keep CLSI and EUCAST guidelines:
   filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
+  mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
+         MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
   # set a nice layout:
   transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
             method = TESTMETHOD,
@@ -36,11 +38,17 @@ tbl_disk <- rsi_translation %>%
 rsi_translation <- bind_rows(tbl_mic, tbl_disk) %>%
   rename(disk_dose = dose_disk) %>% 
   mutate(disk_dose = gsub("µ", "u", disk_dose)) %>% 
-  select(-ends_with("_mic"), -ends_with("_disk")) %>%
+  select(-ends_with("_mic"), -ends_with("_disk"))
+
+# add new EUCAST with read_EUCAST.R
+rsi_translation <- rsi_translation %>%
+  bind_rows(new_EUCAST) %>% 
+  mutate(uti = site %like% "(UTI|urinary)") %>% 
   as.data.frame(stringsAsFactors = FALSE) %>%
   # force classes again
   mutate(mo = as.mo(mo),
-         ab = as.ab(ab))
+         ab = as.ab(ab)) %>% 
+  arrange(desc(guideline), ab, mo, method)
 
 # save to package
 usethis::use_data(rsi_translation, overwrite = TRUE)

data-raw/snomed.R

@@ -0,0 +1,109 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://gitlab.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# 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.                                        #
+#                                                                      #
+# 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.              #
+# Visit our website for more info: https://msberends.gitlab.io/AMR.    #
+# ==================================================================== #
+
+library(AMR)
+library(tidyverse)
+
+# go to https://www.nictiz.nl/standaardisatie/terminologiecentrum/referentielijsten/micro-organismen/
+# read the table from clipboard
+snomed <- clipr::read_clip_tbl()
+# snomed <- snomed %>%
+#   transmute(fullname = trimws(gsub("^genus", "", Omschrijving, ignore.case = TRUE)),
+#             snomed = as.integer(Id))
+snomed <- snomed %>%
+  transmute(fullname = mo_name(Omschrijving),
+            snomed = as.integer(Id)) %>% 
+  filter(!fullname %like% "unknown")
+snomed_trans <- snomed %>%
+  group_by(fullname) %>%
+  mutate(snomed_list = list(snomed)) %>%
+  ungroup() %>%
+  select(fullname, snomed = snomed_list) %>%
+  distinct(fullname, .keep_all = TRUE)
+
+microorganisms <- AMR::microorganisms %>% 
+  left_join(snomed_trans)
+# remove the NULLs, set to NA
+microorganisms$snomed <- lapply(microorganisms$snomed, function(x) if (length(x) == 0)  NA else x)
+
+microorganisms <- dataset_UTF8_to_ASCII(microorganisms)
+
+usethis::use_data(microorganisms, overwrite = TRUE)
+rm(microorganisms)
+
+# OLD ---------------------------------------------------------------------
+
+baseUrl <- 'https://browser.ihtsdotools.org/snowstorm/snomed-ct'
+edition <- 'MAIN'
+version <- '2019-07-31'
+
+microorganisms.snomed <- data.frame(conceptid = character(0),
+                                    mo = character(0),
+                                    stringsAsFactors = FALSE)
+microorganisms$snomed <- ""
+
+# for (i in 1:50) {
+for (i in 1:1000) {
+  
+  if (i %% 10 == 0) {
+    cat(paste0(i, " - ", cleaner::percentage(i / nrow(microorganisms)), "\n"))
+  }
+  
+  mo_data <- microorganisms %>% 
+    filter(mo == microorganisms$mo[i]) %>% 
+    as.list()
+  
+  if (!mo_data$rank %in% c("genus", "species")) {
+    next
+  }
+  
+  searchTerm <- paste0(
+    ifelse(mo_data$rank == "genus", "Genus ", ""),
+    mo_data$fullname, 
+    " (organism)")
+  
+  url <- paste0(baseUrl, '/browser/',
+                edition, '/', 
+                version, 
+                '/descriptions?term=', curl::curl_escape(searchTerm),
+                '&mode=fullText&activeFilter=true&limit=', 250)
+  results <- url %>% 
+    httr::GET() %>%
+    httr::content(type = "text", encoding = "UTF-8") %>% 
+    jsonlite::fromJSON(flatten = TRUE) %>% 
+    .$items
+  if (NROW(results) == 0) {
+    next
+  } else {
+    message("Adding ", crayon::italic(mo_data$fullname))
+  }
+  
+  tryCatch(
+    microorganisms$snomed[i] <- results %>% filter(term == searchTerm) %>% pull(concept.conceptId),
+    error = function(e) invisible()
+  )
+  
+  if (nrow(results) > 1) {
+      microorganisms.snomed <- microorganisms.snomed %>% 
+        bind_rows(tibble(conceptid = results %>% filter(term != searchTerm) %>% pull(concept.conceptId) %>% unique(),
+                         mo = as.character(mo_data$mo)))
+  }
+}

data-raw/whonet_bugfixes.R

@@ -0,0 +1,11 @@
+# WHONET fixes
+microorganisms.codes[which(microorganisms.codes$code == "SAP"), "mo"] <- as.mo("staphylococcus")
+microorganisms.codes[which(microorganisms.codes$code == "PAE"), "mo"] <- as.mo("pseudomonas aeruginosa")
+microorganisms.codes[which(microorganisms.codes$code == "ANI"), "mo"] <- as.mo("aspergillus nidulans")
+microorganisms.codes[which(microorganisms.codes$code == "CAL"), "mo"] <- as.mo("candida albicans")
+microorganisms.codes[which(microorganisms.codes$code == "ENT"), "mo"] <- as.mo("enterococcus")
+microorganisms.codes[which(microorganisms.codes$code == "STR"), "mo"] <- as.mo("streptococcus")
+microorganisms.codes[which(microorganisms.codes$code == "CDF"), "mo"] <- as.mo("clostridium difficile")
+microorganisms.codes[which(microorganisms.codes$code == "HA-"), "mo"] <- as.mo("haemophilus influenzae")
+usethis::use_data(microorganisms.codes, overwrite = TRUE)
+rm(microorganisms.codes)

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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
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+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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docs/articles/EUCAST.html

@@ -16,9 +16,7 @@
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+<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
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@@ -41,7 +39,7 @@
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@@ -166,13 +164,7 @@
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@@ -187,7 +179,7 @@
       <h1>How to apply EUCAST rules</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">17 February 2020</h4>
       
       
       <div class="hidden name"><code>EUCAST.Rmd</code></div>
@@ -203,25 +195,169 @@
 <blockquote>
 <p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
 </blockquote>
-<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 9.0, 2019). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
+<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 10.0, 2020). Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
 </div>
 <div id="examples" class="section level2">
 <h2 class="hasAnchor">
 <a href="#examples" class="anchor"></a>Examples</h2>
-<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
-<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solves this:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">oops &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>, </a>
-<a class="sourceLine" id="cb1-2" data-line-number="2">                          <span class="st">"Escherichia"</span>),</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">                   <span class="dt">ampicillin =</span> <span class="st">"S"</span>)</a>
-<a class="sourceLine" id="cb1-4" data-line-number="4">oops</a>
-<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">#            mo ampicillin</span></a>
-<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co"># 1  Klebsiella          S</span></a>
-<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co"># 2 Escherichia          S</span></a>
-<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
-<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(oops, <span class="dt">info =</span> <span class="ot">FALSE</span>)</a>
-<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co">#            mo ampicillin</span></a>
-<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co"># 1  Klebsiella          R</span></a>
-<a class="sourceLine" id="cb1-12" data-line-number="12"><span class="co"># 2 Escherichia          S</span></a></code></pre></div>
+<p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
+<p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be used with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>oops &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Klebsiella"</span>, </span>
+<span id="cb1-2"><a href="#cb1-2"></a>                          <span class="st">"Escherichia"</span>),</span>
+<span id="cb1-3"><a href="#cb1-3"></a>                   <span class="dt">ampicillin =</span> <span class="st">"S"</span>)</span>
+<span id="cb1-4"><a href="#cb1-4"></a>oops</span>
+<span id="cb1-5"><a href="#cb1-5"></a><span class="co">#            mo ampicillin</span></span>
+<span id="cb1-6"><a href="#cb1-6"></a><span class="co"># 1  Klebsiella          S</span></span>
+<span id="cb1-7"><a href="#cb1-7"></a><span class="co"># 2 Escherichia          S</span></span>
+<span id="cb1-8"><a href="#cb1-8"></a></span>
+<span id="cb1-9"><a href="#cb1-9"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(oops, <span class="dt">info =</span> <span class="ot">FALSE</span>)</span>
+<span id="cb1-10"><a href="#cb1-10"></a><span class="co">#            mo ampicillin</span></span>
+<span id="cb1-11"><a href="#cb1-11"></a><span class="co"># 1  Klebsiella          R</span></span>
+<span id="cb1-12"><a href="#cb1-12"></a><span class="co"># 2 Escherichia          S</span></span></code></pre></div>
+<p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em> and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1"></a>data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"Staphylococcus aureus"</span>,</span>
+<span id="cb2-2"><a href="#cb2-2"></a>                          <span class="st">"Enterococcus faecalis"</span>,</span>
+<span id="cb2-3"><a href="#cb2-3"></a>                          <span class="st">"Escherichia coli"</span>,</span>
+<span id="cb2-4"><a href="#cb2-4"></a>                          <span class="st">"Klebsiella pneumoniae"</span>,</span>
+<span id="cb2-5"><a href="#cb2-5"></a>                          <span class="st">"Pseudomonas aeruginosa"</span>),</span>
+<span id="cb2-6"><a href="#cb2-6"></a>                   <span class="dt">VAN =</span> <span class="st">"-"</span>,       <span class="co"># Vancomycin</span></span>
+<span id="cb2-7"><a href="#cb2-7"></a>                   <span class="dt">AMX =</span> <span class="st">"-"</span>,       <span class="co"># Amoxicillin</span></span>
+<span id="cb2-8"><a href="#cb2-8"></a>                   <span class="dt">COL =</span> <span class="st">"-"</span>,       <span class="co"># Colistin</span></span>
+<span id="cb2-9"><a href="#cb2-9"></a>                   <span class="dt">CAZ =</span> <span class="st">"-"</span>,       <span class="co"># Ceftazidime</span></span>
+<span id="cb2-10"><a href="#cb2-10"></a>                   <span class="dt">CXM =</span> <span class="st">"-"</span>,       <span class="co"># Cefuroxime</span></span>
+<span id="cb2-11"><a href="#cb2-11"></a>                   <span class="dt">PEN =</span> <span class="st">"S"</span>,       <span class="co"># Penicillin G</span></span>
+<span id="cb2-12"><a href="#cb2-12"></a>                   <span class="dt">FOX =</span> <span class="st">"S"</span>,       <span class="co"># Cefoxitin</span></span>
+<span id="cb2-13"><a href="#cb2-13"></a>                   <span class="dt">stringsAsFactors =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a>data</span></code></pre></div>
+<table class="table">
+<thead><tr class="header">
+<th align="left">mo</th>
+<th align="center">VAN</th>
+<th align="center">AMX</th>
+<th align="center">COL</th>
+<th align="center">CAZ</th>
+<th align="center">CXM</th>
+<th align="center">PEN</th>
+<th align="center">FOX</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Staphylococcus aureus</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+<tr class="even">
+<td align="left">Enterococcus faecalis</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+<tr class="odd">
+<td align="left">Escherichia coli</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+<tr class="even">
+<td align="left">Klebsiella pneumoniae</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+<tr class="odd">
+<td align="left">Pseudomonas aeruginosa</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+</tbody>
+</table>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">info =</span> <span class="ot">FALSE</span>)</span></code></pre></div>
+<table class="table">
+<thead><tr class="header">
+<th align="left">mo</th>
+<th align="center">VAN</th>
+<th align="center">AMX</th>
+<th align="center">COL</th>
+<th align="center">CAZ</th>
+<th align="center">CXM</th>
+<th align="center">PEN</th>
+<th align="center">FOX</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Staphylococcus aureus</td>
+<td align="center">-</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+</tr>
+<tr class="even">
+<td align="left">Enterococcus faecalis</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">R</td>
+</tr>
+<tr class="odd">
+<td align="left">Escherichia coli</td>
+<td align="center">R</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">R</td>
+<td align="center">S</td>
+</tr>
+<tr class="even">
+<td align="left">Klebsiella pneumoniae</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">R</td>
+<td align="center">S</td>
+</tr>
+<tr class="odd">
+<td align="left">Pseudomonas aeruginosa</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">-</td>
+<td align="center">-</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+</tr>
+</tbody>
+</table>
 </div>
   </div>
 
@@ -242,7 +378,7 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">
@@ -253,20 +389,7 @@
 </div>
 
   
-<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script><script>
-  docsearch({
-    
-    
-    apiKey: 'f737050abfd4d726c63938e18f8c496e',
-    indexName: 'amr',
-    inputSelector: 'input#search-input.form-control',
-    transformData: function(hits) {
-      return hits.map(function (hit) {
-        hit.url = updateHitURL(hit);
-        return hit;
-      });
-    }
-  });
-</script>
-</body>
+
+
+  </body>
 </html>

docs/articles/MDR.html

@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
       </span>
     </div>
 
@@ -187,7 +187,7 @@
       <h1>How to determine multi-drug resistance (MDR)</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">26 January 2020</h4>
       
       
       <div class="hidden name"><code>MDR.Rmd</code></div>
@@ -306,19 +306,19 @@ Unique: 2</p>
 <p>The data set now looks like this:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
 <a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
-<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1          S         S            I          R            R            S</span></a>
-<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2          S         S            R          R            I            S</span></a>
-<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3          S         S            S          I            R            I</span></a>
-<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4          R         R            S          R            R            S</span></a>
-<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5          R         R            S          R            I            S</span></a>
-<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6          R         R            R          R            S            R</span></a>
+<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1          I         S            R          S            S            R</span></a>
+<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2          S         R            R          R            S            S</span></a>
+<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3          S         S            R          S            R            I</span></a>
+<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4          S         S            S          R            S            R</span></a>
+<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5          R         S            S          S            S            I</span></a>
+<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6          S         S            R          R            R            S</span></a>
 <a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co">#   kanamycin</span></a>
 <a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># 1         S</span></a>
-<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2         I</span></a>
-<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3         I</span></a>
-<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4         R</span></a>
-<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5         R</span></a>
-<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6         S</span></a></code></pre></div>
+<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2         S</span></a>
+<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3         R</span></a>
+<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4         I</span></a>
+<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5         S</span></a>
+<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6         R</span></a></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</a></code></pre></div>
 <p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@@ -335,7 +335,7 @@ Unique: 2</p>
 <a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Author:    WHO (World Health Organization)</span></a>
 <a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
 <a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># </span></a>
-<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4377 MDROs out of 5000 tested isolates (87.5%)</span></a></code></pre></div>
+<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4338 MDROs out of 5000 tested isolates (86.8%)</span></a></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
 <p><strong>Frequency table</strong></p>
@@ -356,40 +356,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3240</td>
-<td align="right">64.80%</td>
-<td align="right">3240</td>
-<td align="right">64.80%</td>
+<td align="right">3217</td>
+<td align="right">64.34%</td>
+<td align="right">3217</td>
+<td align="right">64.34%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
-<td align="left">Multi-drug-resistant</td>
-<td align="right">647</td>
-<td align="right">12.94%</td>
-<td align="right">3887</td>
-<td align="right">77.74%</td>
+<td align="left">Negative</td>
+<td align="right">662</td>
+<td align="right">13.24%</td>
+<td align="right">3879</td>
+<td align="right">77.58%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
-<td align="left">Negative</td>
-<td align="right">623</td>
-<td align="right">12.46%</td>
-<td align="right">4510</td>
-<td align="right">90.20%</td>
+<td align="left">Multi-drug-resistant</td>
+<td align="right">632</td>
+<td align="right">12.64%</td>
+<td align="right">4511</td>
+<td align="right">90.22%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">304</td>
-<td align="right">6.08%</td>
-<td align="right">4814</td>
-<td align="right">96.28%</td>
+<td align="right">280</td>
+<td align="right">5.60%</td>
+<td align="right">4791</td>
+<td align="right">95.82%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">186</td>
-<td align="right">3.72%</td>
+<td align="right">209</td>
+<td align="right">4.18%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -407,7 +407,7 @@ Unique: 5</p>
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">

docs/articles/SPSS.html

@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
       </span>
     </div>
 
@@ -187,7 +187,7 @@
       <h1>How to import data from SPSS / SAS / Stata</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">26 January 2020</h4>
       
       
       <div class="hidden name"><code>SPSS.Rmd</code></div>
@@ -237,7 +237,7 @@
 <li>
 <p><strong>R is (nowadays) the preferred analysis software in academic papers.</strong></p>
 <p>At present, R is among the world most powerful statistical languages, and it is generally very popular in science (Bollmann <em>et al.</em>, 2017). For all the above reasons, the number of references to R as an analysis method in academic papers <a href="https://r4stats.com/2014/08/20/r-passes-spss-in-scholarly-use-stata-growing-rapidly/">is rising continuously</a> and has even surpassed SPSS for academic use (Muenchen, 2014).</p>
-<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2019, I don’t see any reason why SPSS would be of any better use than R.</p>
+<p>I believe that the thing with SPSS is, that it has always had a great user interface which is very easy to learn and use. Back when they developed it, they had very little competition, let alone from R. R didn’t even had a professional user interface until the last decade (called RStudio, see below). How people used R between the nineties and 2010 is almost completely incomparable to how R is being used now. The language itself <a href="https://www.tidyverse.org/packages/">has been restyled completely</a> by volunteers who are dedicated professionals in the field of data science. SPSS was great when there was nothing else that could compete. But now in 2020, I don’t see any reason why SPSS would be of any better use than R.</p>
 </li>
 </ul>
 <p>To demonstrate the first point:</p>
@@ -403,7 +403,7 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">

docs/articles/WHONET.html

@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
       </span>
     </div>
 
@@ -187,7 +187,7 @@
       <h1>How to work with WHONET data</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">26 January 2020</h4>
       
       
       <div class="hidden name"><code>WHONET.Rmd</code></div>
@@ -394,7 +394,7 @@ Unique: 3</p>
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">

docs/articles/benchmarks.html

@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9021</span>
       </span>
     </div>
 
@@ -187,7 +187,7 @@
       <h1>Benchmarks</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">10 February 2020</h4>
       
       
       <div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -196,12 +196,12 @@
 
     
     
-<p><small>Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class="uri">https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd</a></small></p>
 <p>One of the most important features of this package is the complete microbial taxonomic database, supplied by the <a href="http://catalogueoflife.org">Catalogue of Life</a>. We created a function <code><a href="../reference/as.mo.html">as.mo()</a></code> that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.</p>
 <p>Using the <code>microbenchmark</code> package, we can review the calculation performance of this function. Its function <code><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark()</a></code> runs different input expressions independently of each other and measures their time-to-result.</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(microbenchmark)</a>
 <a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(AMR)</a></code></pre></div>
-<p>In the next test, we try to ‘coerce’ different input values for <em>Staphylococcus aureus</em>. The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
+<p>In the next test, we try to ‘coerce’ different input values into the microbial code of <em>Staphylococcus aureus</em>. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.</p>
+<p>The actual result is the same every time: it returns its microorganism code <code>B_STPHY_AURS</code> (<em>B</em> stands for <em>Bacteria</em>, the taxonomic kingdom).</p>
 <p>But the calculation time differs a lot:</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">S.aureus &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(</a>
 <a class="sourceLine" id="cb2-2" data-line-number="2">  <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"sau"</span>), <span class="co"># WHONET code</span></a>
@@ -221,50 +221,47 @@
 <a class="sourceLine" id="cb2-16" data-line-number="16">  <span class="dt">times =</span> <span class="dv">10</span>)</a>
 <a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
 <a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
-<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co">#                                   expr min  lq mean median  uq max neval</span></a>
-<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co">#                           as.mo("sau")  11  11   15     12  14  39    10</span></a>
-<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co">#                          as.mo("stau")  36  38   49     48  60  65    10</span></a>
-<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co">#                          as.mo("STAU")  36  38   46     40  59  71    10</span></a>
-<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co">#                        as.mo("staaur")  11  11   21     11  37  37    10</span></a>
-<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co">#                        as.mo("STAAUR")  11  11   12     12  12  17    10</span></a>
-<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co">#                     as.mo("S. aureus")  26  29   36     32  48  53    10</span></a>
-<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co">#                      as.mo("S aureus")  25  27   37     29  52  64    10</span></a>
-<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co">#         as.mo("Staphylococcus aureus")  33  34   39     36  45  53    10</span></a>
-<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 660 720  740    740 760 800    10</span></a>
-<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co">#       as.mo("Sthafilokkockus aaureuz") 350 360  410    380 400 660    10</span></a>
-<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co">#                          as.mo("MRSA")  11  11   14     12  12  36    10</span></a>
-<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co">#                          as.mo("VISA")  21  23   27     26  28  47    10</span></a>
-<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co">#                          as.mo("VRSA")  21  22   30     23  44  52    10</span></a>
-<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co">#                        as.mo(22242419)  20  20   24     21  21  52    10</span></a></code></pre></div>
-<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="562.5"></p>
-<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
-<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
+<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co">#                                   expr   min    lq  mean median    uq max neval</span></a>
+<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co">#                           as.mo("sau")   8.0   8.2  11.0    8.4   8.6  34    10</span></a>
+<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co">#                          as.mo("stau")  37.0  37.0  41.0   38.0  40.0  65    10</span></a>
+<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co">#                          as.mo("STAU")  37.0  38.0  47.0   41.0  62.0  69    10</span></a>
+<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co">#                        as.mo("staaur")   8.1   8.2  16.0    8.4   8.8  57    10</span></a>
+<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co">#                        as.mo("STAAUR")   8.1   8.3  11.0    8.5   8.9  34    10</span></a>
+<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co">#                     as.mo("S. aureus")  14.0  14.0  21.0   14.0  36.0  37    10</span></a>
+<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co">#                      as.mo("S aureus")  13.0  14.0  20.0   15.0  16.0  47    10</span></a>
+<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co">#         as.mo("Staphylococcus aureus")   4.7   4.8   8.6    4.9   6.2  39    10</span></a>
+<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co">#  as.mo("Staphylococcus aureus (MRSA)") 640.0 650.0 680.0  660.0 680.0 790    10</span></a>
+<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co">#       as.mo("Sthafilokkockus aaureuz") 330.0 350.0 390.0  390.0 430.0 500    10</span></a>
+<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co">#                          as.mo("MRSA")   8.0   8.5  17.0    9.0  33.0  43    10</span></a>
+<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co">#                          as.mo("VISA")  24.0  24.0  36.0   30.0  47.0  56    10</span></a>
+<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co">#                          as.mo("VRSA")  24.0  25.0  60.0   36.0  50.0 270    10</span></a>
+<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co">#                        as.mo(22242419) 120.0 120.0 130.0  130.0 140.0 150    10</span></a></code></pre></div>
+<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
+<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second.</p>
+<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
 <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">M.semesiae &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"metsem"</span>),</a>
-<a class="sourceLine" id="cb3-2" data-line-number="2">                               <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),</a>
-<a class="sourceLine" id="cb3-3" data-line-number="3">                               <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),</a>
-<a class="sourceLine" id="cb3-4" data-line-number="4">                               <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M.  semesiae"</span>),</a>
-<a class="sourceLine" id="cb3-5" data-line-number="5">                               <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),</a>
-<a class="sourceLine" id="cb3-6" data-line-number="6">                               <span class="dt">times =</span> <span class="dv">10</span>)</a>
+<a class="sourceLine" id="cb3-2" data-line-number="2">                             <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"METSEM"</span>),</a>
+<a class="sourceLine" id="cb3-3" data-line-number="3">                             <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M. semesiae"</span>),</a>
+<a class="sourceLine" id="cb3-4" data-line-number="4">                             <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"M.  semesiae"</span>),</a>
+<a class="sourceLine" id="cb3-5" data-line-number="5">                             <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Methanosarcina semesiae"</span>),</a>
+<a class="sourceLine" id="cb3-6" data-line-number="6">                             <span class="dt">times =</span> <span class="dv">10</span>)</a>
 <a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
 <a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
-<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#                              expr    min      lq   mean  median      uq     max</span></a>
-<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co">#                   as.mo("metsem") 1501.0 1506.00 1665.0 1569.00 1788.00 2141.00</span></a>
-<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co">#                   as.mo("METSEM") 1586.0 1610.00 1727.0 1675.00 1793.00 2002.00</span></a>
-<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co">#              as.mo("M. semesiae") 2266.0 2335.00 2587.0 2418.00 2524.00 3676.00</span></a>
-<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co">#             as.mo("M.  semesiae") 2143.0 2252.00 2334.0 2331.00 2396.00 2540.00</span></a>
-<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co">#  as.mo("Methanosarcina semesiae")   34.8   35.74   46.3   39.64   62.28   65.83</span></a>
-<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co">#  neval</span></a>
-<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#     10</span></a>
-<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#     10</span></a>
-<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#     10</span></a>
-<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#     10</span></a>
-<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co">#     10</span></a></code></pre></div>
-<p>That takes 15.6 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are almost fast - these are the most probable input from most data sets.</p>
+<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#                              expr      min       lq     mean   median      uq</span></a>
+<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co">#                   as.mo("metsem") 1422.000 1474.000 1511.000 1515.000 1544.00</span></a>
+<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co">#                   as.mo("METSEM") 1381.000 1446.000 1457.000 1458.000 1477.00</span></a>
+<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co">#              as.mo("M. semesiae")   14.390   14.520   18.050   15.000   17.64</span></a>
+<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co">#             as.mo("M.  semesiae")   14.330   14.570   17.690   14.740   15.14</span></a>
+<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co">#  as.mo("Methanosarcina semesiae")    5.261    5.342    7.848    5.459    5.63</span></a>
+<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co">#      max neval</span></a>
+<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#  1617.00    10</span></a>
+<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#  1520.00    10</span></a>
+<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#    39.73    10</span></a>
+<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#    39.72    10</span></a>
+<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co">#    29.36    10</span></a></code></pre></div>
+<p>That takes 5.6 times as much time on average. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.</p>
 <p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
-<p><img src="benchmarks_files/figure-html/unnamed-chunk-9-1.png" width="562.5"></p>
-<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
-<p><img src="benchmarks_files/figure-html/unnamed-chunk-11-1.png" width="562.5"></p>
-<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds.</p>
+<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="900"></p>
 <p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
 <div id="repetitive-results" class="section level3">
 <h3 class="hasAnchor">
@@ -292,12 +289,12 @@
 <a class="sourceLine" id="cb4-20" data-line-number="20"></a>
 <a class="sourceLine" id="cb4-21" data-line-number="21"><span class="co"># now let's see:</span></a>
 <a class="sourceLine" id="cb4-22" data-line-number="22">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(x),</a>
-<a class="sourceLine" id="cb4-23" data-line-number="23">                         <span class="dt">times =</span> <span class="dv">10</span>)</a>
+<a class="sourceLine" id="cb4-23" data-line-number="23">                         <span class="dt">times =</span> <span class="dv">100</span>)</a>
 <a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co">#        expr min  lq mean median  uq max neval</span></a>
-<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co">#  mo_name(x) 655 668  715    717 751 797    10</span></a></code></pre></div>
-<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (717 ms). You only lose time on your unique input values.</p>
+<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co">#  mo_name(x) 566 598  628    621 645 782   100</span></a></code></pre></div>
+<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.62 seconds (620 ms). You only lose time on your unique input values.</p>
 </div>
 <div id="precalculated-results" class="section level3">
 <h3 class="hasAnchor">
@@ -309,10 +306,10 @@
 <a class="sourceLine" id="cb5-4" data-line-number="4">                         <span class="dt">times =</span> <span class="dv">10</span>)</a>
 <a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
-<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co">#  expr   min     lq   mean median     uq   max neval</span></a>
-<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co">#     A  6.70  6.710  9.690   7.18  7.850 31.90    10</span></a>
-<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co">#     B 26.20 27.100 32.400  28.80 32.100 58.80    10</span></a>
-<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co">#     C  0.78  0.837  0.924   0.88  0.965  1.24    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co">#  expr    min     lq  mean median     uq   max neval</span></a>
+<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co">#     A  6.120  6.540  7.44  6.900  8.830  9.12    10</span></a>
+<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co">#     B 13.600 13.800 14.50 14.200 15.000 16.30    10</span></a>
+<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co">#     C  0.841  0.859  3.82  0.876  0.917 30.30    10</span></a></code></pre></div>
 <p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
 <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
 <a class="sourceLine" id="cb6-2" data-line-number="2">                         <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@@ -326,15 +323,15 @@
 <a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
 <a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
 <a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co">#  expr   min    lq  mean median    uq   max neval</span></a>
-<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co">#     A 0.444 0.449 0.473  0.460 0.466 0.630    10</span></a>
-<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co">#     B 0.483 0.496 0.511  0.505 0.535 0.539    10</span></a>
-<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co">#     C 0.709 0.839 0.850  0.846 0.886 0.921    10</span></a>
-<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co">#     D 0.463 0.483 0.521  0.499 0.548 0.694    10</span></a>
-<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co">#     E 0.433 0.451 0.493  0.484 0.513 0.611    10</span></a>
-<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co">#     F 0.434 0.450 0.481  0.458 0.484 0.582    10</span></a>
-<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co">#     G 0.434 0.443 0.471  0.455 0.489 0.577    10</span></a>
-<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co">#     H 0.434 0.436 0.471  0.451 0.480 0.614    10</span></a></code></pre></div>
-<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
+<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co">#     A 0.517 0.522 0.570  0.540 0.575 0.756    10</span></a>
+<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co">#     B 0.536 0.550 0.584  0.559 0.579 0.801    10</span></a>
+<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co">#     C 0.696 0.776 0.804  0.828 0.841 0.908    10</span></a>
+<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co">#     D 0.531 0.552 0.597  0.576 0.616 0.784    10</span></a>
+<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co">#     E 0.520 0.529 0.549  0.534 0.569 0.626    10</span></a>
+<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co">#     F 0.483 0.491 0.519  0.517 0.521 0.580    10</span></a>
+<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co">#     G 0.509 0.514 0.545  0.520 0.537 0.763    10</span></a>
+<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co">#     H 0.464 0.514 0.555  0.542 0.593 0.698    10</span></a></code></pre></div>
+<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
 </div>
 <div id="results-in-other-languages" class="section level3">
 <h3 class="hasAnchor">
@@ -356,17 +353,17 @@
 <a class="sourceLine" id="cb7-14" data-line-number="14">                         <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
 <a class="sourceLine" id="cb7-15" data-line-number="15">                         <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
 <a class="sourceLine" id="cb7-16" data-line-number="16">                         <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
-<a class="sourceLine" id="cb7-17" data-line-number="17">                         <span class="dt">times =</span> <span class="dv">10</span>)</a>
+<a class="sourceLine" id="cb7-17" data-line-number="17">                         <span class="dt">times =</span> <span class="dv">100</span>)</a>
 <a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
 <a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
-<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co">#  expr   min    lq  mean median    uq   max neval</span></a>
-<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co">#    en 22.05 22.65 29.93  25.35 27.03 53.36    10</span></a>
-<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co">#    de 22.86 23.16 30.45  27.22 28.33 62.68    10</span></a>
-<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co">#    nl 28.99 29.69 34.37  30.32 31.78 65.15    10</span></a>
-<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co">#    es 22.45 23.17 30.84  23.73 28.02 64.67    10</span></a>
-<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co">#    it 22.76 24.59 30.36  26.23 29.97 66.70    10</span></a>
-<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co">#    fr 23.00 24.20 30.70  27.00 29.22 51.23    10</span></a>
-<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co">#    pt 23.31 24.41 26.92  27.31 28.39 31.00    10</span></a></code></pre></div>
+<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co">#  expr   min    lq  mean median    uq    max neval</span></a>
+<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co">#    en 23.52 25.12 30.94  26.03 26.90  68.07   100</span></a>
+<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co">#    de 24.94 26.64 33.82  27.81 30.86 152.10   100</span></a>
+<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co">#    nl 30.28 32.60 37.42  33.81 35.15  72.52   100</span></a>
+<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co">#    es 24.86 26.55 31.91  27.42 28.91  80.24   100</span></a>
+<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co">#    it 24.54 26.61 32.10  27.45 28.35  69.43   100</span></a>
+<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co">#    fr 24.75 26.30 30.43  27.50 28.37  64.56   100</span></a>
+<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co">#    pt 24.95 26.38 31.37  27.32 28.38  66.08   100</span></a></code></pre></div>
 <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
 </div>
   </div>
@@ -380,7 +377,7 @@
 
 
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-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
 </div>
 
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docs/articles/index.html

@@ -40,12 +40,6 @@
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-
 
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@@ -84,7 +78,7 @@
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         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
       </span>
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@@ -210,12 +204,6 @@
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-      <form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
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-          <input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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@@ -250,7 +238,7 @@
 
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-  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">
@@ -261,23 +249,6 @@
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
-<script>
-  docsearch({
-    
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-    apiKey: 'f737050abfd4d726c63938e18f8c496e',
-    indexName: 'amr',
-    inputSelector: 'input#search-input.form-control',
-    transformData: function(hits) {
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   </body>

docs/articles/resistance_predict.html

@@ -41,7 +41,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9013</span>
       </span>
     </div>
 
@@ -187,7 +187,7 @@
       <h1>How to predict antimicrobial resistance</h1>
                         <h4 class="author">Matthijs S. Berends</h4>
             
-            <h4 class="date">29 November 2019</h4>
+            <h4 class="date">26 January 2020</h4>
       
       
       <div class="hidden name"><code>resistance_predict.Rmd</code></div>
@@ -282,7 +282,8 @@
 <a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># 24 2026 0.42496142 0.3390173 0.5109056           NA         NA 0.42496142</span></a>
 <a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># 25 2027 0.45218939 0.3593720 0.5450068           NA         NA 0.45218939</span></a>
 <a class="sourceLine" id="cb4-28" data-line-number="28"><span class="co"># 26 2028 0.47970658 0.3804212 0.5789920           NA         NA 0.47970658</span></a>
-<a class="sourceLine" id="cb4-29" data-line-number="29"><span class="co"># 27 2029 0.50734745 0.4021241 0.6125708           NA         NA 0.50734745</span></a></code></pre></div>
+<a class="sourceLine" id="cb4-29" data-line-number="29"><span class="co"># 27 2029 0.50734745 0.4021241 0.6125708           NA         NA 0.50734745</span></a>
+<a class="sourceLine" id="cb4-30" data-line-number="30"><span class="co"># 28 2030 0.53494347 0.4244247 0.6454622           NA         NA 0.53494347</span></a></code></pre></div>
 <p>The function <code>plot</code> is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:</p>
 <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(predict_TZP)</a></code></pre></div>
 <p><img src="resistance_predict_files/figure-html/unnamed-chunk-4-1.png" width="720"></p>
@@ -383,7 +384,7 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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