diff --git a/DESCRIPTION b/DESCRIPTION index 88dec141..273cf953 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.9.0.9008 -Date: 2020-01-05 +Version: 0.9.0.9009 +Date: 2020-01-08 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), @@ -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) diff --git a/NEWS.md b/NEWS.md index 22014323..ba66451f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,15 @@ -# AMR 0.9.0.9008 -## Last updated: 05-Jan-2020 +# AMR 0.9.0.9009 +## Last updated: 08-Jan-2020 ### Changes * Speed improvement for `as.mo()` (and consequently all `mo_*` functions that use `as.mo()` internally), especially for the *G. species* format (G for genus), like *E. coli* and *K penumoniae* * 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 diff --git a/R/ab.R b/R/ab.R index 6ebd8f39..84b0929c 100755 --- a/R/ab.R +++ b/R/ab.R @@ -43,7 +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") @@ -54,8 +54,14 @@ #' 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") +#' ab_atc("cephthriaxone") +#' ab_atc("seephthriaaksone") #' -#' # 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" @@ -87,6 +93,10 @@ 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)) diff --git a/R/ab_property.R b/R/ab_property.R index d7404609..a077b665 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -72,6 +72,12 @@ #' ab_name("floxapen") # "Flucloxacillin" #' ab_name(21319) # "Flucloxacillin" (using CID) #' ab_name("J01CF05") # "Flucloxacillin" (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) { diff --git a/_pkgdown.yml b/_pkgdown.yml index 7cd77235..13e0b910 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -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 diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 521af24e..6b9ddd92 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -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 diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 5174e282..0762f555 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/docs/404.html b/docs/404.html index d5d6fe44..30b5159c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9008 + 0.9.0.9009 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index eb22a69c..ce422108 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9008 + 0.9.0.9009 diff --git a/docs/articles/index.html b/docs/articles/index.html index 7d4f3efa..3f33fc1c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9008 + 0.9.0.9009 diff --git a/docs/authors.html b/docs/authors.html index 39a5cf78..eb17b5d9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.9.0.9008 + 0.9.0.9009 @@ -238,7 +238,7 @@ 

@Article{,
   title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
-  author = {Matthijs S Berends and Christian F Luz and Alexander W Friedrich and Bhanu N M Sinha and Casper J Albers and Corinna Glasner},
+  author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
   journal = {bioRxiv},
   publisher = {Cold Spring Harbor Laboratory},
   year = {2019},
diff --git a/docs/index.html b/docs/index.html
index 5f176c1c..486cc9f2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -45,7 +45,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 3c9b8614..bc850f50 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -84,7 +84,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
@@ -231,13 +231,13 @@
       
     
 
-    

+    

 

-AMR 0.9.0.9008 Unreleased 
+AMR 0.9.0.9009 Unreleased 
 

-

+

 

-Last updated: 05-Jan-2020
+Last updated: 08-Jan-2020
 

 

 

@@ -248,6 +248,14 @@
 
  • 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
 
    • 
+
  • 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, so e.g. ab_ddd("Rimactazid") will now return NA.
      • 
+
    • Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (SMX) to trimethoprim/sulfamethoxazole (SXT)
      • 
+
    
+
    • 
 
 
    
 
    
@@ -1418,7 +1426,7 @@ Using as.mo(..., allow_uncertain = 3)
       
    Contents
    
       
      
-        
    • 0.9.0.9008
      • 
+        
    • 0.9.0.9009
      • 
         
    • 0.9.0
      • 
         
    • 0.8.0
      • 
         
    • 0.7.1
      • 
diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html
index 3c44bb1b..c61a0035 100644
--- a/docs/reference/AMR-deprecated.html
+++ b/docs/reference/AMR-deprecated.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
    
 
diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html
index a64275ec..81fd5d1b 100644
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
    
 
@@ -356,7 +356,13 @@ The lifecycle of this function is maturing<
 ab_name("fluklox")   # "Flucloxacillin"
 ab_name("floxapen")  # "Flucloxacillin"
 ab_name(21319)       # "Flucloxacillin" (using CID)
-ab_name("J01CF05")   # "Flucloxacillin" (using ATC)
    +ab_name("J01CF05") # "Flucloxacillin" (using ATC) + +# spelling from different languages and dyslexia are no problem +ab_atc("ceftriaxon") +ab_atc("cephtriaxone") +ab_atc("cephthriaxone") +ab_atc("seephthriaaksone") diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 9c6a427c..61e269d9 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -85,7 +85,7 @@ AMR (for R) - 0.9.0.9007 + 0.9.0.9009 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 5f14951a..9d1fcb9d 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -85,7 +85,7 @@ AMR (for R) - 0.9.0.9007 + 0.9.0.9009 @@ -293,7 +293,7 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru

    antibiotics for the dataframe that is being used to determine ATCs.

    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")
@@ -305,7 +305,13 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru
 as.ab("Erythrocin")   # trade name
 as.ab("Romycin")      # trade name
 
-# Use ab_* functions to get a specific properties (see ?ab_property);
+# spelling from different languages and dyslexia are no problem
+ab_atc("ceftriaxon")
+ab_atc("cephtriaxone")
+ab_atc("cephthriaxone")
+ab_atc("seephthriaaksone")
+
+# use ab_* functions to get a specific properties (see ?ab_property);
 # they use as.ab() internally:
 ab_name("J01FA01")    # "Erythromycin"
 ab_name("eryt")       # "Erythromycin"
    
diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html
index 6cc66ee1..c9de77ee 100644
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html
index 6b8fd67f..a513bc23 100644
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 0d7f2519..8abed42f 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html
index d2248746..4ba152c4 100644
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html
index f57f8c51..9a0539af 100644
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@@ -86,7 +86,7 @@ This function requires an internet connection." />
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/availability.html b/docs/reference/availability.html
index 3099d71b..ef3b2ea1 100644
--- a/docs/reference/availability.html
+++ b/docs/reference/availability.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html
index 20ca48c4..0e647492 100644
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/count.html b/docs/reference/count.html
index e8dc2a96..7302ed74 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html
index bdf75109..818813ae 100644
--- a/docs/reference/eucast_rules.html
+++ b/docs/reference/eucast_rules.html
@@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/extended-functions.html b/docs/reference/extended-functions.html
index d76904ff..12664884 100644
--- a/docs/reference/extended-functions.html
+++ b/docs/reference/extended-functions.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html
index 245ac726..0bb26635 100644
--- a/docs/reference/filter_ab_class.html
+++ b/docs/reference/filter_ab_class.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html
index acfa950d..cf7f3c19 100644
--- a/docs/reference/g.test.html
+++ b/docs/reference/g.test.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index 5dc8b5cf..a74f000a 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html
index 6b2ecce0..09e683de 100644
--- a/docs/reference/guess_ab_col.html
+++ b/docs/reference/guess_ab_col.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b49c3488..f7cb2416 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -84,7 +84,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
@@ -517,6 +517,12 @@
           
    WHOCC 
    
         
         
    WHOCC: WHO Collaborating Centre for Drug Statistics Methodology
    
+      
+        
+        
+          
    lifecycle 
    
+        
+        
    Lifecycles of functions in the AMR package
    
       
     
       
diff --git a/docs/reference/join.html b/docs/reference/join.html
index e158f206..46efe370 100644
--- a/docs/reference/join.html
+++ b/docs/reference/join.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html
index fa1ec9c7..ff9e6057 100644
--- a/docs/reference/key_antibiotics.html
+++ b/docs/reference/key_antibiotics.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html
index e54eaadc..69ba3a99 100644
--- a/docs/reference/kurtosis.html
+++ b/docs/reference/kurtosis.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html
index 08cdc312..a22e1a42 100644
--- a/docs/reference/lifecycle.html
+++ b/docs/reference/lifecycle.html
@@ -87,7 +87,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/like.html b/docs/reference/like.html
index 9a5683b8..23d68e0f 100644
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html
index 5bf3ae40..3fd6f62f 100644
--- a/docs/reference/mdro.html
+++ b/docs/reference/mdro.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html
index 12f588c0..420914d0 100644
--- a/docs/reference/mo_source.html
+++ b/docs/reference/mo_source.html
@@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/p_symbol.html b/docs/reference/p_symbol.html
index eec1d452..96f1dc34 100644
--- a/docs/reference/p_symbol.html
+++ b/docs/reference/p_symbol.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html
index 78effc2b..8849206b 100644
--- a/docs/reference/proportion.html
+++ b/docs/reference/proportion.html
@@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/read.4D.html b/docs/reference/read.4D.html
index b5bcd252..20dd3106 100644
--- a/docs/reference/read.4D.html
+++ b/docs/reference/read.4D.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html
index 01f2abcb..c357b381 100644
--- a/docs/reference/resistance_predict.html
+++ b/docs/reference/resistance_predict.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html
index 3286082f..cc51ae32 100644
--- a/docs/reference/skewness.html
+++ b/docs/reference/skewness.html
@@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
       
       
         AMR (for R)
-        0.9.0.9008
+        0.9.0.9009
       
     
 
diff --git a/docs/reference/translate.html b/docs/reference/translate.html
index bc1aad71..163b1fea 100644
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@@ -85,7 +85,7 @@
       
       
         AMR (for R)
-        0.9.0.9007
+        0.9.0.9009
       
     
 
diff --git a/inst/CITATION b/inst/CITATION
index 2e229915..66ddc1d0 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -3,7 +3,7 @@ citHeader("To cite our AMR package in publications, please use (for now):")
 citEntry(
   entry        = "Article",
   title        = "AMR - An R Package for Working with Antimicrobial Resistance Data",
-  author       = "Matthijs S Berends and Christian F Luz and Alexander W Friedrich and Bhanu N M Sinha and Casper J Albers and Corinna Glasner",
+  author       = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner",
   journal      = "bioRxiv",
   publisher    = "Cold Spring Harbor Laboratory",
   year         = 2019,
diff --git a/man/ab_property.Rd b/man/ab_property.Rd
index 040c6c65..4d927116 100644
--- a/man/ab_property.Rd
+++ b/man/ab_property.Rd
@@ -116,6 +116,12 @@ ab_name("fluklox")   # "Flucloxacillin"
 ab_name("floxapen")  # "Flucloxacillin"
 ab_name(21319)       # "Flucloxacillin" (using CID)
 ab_name("J01CF05")   # "Flucloxacillin" (using ATC)
+
+# spelling from different languages and dyslexia are no problem
+ab_atc("ceftriaxon")
+ab_atc("cephtriaxone")
+ab_atc("cephthriaxone")
+ab_atc("seephthriaaksone")
 }
 \seealso{
 \link{antibiotics}
diff --git a/man/as.ab.Rd b/man/as.ab.Rd
index 27581739..9551e35b 100644
--- a/man/as.ab.Rd
+++ b/man/as.ab.Rd
@@ -59,7 +59,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
 }
 
 \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")
@@ -71,7 +71,13 @@ as.ab("eritromicine") # spelled wrong, yet works
 as.ab("Erythrocin")   # trade name
 as.ab("Romycin")      # trade name
 
-# Use ab_* functions to get a specific properties (see ?ab_property);
+# spelling from different languages and dyslexia are no problem
+ab_atc("ceftriaxon")
+ab_atc("cephtriaxone")
+ab_atc("cephthriaxone")
+ab_atc("seephthriaaksone")
+
+# use ab_* functions to get a specific properties (see ?ab_property);
 # they use as.ab() internally:
 ab_name("J01FA01")    # "Erythromycin"
 ab_name("eryt")       # "Erythromycin"