DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.5.0.9020
-Date: 2021-02-18
+Version: 1.5.0.9018
+Date: 2021-02-09
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.5.0.9020
-## <small>Last updated: 18 February 2021</small>
+# AMR 1.5.0.9018
+## <small>Last updated:  9 February 2021</small>
 
 ### New
 * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@@ -7,10 +7,10 @@
   * Added data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way 
   * Existing data set `example_isolates` now reflects the latest EUCAST rules
 * Added argument `only_rsi_columns` for some functions, which defaults to `FALSE`, to indicate if the functions must only be applied to columns that are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
-  * All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglycosides()`, `carbapenems()`, `penicillins()`)
-  * All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglycosides()`, `filter_carbapenems()`, `filter_penicillins()`)
+  * All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglocysides()`, `carbapenems()`, `penicillins()`)
+  * All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglocysides()`, `filter_carbapenems()`, `filter_penicillins()`)
   * `eucast_rules()`
-  * `mdro()` (including wrappers such as `brmo()`, `mrgn()` and `eucast_exceptional_phenotypes()`)
+  * `mdro()` (including wrappers such as `brmo()`, `mrgn` and `eucast_exceptional_phenotypes()`)
   * `guess_ab_col()`
 * Functions `oxazolidinones()` (an antibiotic selector function) and `filter_oxazolidinones()` (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
   ```r
@@ -57,7 +57,6 @@
 * Updated colours of values R, S and I in tibble printing
 * Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
 * Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
-* Fix for `mo_name()` when used in other languages than English
 
 ### Other
 * Big documentation updates

R/aa_helper_functions.R

@@ -82,27 +82,20 @@ check_dataset_integrity <- function() {
   # exception for example_isolates
   overwritten <- overwritten[overwritten != "example_isolates"]
   if (length(overwritten) > 0) {
-    if (length(overwritten) > 1) {
-      plural <- c("s are", "", "s")
-    } else {
-      plural <- c(" is", "s", "")
-    }
-    warning_("The following data set", plural[1],
-             " overwritten by your global environment and prevent", plural[2], 
-             " the AMR package from working correctly: ",
+    warning_(ifelse(length(overwritten) == 1,
+                    "The following data set is overwritten by your global environment and prevents the AMR package from working correctly: ",
+                    "The following data sets are overwritten by your global environment and prevent the AMR package from working correctly: "),
              vector_and(overwritten, quotes = "'"),
-             ".\nPlease rename your object", plural[3], ".", call = FALSE)
+             ".\nPlease rename your object(s).", call = FALSE)
   }
   # check if other packages did not overwrite our data sets
-  valid_microorganisms <- TRUE
-  valid_antibiotics <- TRUE
   tryCatch({
-    valid_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
+    check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
                                   "class", "order", "family", "genus",
                                   "species", "subspecies", "rank",
                                   "species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
                                 na.rm = TRUE)
-    valid_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
+    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),
@@ -111,7 +104,7 @@ check_dataset_integrity <- function() {
     # package not yet loaded
     require("AMR")
   })
-  stop_if(!valid_microorganisms | !valid_antibiotics,
+  stop_if(!check_microorganisms | !check_antibiotics,
           "the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
   invisible(TRUE)
 }

R/ab_class_selectors.R

@@ -43,7 +43,7 @@
 #' # See ?example_isolates.
 #' 
 #' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
-#' example_isolates[, carbapenems()]
+#' example_isolates[, c(carbapenems())]
 #' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
 #' example_isolates[, c("mo", aminoglycosides())]
 #' 

R/mo_property.R

@@ -172,10 +172,7 @@ mo_name <- function(x, language = get_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
-                language = language,
-                only_unknown = FALSE,
-                affect_mo_name = TRUE)
+  translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
@@ -217,7 +214,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   
   shortnames[is.na(x.mo)] <- NA_character_
   load_mo_failures_uncertainties_renamed(metadata)
-  translate_AMR(shortnames, language = language, only_unknown = FALSE, affect_mo_name = TRUE)
+  translate_AMR(shortnames, language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property

R/translate.R

@@ -123,7 +123,7 @@ coerce_language_setting <- function(lang) {
 }
 
 # translate strings based on inst/translations.tsv
-translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, affect_mo_name = FALSE) {
+translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
   
   if (is.null(language)) {
     return(from)
@@ -146,13 +146,10 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
   if (only_unknown == TRUE) {
     df_trans <- subset(df_trans, pattern %like% "unknown")
   }
-  if (affect_mo_name == TRUE) {
-    df_trans <- subset(df_trans, affect_mo_name == TRUE)
-  }
   
-  # default: case sensitive if value if 'ignore.case' is missing:
+  # default case sensitive if value if 'ignore.case' is missing:
   df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
-  # default: not using regular expressions (fixed = TRUE) if 'fixed' is missing:
+  # default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
   df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
   
   # check if text to look for is in one of the patterns
@@ -170,8 +167,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
                                                      replacement = df_trans$replacement[i],
                                                      x = from_unique_translated,
                                                      ignore.case = df_trans$ignore.case[i], 
-                                                     fixed = df_trans$fixed[i],
-                                                     perl = !df_trans$fixed[i]))
+                                                     fixed = df_trans$fixed[i]))
   
   # force UTF-8 for diacritics
   from_unique_translated <- enc2utf8(from_unique_translated)

README.md

@@ -10,7 +10,7 @@
 
 <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
 
-The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](data-raw).
+The latest built **source package** (`AMR_x.x.x.tar.gz`) can be found in folder [/data-raw/](data-raw).
 
 `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
  
@@ -20,7 +20,7 @@ This package is fully independent of any other R package and works on Windows, m
 
 This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package.
 
-*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to our university's Gitea server (https://git.web.rug.nl/P281424/AMR) and to GitLab (https://gitlab.com/msberends/AMR).*
+*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*
 
 ### How to get this package
 Please see [our website](https://msberends.github.io/AMR/#get-this-package).

data-raw/reproduction_of_microorganisms.R

@@ -25,22 +25,20 @@
 
 # Reproduction of the `microorganisms` data set
 
-# Data retrieved from the Catalogue of Life (CoL):
-# https://download.catalogueoflife.org/col/monthly/life/
-# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2020-12-01_dwca.zip)
+# Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
+# https://opendata.eol.org/dataset/catalogue-of-life/
 # Data retrieved from the Global Biodiversity Information Facility (GBIF): 
 # https://doi.org/10.15468/rffz4x
 #
-# And from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
-# (register first) https://lpsn.dsmz.de/downloads
-# download the latest CSV file.
+# And from the Leibniz Institute: German Collection of Microorganisms and Cell Cultures (DSMZ)
+# (register first at https://bacdive.dsmz.de/api/pnu/registration/register/ and use API as done below)
 
 library(dplyr)
 library(AMR)
 # also needed: data.table, httr, jsonlite, cleaner, stringr
 
 # unzip and extract taxa.txt (both around 1.5 GB, 3.7-3.9M rows) from Col and GBIF, then:
-data_col_raw <- data.table::fread("data-raw/taxon.tsv", quote = "")
+data_col_raw <- data.table::fread("data-raw/taxon.tab", quote = "")
 data_gbif <- data.table::fread("data-raw/taxa.txt", quote = "")
 
 # merge the two

data-raw/translations.tsv

@@ -1,412 +1,407 @@
-lang	pattern	replacement	fixed	ignore.case	affect_mo_name
-de	Coagulase-negative Staphylococcus	Koagulase-negative Staphylococcus	FALSE	FALSE	TRUE
-de	Coagulase-positive Staphylococcus	Koagulase-positive Staphylococcus	FALSE	FALSE	TRUE
-de	Beta-haemolytic Streptococcus	Beta-hämolytischer Streptococcus	FALSE	FALSE	TRUE
-de	unknown Gram-negatives	unbekannte Gramnegativen	FALSE	FALSE	TRUE
-de	unknown Gram-positives	unbekannte Grampositiven	FALSE	FALSE	TRUE
-de	unknown fungus	unbekannter Pilze	FALSE	FALSE	TRUE
-de	unknown yeast	unbekannte Hefe	FALSE	FALSE	TRUE
-de	unknown name	unbekannte Name	FALSE	FALSE	TRUE
-de	unknown kingdom	unbekanntes Reich	FALSE	FALSE	TRUE
-de	unknown phylum	unbekannter Stamm	FALSE	FALSE	TRUE
-de	unknown class	unbekannte Klasse	FALSE	FALSE	TRUE
-de	unknown order	unbekannte Ordnung	FALSE	FALSE	TRUE
-de	unknown family	unbekannte Familie	FALSE	FALSE	TRUE
-de	unknown genus	unbekannte Gattung	FALSE	FALSE	TRUE
-de	unknown species	unbekannte Art	FALSE	FALSE	TRUE
-de	unknown subspecies	unbekannte Unterart	FALSE	FALSE	TRUE
-de	unknown rank	unbekannter Rang	FALSE	FALSE	TRUE
-de	CoNS	KNS	TRUE	FALSE	TRUE
-de	CoPS	KPS	TRUE	FALSE	TRUE
-de	Gram-negative	Gramnegativ	FALSE	FALSE	FALSE
-de	Gram-positive	Grampositiv	FALSE	FALSE	FALSE
-de	^Bacteria$	Bakterien	FALSE	FALSE	FALSE
-de	^Fungi$	Pilze	FALSE	FALSE	FALSE
-de	^Yeasts$	Hefen	FALSE	FALSE	FALSE
-de	^Protozoa$	Protozoen	FALSE	FALSE	FALSE
-de	biogroup	Biogruppe	FALSE	FALSE	FALSE
-de	biotype	Biotyp	FALSE	FALSE	FALSE
-de	vegetative	vegetativ	FALSE	FALSE	FALSE
-de	([([ ]*?)group	\\1Gruppe	FALSE	FALSE	FALSE
-de	([([ ]*?)Group	\\1Gruppe	FALSE	FALSE	FALSE
-de	no .*growth	keine? .*wachstum	FALSE	TRUE	FALSE
-de	(^| )no|not	keine?	FALSE	TRUE	FALSE
-nl	Coagulase-negative Staphylococcus	Coagulase-negatieve Staphylococcus	FALSE	FALSE	TRUE
-nl	Coagulase-positive Staphylococcus	Coagulase-positieve Staphylococcus	FALSE	FALSE	TRUE
-nl	Beta-haemolytic Streptococcus	Beta-hemolytische Streptococcus	FALSE	FALSE	TRUE
-nl	unknown Gram-negatives	onbekende Gram-negatieven	FALSE	FALSE	TRUE
-nl	unknown Gram-positives	onbekende Gram-positieven	FALSE	FALSE	TRUE
-nl	unknown fungus	onbekende schimmel	FALSE	FALSE	TRUE
-nl	unknown yeast	onbekende gist	FALSE	FALSE	TRUE
-nl	unknown name	onbekende naam	FALSE	FALSE	TRUE
-nl	unknown kingdom	onbekend koninkrijk	FALSE	FALSE	TRUE
-nl	unknown phylum	onbekend fylum	FALSE	FALSE	TRUE
-nl	unknown class	onbekende klasse	FALSE	FALSE	TRUE
-nl	unknown order	onbekende orde	FALSE	FALSE	TRUE
-nl	unknown family	onbekende familie	FALSE	FALSE	TRUE
-nl	unknown genus	onbekend geslacht	FALSE	FALSE	TRUE
-nl	unknown species	onbekende soort	FALSE	FALSE	TRUE
-nl	unknown subspecies	onbekende ondersoort	FALSE	FALSE	TRUE
-nl	unknown rank	onbekende rang	FALSE	FALSE	TRUE
-nl	CoNS	CNS	TRUE	FALSE	TRUE
-nl	CoPS	CPS	TRUE	FALSE	TRUE
-nl	Gram-negative	Gram-negatief	FALSE	FALSE	FALSE
-nl	Gram-positive	Gram-positief	FALSE	FALSE	FALSE
-nl	^Bacteria$	Bacteriën	FALSE	FALSE	FALSE
-nl	^Fungi$	Schimmels	FALSE	FALSE	FALSE
-nl	^Yeasts$	Gisten	FALSE	FALSE	FALSE
-nl	^Protozoa$	Protozoën	FALSE	FALSE	FALSE
-nl	biogroup	biogroep	FALSE	FALSE	FALSE
-nl	vegetative	vegetatief	FALSE	FALSE	FALSE
-nl	([([ ]*?)group	\\1groep	FALSE	FALSE	FALSE
-nl	([([ ]*?)Group	\\1Groep	FALSE	FALSE	FALSE
-nl	antibiotic	antibioticum	FALSE	FALSE	FALSE
-nl	Antibiotic	Antibioticum	FALSE	FALSE	FALSE
-nl	Drug	Middel	FALSE	FALSE	FALSE
-nl	drug	middel	FALSE	FALSE	FALSE
-nl	no .*growth	geen .*groei	FALSE	TRUE	FALSE
-nl	no|not	geen|niet	FALSE	TRUE	FALSE
-es	Coagulase-negative Staphylococcus	Staphylococcus coagulasa negativo	FALSE	FALSE	TRUE
-es	Coagulase-positive Staphylococcus	Staphylococcus coagulasa positivo	FALSE	FALSE	TRUE
-es	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE	TRUE
-es	unknown Gram-negatives	Gram negativos desconocidos	FALSE	FALSE	TRUE
-es	unknown Gram-positives	Gram positivos desconocidos	FALSE	FALSE	TRUE
-es	unknown fungus	hongo desconocido	FALSE	FALSE	TRUE
-es	unknown yeast	levadura desconocida	FALSE	FALSE	TRUE
-es	unknown name	nombre desconocido	FALSE	FALSE	TRUE
-es	unknown kingdom	reino desconocido	FALSE	FALSE	TRUE
-es	unknown phylum	filo desconocido	FALSE	FALSE	TRUE
-es	unknown class	clase desconocida	FALSE	FALSE	TRUE
-es	unknown order	orden desconocido	FALSE	FALSE	TRUE
-es	unknown family	familia desconocida	FALSE	FALSE	TRUE
-es	unknown genus	género desconocido	FALSE	FALSE	TRUE
-es	unknown species	especie desconocida	FALSE	FALSE	TRUE
-es	unknown subspecies	subespecie desconocida	FALSE	FALSE	TRUE
-es	unknown rank	rango desconocido	FALSE	FALSE	TRUE
-es	CoNS	SCN	TRUE	FALSE	TRUE
-es	CoPS	SCP	TRUE	FALSE	TRUE
-es	Gram-negative	Gram negativo	FALSE	FALSE	FALSE
-es	Gram-positive	Gram positivo	FALSE	FALSE	FALSE
-es	^Bacteria$	Bacterias	FALSE	FALSE	FALSE
-es	^Fungi$	Hongos	FALSE	FALSE	FALSE
-es	^Yeasts$	Levaduras	FALSE	FALSE	FALSE
-es	^Protozoa$	Protozoarios	FALSE	FALSE	FALSE
-es	biogroup	biogrupo	FALSE	FALSE	FALSE
-es	biotype	biotipo	FALSE	FALSE	FALSE
-es	vegetative	vegetativo	FALSE	FALSE	FALSE
-es	([([ ]*?)group	\\1grupo	FALSE	FALSE	FALSE
-es	([([ ]*?)Group	\\1Grupo	FALSE	FALSE	FALSE
-es	no .*growth	no .*crecimientonon	FALSE	TRUE	FALSE
-es	no|not	no|sin	FALSE	TRUE	FALSE
-it	Coagulase-negative Staphylococcus	Staphylococcus negativo coagulasi	FALSE	FALSE	TRUE
-it	Coagulase-positive Staphylococcus	Staphylococcus positivo coagulasi	FALSE	FALSE	TRUE
-it	Beta-haemolytic Streptococcus	Streptococcus Beta-emolitico	FALSE	FALSE	TRUE
-it	unknown Gram-negatives	Gram negativi sconosciuti	FALSE	FALSE	TRUE
-it	unknown Gram-positives	Gram positivi sconosciuti	FALSE	FALSE	TRUE
-it	unknown fungus	fungo sconosciuto	FALSE	FALSE	TRUE
-it	unknown yeast	lievito sconosciuto	FALSE	FALSE	TRUE
-it	unknown name	nome sconosciuto	FALSE	FALSE	TRUE
-it	unknown kingdom	regno sconosciuto	FALSE	FALSE	TRUE
-it	unknown phylum	phylum sconosciuto	FALSE	FALSE	TRUE
-it	unknown class	classe sconosciuta	FALSE	FALSE	TRUE
-it	unknown order	ordine sconosciuto	FALSE	FALSE	TRUE
-it	unknown family	famiglia sconosciuta	FALSE	FALSE	TRUE
-it	unknown genus	genere sconosciuto	FALSE	FALSE	TRUE
-it	unknown species	specie sconosciute	FALSE	FALSE	TRUE
-it	unknown subspecies	sottospecie sconosciute	FALSE	FALSE	TRUE
-it	unknown rank	grado sconosciuto	FALSE	FALSE	TRUE
-it	Gram-negative	Gram negativo	FALSE	FALSE	FALSE
-it	Gram-positive	Gram positivo	FALSE	FALSE	FALSE
-it	^Bacteria$	Batteri	FALSE	FALSE	FALSE
-it	^Fungi$	Funghi	FALSE	FALSE	FALSE
-it	^Yeasts$	Lieviti	FALSE	FALSE	FALSE
-it	^Protozoa$	Protozoi	FALSE	FALSE	FALSE
-it	biogroup	biogruppo	FALSE	FALSE	FALSE
-it	biotype	biotipo	FALSE	FALSE	FALSE
-it	vegetative	vegetativo	FALSE	FALSE	FALSE
-it	([([ ]*?)group	\\1gruppo	FALSE	FALSE	FALSE
-it	([([ ]*?)Group	\\1Gruppo	FALSE	FALSE	FALSE
-it	no .*growth	sem .*crescimento	FALSE	TRUE	FALSE
-it	no|not	sem	FALSE	TRUE	FALSE
-fr	Coagulase-negative Staphylococcus	Staphylococcus à coagulase négative	FALSE	FALSE	TRUE
-fr	Coagulase-positive Staphylococcus	Staphylococcus à coagulase positif	FALSE	FALSE	TRUE
-fr	Beta-haemolytic Streptococcus	Streptococcus Bêta-hémolytique	FALSE	FALSE	TRUE
-fr	unknown Gram-negatives	Gram négatifs inconnus	FALSE	FALSE	TRUE
-fr	unknown Gram-positives	Gram positifs inconnus	FALSE	FALSE	TRUE
-fr	unknown fungus	champignon inconnu	FALSE	FALSE	TRUE
-fr	unknown yeast	levure inconnue	FALSE	FALSE	TRUE
-fr	unknown name	nom inconnu	FALSE	FALSE	TRUE
-fr	unknown kingdom	règme inconnu	FALSE	FALSE	TRUE
-fr	unknown phylum	embranchement inconnu	FALSE	FALSE	TRUE
-fr	unknown class	classe inconnue	FALSE	FALSE	TRUE
-fr	unknown order	ordre inconnu	FALSE	FALSE	TRUE
-fr	unknown family	famille inconnue	FALSE	FALSE	TRUE
-fr	unknown genus	genre inconnu	FALSE	FALSE	TRUE
-fr	unknown species	espèce inconnue	FALSE	FALSE	TRUE
-fr	unknown subspecies	sous-espèce inconnue	FALSE	FALSE	TRUE
-fr	unknown rank	rang inconnu	FALSE	FALSE	TRUE
-fr	Gram-negative	Gram négatif	FALSE	FALSE	FALSE
-fr	Gram-positive	Gram positif	FALSE	FALSE	FALSE
-fr	^Bacteria$	Bactéries	FALSE	FALSE	FALSE
-fr	^Fungi$	Champignons	FALSE	FALSE	FALSE
-fr	^Yeasts$	Levures	FALSE	FALSE	FALSE
-fr	^Protozoa$	Protozoaires	FALSE	FALSE	FALSE
-fr	biogroup	biogroupe	FALSE	FALSE	FALSE
-fr	vegetative	végétatif	FALSE	FALSE	FALSE
-fr	([([ ]*?)group	\\1groupe	FALSE	FALSE	FALSE
-fr	([([ ]*?)Group	\\1Groupe	FALSE	FALSE	FALSE
-fr	no .*growth	pas .*croissance	FALSE	TRUE	FALSE
-fr	no|not	non	FALSE	TRUE	FALSE
-pt	Coagulase-negative Staphylococcus	Staphylococcus coagulase negativo	FALSE	FALSE	TRUE
-pt	Coagulase-positive Staphylococcus	Staphylococcus coagulase positivo	FALSE	FALSE	TRUE
-pt	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE	TRUE
-pt	unknown Gram-negatives	Gram negativos desconhecidos	FALSE	FALSE	TRUE
-pt	unknown Gram-positives	Gram positivos desconhecidos	FALSE	FALSE	TRUE
-pt	unknown fungus	fungo desconhecido	FALSE	FALSE	TRUE
-pt	unknown yeast	levedura desconhecida	FALSE	FALSE	TRUE
-pt	unknown name	nome desconhecido	FALSE	FALSE	TRUE
-pt	unknown kingdom	reino desconhecido	FALSE	FALSE	TRUE
-pt	unknown phylum	filo desconhecido	FALSE	FALSE	TRUE
-pt	unknown class	classe desconhecida	FALSE	FALSE	TRUE
-pt	unknown order	ordem desconhecido	FALSE	FALSE	TRUE
-pt	unknown family	família desconhecida	FALSE	FALSE	TRUE
-pt	unknown genus	gênero desconhecido	FALSE	FALSE	TRUE
-pt	unknown species	espécies desconhecida	FALSE	FALSE	TRUE
-pt	unknown subspecies	subespécies desconhecida	FALSE	FALSE	TRUE
-pt	unknown rank	classificação desconhecido	FALSE	FALSE	TRUE
-pt	Gram-negative	Gram negativo	FALSE	FALSE	FALSE
-pt	Gram-positive	Gram positivo	FALSE	FALSE	FALSE
-pt	^Bacteria$	Bactérias	FALSE	FALSE	FALSE
-pt	^Fungi$	Fungos	FALSE	FALSE	FALSE
-pt	^Yeasts$	Leveduras	FALSE	FALSE	FALSE
-pt	^Protozoa$	Protozoários	FALSE	FALSE	FALSE
-pt	biogroup	biogrupo	FALSE	FALSE	FALSE
-pt	biotype	biótipo	FALSE	FALSE	FALSE
-pt	vegetative	vegetativo	FALSE	FALSE	FALSE
-pt	([([ ]*?)group	\\1grupo	FALSE	FALSE	FALSE
-pt	([([ ]*?)Group	\\1Grupo	FALSE	FALSE	FALSE
-pt	no .*growth	sem .*crescimento	FALSE	TRUE	FALSE
-pt	no|not	sem	FALSE	TRUE	FALSE
-de	clavulanic acid	Clavulansäure	FALSE	TRUE	FALSE
-nl	4-aminosalicylic acid	4-aminosalicylzuur	TRUE	FALSE	FALSE
-nl	Adefovir dipivoxil	Adefovir	TRUE	FALSE	FALSE
-nl	Aldesulfone sodium	Aldesulfon	TRUE	FALSE	FALSE
-nl	Amikacin	Amikacine	TRUE	FALSE	FALSE
-nl	Amoxicillin	Amoxicilline	TRUE	FALSE	FALSE
-nl	Amoxicillin/beta-lactamase inhibitor	Amoxicilline/enzymremmer	TRUE	FALSE	FALSE
-nl	Amphotericin B	Amfotericine B	TRUE	FALSE	FALSE
-nl	Ampicillin	Ampicilline	TRUE	FALSE	FALSE
-nl	Ampicillin/beta-lactamase inhibitor	Ampicilline/enzymremmer	TRUE	FALSE	FALSE
-nl	Anidulafungin	Anidulafungine	TRUE	FALSE	FALSE
-nl	Azidocillin	Azidocilline	TRUE	FALSE	FALSE
-nl	Azithromycin	Azitromycine	TRUE	FALSE	FALSE
-nl	Azlocillin	Azlocilline	TRUE	FALSE	FALSE
-nl	Bacampicillin	Bacampicilline	TRUE	FALSE	FALSE
-nl	Bacitracin	Bacitracine	TRUE	FALSE	FALSE
-nl	Benzathine benzylpenicillin	Benzylpenicillinebenzathine	TRUE	FALSE	FALSE
-nl	Benzathine phenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine	TRUE	FALSE	FALSE
-nl	Benzylpenicillin	Benzylpenicilline	TRUE	FALSE	FALSE
-nl	Calcium aminosalicylate	Aminosalicylzuur	TRUE	FALSE	FALSE
-nl	Capreomycin	Capreomycine	TRUE	FALSE	FALSE
-nl	Carbenicillin	Carbenicilline	TRUE	FALSE	FALSE
-nl	Carindacillin	Carindacilline	TRUE	FALSE	FALSE
-nl	Caspofungin	Caspofungine	TRUE	FALSE	FALSE
-nl	Ce(f|ph)acetrile	Cefacetril	FALSE	FALSE	FALSE
-nl	Ce(f|ph)alexin	Cefalexine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)alotin	Cefalotine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)amandole	Cefamandol	FALSE	FALSE	FALSE
-nl	Ce(f|ph)apirin	Cefapirine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)azedone	Cefazedon	FALSE	FALSE	FALSE
-nl	Ce(f|ph)azolin	Cefazoline	FALSE	FALSE	FALSE
-nl	Ce(f|ph)alothin	Cefalotine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)alexin	Cefalexine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)epime	Cefepim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)ixime	Cefixim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)menoxime	Cefmenoxim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)metazole	Cefmetazol	FALSE	FALSE	FALSE
-nl	Ce(f|ph)odizime	Cefodizim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)onicid	Cefonicide	FALSE	FALSE	FALSE
-nl	Ce(f|ph)operazone	Cefoperazon	FALSE	FALSE	FALSE
-nl	Ce(f|ph)operazone/beta-lactamase inhibitor	Cefoperazon/enzymremmer	FALSE	FALSE	FALSE
-nl	Ce(f|ph)otaxime	Cefotaxim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)oxitin	Cefoxitine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)pirome	Cefpirom	FALSE	FALSE	FALSE
-nl	Ce(f|ph)podoxime	Cefpodoxim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)radine	Cefradine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)sulodin	Cefsulodine	FALSE	FALSE	FALSE
-nl	Ce(f|ph)tazidime	Ceftazidim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)tezole	Ceftezol	FALSE	FALSE	FALSE
-nl	Ce(f|ph)tizoxime	Ceftizoxim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)triaxone	Ceftriaxon	FALSE	FALSE	FALSE
-nl	Ce(f|ph)uroxime	Cefuroxim	FALSE	FALSE	FALSE
-nl	Ce(f|ph)uroxime/metronidazole	Cefuroxim/andere antibacteriele middelen	FALSE	FALSE	FALSE
-nl	Chloramphenicol	Chlooramfenicol	TRUE	FALSE	FALSE
-nl	Chlortetracycline	Chloortetracycline	TRUE	FALSE	FALSE
-nl	Cinoxacin	Cinoxacine	TRUE	FALSE	FALSE
-nl	Ciprofloxacin	Ciprofloxacine	TRUE	FALSE	FALSE
-nl	Clarithromycin	Claritromycine	TRUE	FALSE	FALSE
-nl	Clavulanic acid	Clavulaanzuur	TRUE	FALSE	FALSE
-nl	clavulanic acid	clavulaanzuur	TRUE	FALSE	FALSE
-nl	Clindamycin	Clindamycine	TRUE	FALSE	FALSE
-nl	Clometocillin	Clometocilline	TRUE	FALSE	FALSE
-nl	Clotrimazole	Clotrimazol	TRUE	FALSE	FALSE
-nl	Cloxacillin	Cloxacilline	TRUE	FALSE	FALSE
-nl	Colistin	Colistine	TRUE	FALSE	FALSE
-nl	Dapsone	Dapson	TRUE	FALSE	FALSE
-nl	Daptomycin	Daptomycine	TRUE	FALSE	FALSE
-nl	Dibekacin	Dibekacine	TRUE	FALSE	FALSE
-nl	Dicloxacillin	Dicloxacilline	TRUE	FALSE	FALSE
-nl	Dirithromycin	Diritromycine	TRUE	FALSE	FALSE
-nl	Econazole	Econazol	TRUE	FALSE	FALSE
-nl	Enoxacin	Enoxacine	TRUE	FALSE	FALSE
-nl	Epicillin	Epicilline	TRUE	FALSE	FALSE
-nl	Erythromycin	Erytromycine	TRUE	FALSE	FALSE
-nl	Ethambutol/isoniazid	Ethambutol/isoniazide	TRUE	FALSE	FALSE
-nl	Fleroxacin	Fleroxacine	TRUE	FALSE	FALSE
-nl	Flucloxacillin	Flucloxacilline	TRUE	FALSE	FALSE
-nl	Fluconazole	Fluconazol	TRUE	FALSE	FALSE
-nl	Flucytosine	Fluorocytosine	TRUE	FALSE	FALSE
-nl	Flurithromycin	Fluritromycine	TRUE	FALSE	FALSE
-nl	Fosfomycin	Fosfomycine	TRUE	FALSE	FALSE
-nl	Fusidic acid	Fusidinezuur	TRUE	FALSE	FALSE
-nl	Gatifloxacin	Gatifloxacine	TRUE	FALSE	FALSE
-nl	Gemifloxacin	Gemifloxacine	TRUE	FALSE	FALSE
-nl	Gentamicin	Gentamicine	TRUE	FALSE	FALSE
-nl	Grepafloxacin	Grepafloxacine	TRUE	FALSE	FALSE
-nl	Hachimycin	Hachimycine	TRUE	FALSE	FALSE
-nl	Hetacillin	Hetacilline	TRUE	FALSE	FALSE
-nl	Imipenem/cilastatin	Imipenem/enzymremmer	TRUE	FALSE	FALSE
-nl	Inosine pranobex	Inosiplex	TRUE	FALSE	FALSE
-nl	Isepamicin	Isepamicine	TRUE	FALSE	FALSE
-nl	Isoconazole	Isoconazol	TRUE	FALSE	FALSE
-nl	Isoniazid	Isoniazide	TRUE	FALSE	FALSE
-nl	Itraconazole	Itraconazol	TRUE	FALSE	FALSE
-nl	Josamycin	Josamycine	TRUE	FALSE	FALSE
-nl	Kanamycin	Kanamycine	TRUE	FALSE	FALSE
-nl	Ketoconazole	Ketoconazol	TRUE	FALSE	FALSE
-nl	Levofloxacin	Levofloxacine	TRUE	FALSE	FALSE
-nl	Lincomycin	Lincomycine	TRUE	FALSE	FALSE
-nl	Lomefloxacin	Lomefloxacine	TRUE	FALSE	FALSE
-nl	Lysozyme	Lysozym	TRUE	FALSE	FALSE
-nl	Mandelic acid	Amandelzuur	TRUE	FALSE	FALSE
-nl	Metampicillin	Metampicilline	TRUE	FALSE	FALSE
-nl	Meticillin	Meticilline	TRUE	FALSE	FALSE
-nl	Metisazone	Metisazon	TRUE	FALSE	FALSE
-nl	Metronidazole	Metronidazol	TRUE	FALSE	FALSE
-nl	Mezlocillin	Mezlocilline	TRUE	FALSE	FALSE
-nl	Micafungin	Micafungine	TRUE	FALSE	FALSE
-nl	Miconazole	Miconazol	TRUE	FALSE	FALSE
-nl	Midecamycin	Midecamycine	TRUE	FALSE	FALSE
-nl	Miocamycin	Miocamycine	TRUE	FALSE	FALSE
-nl	Moxifloxacin	Moxifloxacine	TRUE	FALSE	FALSE
-nl	Mupirocin	Mupirocine	TRUE	FALSE	FALSE
-nl	Nalidixic acid	Nalidixinezuur	TRUE	FALSE	FALSE
-nl	Neomycin	Neomycine	TRUE	FALSE	FALSE
-nl	Netilmicin	Netilmicine	TRUE	FALSE	FALSE
-nl	Nitrofurantoin	Nitrofurantoine	TRUE	FALSE	FALSE
-nl	Norfloxacin	Norfloxacine	TRUE	FALSE	FALSE
-nl	Novobiocin	Novobiocine	TRUE	FALSE	FALSE
-nl	Nystatin	Nystatine	TRUE	FALSE	FALSE
-nl	Ofloxacin	Ofloxacine	TRUE	FALSE	FALSE
-nl	Oleandomycin	Oleandomycine	TRUE	FALSE	FALSE
-nl	Ornidazole	Ornidazol	TRUE	FALSE	FALSE
-nl	Oxacillin	Oxacilline	TRUE	FALSE	FALSE
-nl	Oxolinic acid	Oxolinezuur	TRUE	FALSE	FALSE
-nl	Oxytetracycline	Oxytetracycline	TRUE	FALSE	FALSE
-nl	Pazufloxacin	Pazufloxacine	TRUE	FALSE	FALSE
-nl	Pefloxacin	Pefloxacine	TRUE	FALSE	FALSE
-nl	Penamecillin	Penamecilline	TRUE	FALSE	FALSE
-nl	Penicillin	Penicilline	TRUE	FALSE	FALSE
-nl	Pheneticillin	Feneticilline	TRUE	FALSE	FALSE
-nl	Phenoxymethylpenicillin	Fenoxymethylpenicilline	TRUE	FALSE	FALSE
-nl	Pipemidic acid	Pipemidinezuur	TRUE	FALSE	FALSE
-nl	Piperacillin	Piperacilline	TRUE	FALSE	FALSE
-nl	Piperacillin/beta-lactamase inhibitor	Piperacilline/enzymremmer	TRUE	FALSE	FALSE
-nl	Piromidic acid	Piromidinezuur	TRUE	FALSE	FALSE
-nl	Pivampicillin	Pivampicilline	TRUE	FALSE	FALSE
-nl	Polymyxin B	Polymyxine B	TRUE	FALSE	FALSE
-nl	Posaconazole	Posaconazol	TRUE	FALSE	FALSE
-nl	Pristinamycin	Pristinamycine	TRUE	FALSE	FALSE
-nl	Procaine benzylpenicillin	Benzylpenicillineprocaine	TRUE	FALSE	FALSE
-nl	Propicillin	Propicilline	TRUE	FALSE	FALSE
-nl	Prulifloxacin	Prulifloxacine	TRUE	FALSE	FALSE
-nl	Quinupristin/dalfopristin	Quinupristine/dalfopristine	TRUE	FALSE	FALSE
-nl	Ribostamycin	Ribostamycine	TRUE	FALSE	FALSE
-nl	Rifabutin	Rifabutine	TRUE	FALSE	FALSE
-nl	Rifampicin	Rifampicine	TRUE	FALSE	FALSE
-nl	Rifampicin/pyrazinamide/ethambutol/isoniazid	Rifampicine/pyrazinamide/ethambutol/isoniazide	TRUE	FALSE	FALSE
-nl	Rifampicin/pyrazinamide/isoniazid	Rifampicine/pyrazinamide/isoniazide	TRUE	FALSE	FALSE
-nl	Rifampicin/isoniazid	Rifampicine/isoniazide	TRUE	FALSE	FALSE
-nl	Rifamycin	Rifamycine	TRUE	FALSE	FALSE
-nl	Rifaximin	Rifaximine	TRUE	FALSE	FALSE
-nl	Rokitamycin	Rokitamycine	TRUE	FALSE	FALSE
-nl	Rosoxacin	Rosoxacine	TRUE	FALSE	FALSE
-nl	Roxithromycin	Roxitromycine	TRUE	FALSE	FALSE
-nl	Rufloxacin	Rufloxacine	TRUE	FALSE	FALSE
-nl	Sisomicin	Sisomicine	TRUE	FALSE	FALSE
-nl	Sodium aminosalicylate	Aminosalicylzuur	TRUE	FALSE	FALSE
-nl	Sparfloxacin	Sparfloxacine	TRUE	FALSE	FALSE
-nl	Spectinomycin	Spectinomycine	TRUE	FALSE	FALSE
-nl	Spiramycin	Spiramycine	TRUE	FALSE	FALSE
-nl	Spiramycin/metronidazole	Spiramycine/metronidazol	TRUE	FALSE	FALSE
-nl	Staphylococcus immunoglobulin	Stafylokokkenimmunoglobuline	TRUE	FALSE	FALSE
-nl	Streptoduocin	Streptoduocine	TRUE	FALSE	FALSE
-nl	Streptomycin	Streptomycine	TRUE	FALSE	FALSE
-nl	Streptomycin/isoniazid	Streptomycine/isoniazide	TRUE	FALSE	FALSE
-nl	Sulbenicillin	Sulbenicilline	TRUE	FALSE	FALSE
-nl	Sulfadiazine/tetroxoprim	Sulfadiazine/tetroxoprim	TRUE	FALSE	FALSE
-nl	Sulfadiazine/trimethoprim	Sulfadiazine/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfadimidine/trimethoprim	Sulfadimidine/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfafurazole	Sulfafurazol	TRUE	FALSE	FALSE
-nl	Sulfaisodimidine	Sulfisomidine	TRUE	FALSE	FALSE
-nl	Sulfalene	Sulfaleen	TRUE	FALSE	FALSE
-nl	Sulfamazone	Sulfamazon	TRUE	FALSE	FALSE
-nl	Sulfamerazine/trimethoprim	Sulfamerazine/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfamethizole	Sulfamethizol	TRUE	FALSE	FALSE
-nl	Sulfamethoxazole	Sulfamethoxazol	TRUE	FALSE	FALSE
-nl	Sulfamethoxazole/trimethoprim	Sulfamethoxazol/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfametoxydiazine	Sulfamethoxydiazine	TRUE	FALSE	FALSE
-nl	Sulfametrole/trimethoprim	Sulfametrol/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfamoxole	Sulfamoxol	TRUE	FALSE	FALSE
-nl	Sulfamoxole/trimethoprim	Sulfamoxol/trimethoprim	TRUE	FALSE	FALSE
-nl	Sulfaperin	Sulfaperine	TRUE	FALSE	FALSE
-nl	Sulfaphenazole	Sulfafenazol	TRUE	FALSE	FALSE
-nl	Sulfathiazole	Sulfathiazol	TRUE	FALSE	FALSE
-nl	Sulfathiourea	Sulfathioureum	TRUE	FALSE	FALSE
-nl	Sultamicillin	Sultamicilline	TRUE	FALSE	FALSE
-nl	Talampicillin	Talampicilline	TRUE	FALSE	FALSE
-nl	Teicoplanin	Teicoplanine	TRUE	FALSE	FALSE
-nl	Telithromycin	Telitromycine	TRUE	FALSE	FALSE
-nl	Temafloxacin	Temafloxacine	TRUE	FALSE	FALSE
-nl	Temocillin	Temocilline	TRUE	FALSE	FALSE
-nl	Tenofovir disoproxil	Tenofovir	TRUE	FALSE	FALSE
-nl	Terizidone	Terizidon	TRUE	FALSE	FALSE
-nl	Thiamphenicol	Thiamfenicol	TRUE	FALSE	FALSE
-nl	Thioacetazone/isoniazid	Thioacetazon/isoniazide	TRUE	FALSE	FALSE
-nl	Ticarcillin	Ticarcilline	TRUE	FALSE	FALSE
-nl	Ticarcillin/beta-lactamase inhibitor	Ticarcilline/enzymremmer	TRUE	FALSE	FALSE
-nl	Ticarcillin/clavulanic acid	Ticarcilline/clavulaanzuur	TRUE	FALSE	FALSE
-nl	Tinidazole	Tinidazol	TRUE	FALSE	FALSE
-nl	Tobramycin	Tobramycine	TRUE	FALSE	FALSE
-nl	Trimethoprim/sulfamethoxazole	Cotrimoxazol	TRUE	FALSE	FALSE
-nl	Troleandomycin	Troleandomycine	TRUE	FALSE	FALSE
-nl	Trovafloxacin	Trovafloxacine	TRUE	FALSE	FALSE
-nl	Vancomycin	Vancomycine	TRUE	FALSE	FALSE
-nl	Voriconazole	Voriconazol	TRUE	FALSE	FALSE
-nl	Aminoglycosides	Aminoglycosiden	TRUE	FALSE	FALSE
-nl	Amphenicols	Amfenicolen	TRUE	FALSE	FALSE
-nl	Antifungals/antimycotics	Antifungica/antimycotica	TRUE	FALSE	FALSE
-nl	Antimycobacterials	Antimycobacteriele middelen	TRUE	FALSE	FALSE
-nl	Beta-lactams/penicillins	Beta-lactams/penicillines	TRUE	FALSE	FALSE
-nl	Cephalosporins (1st gen.)	Cefalosporines (1e gen.)	TRUE	FALSE	FALSE
-nl	Cephalosporins (2nd gen.)	Cefalosporines (2e gen.)	TRUE	FALSE	FALSE
-nl	Cephalosporins (3rd gen.)	Cefalosporines (3e gen.)	TRUE	FALSE	FALSE
-nl	Cephalosporins (4th gen.)	Cefalosporines (4e gen.)	TRUE	FALSE	FALSE
-nl	Cephalosporins (5th gen.)	Cefalosporines (5e gen.)	TRUE	FALSE	FALSE
-nl	Cephalosporins (unclassified gen.)	Cefalosporines (ongeclassificeerd)	TRUE	FALSE	FALSE
-nl	Cephalosporins	Cefalosporines	TRUE	FALSE	FALSE
-nl	Glycopeptides	Glycopeptiden	TRUE	FALSE	FALSE
-nl	Macrolides/lincosamides	Macroliden/lincosamiden	TRUE	FALSE	FALSE
-nl	Other antibacterials	Overige antibiotica	TRUE	FALSE	FALSE
-nl	Polymyxins	Polymyxines	TRUE	FALSE	FALSE
-nl	Quinolones	Quinolonen	TRUE	FALSE	FALSE
+lang	pattern	replacement	fixed	ignore.case
+de	Coagulase-negative Staphylococcus	Koagulase-negative Staphylococcus	FALSE	FALSE
+de	Coagulase-positive Staphylococcus	Koagulase-positive Staphylococcus	FALSE	FALSE
+de	Beta-haemolytic Streptococcus	Beta-hämolytischer Streptococcus	FALSE	FALSE
+de	unknown Gram-negatives	unbekannte Gramnegativen	FALSE	FALSE
+de	unknown Gram-positives	unbekannte Grampositiven	FALSE	FALSE
+de	unknown name	unbekannte Name	FALSE	FALSE
+de	unknown kingdom	unbekanntes Reich	FALSE	FALSE
+de	unknown phylum	unbekannter Stamm	FALSE	FALSE
+de	unknown class	unbekannte Klasse	FALSE	FALSE
+de	unknown order	unbekannte Ordnung	FALSE	FALSE
+de	unknown family	unbekannte Familie	FALSE	FALSE
+de	unknown genus	unbekannte Gattung	FALSE	FALSE
+de	unknown species	unbekannte Art	FALSE	FALSE
+de	unknown subspecies	unbekannte Unterart	FALSE	FALSE
+de	unknown rank	unbekannter Rang	FALSE	FALSE
+de	CoNS	KNS	TRUE	FALSE
+de	CoPS	KPS	TRUE	FALSE
+de	Gram-negative	Gramnegativ	FALSE	FALSE
+de	Gram-positive	Grampositiv	FALSE	FALSE
+de	Bacteria	Bakterien	FALSE	FALSE
+de	Fungi	Pilze	FALSE	FALSE
+de	Yeasts	Hefen	FALSE	FALSE
+de	Protozoa	Protozoen	FALSE	FALSE
+de	biogroup	Biogruppe	FALSE	FALSE
+de	biotype	Biotyp	FALSE	FALSE
+de	vegetative	vegetativ	FALSE	FALSE
+de	([([ ]*?)group	\\1Gruppe	FALSE	FALSE
+de	([([ ]*?)Group	\\1Gruppe	FALSE	FALSE
+de	no .*growth	keine? .*wachstum	FALSE	TRUE
+de	no|not	keine?	FALSE	TRUE
+
+nl	Coagulase-negative Staphylococcus	Coagulase-negatieve Staphylococcus	FALSE	FALSE
+nl	Coagulase-positive Staphylococcus	Coagulase-positieve Staphylococcus	FALSE	FALSE
+nl	Beta-haemolytic Streptococcus	Beta-hemolytische Streptococcus	FALSE	FALSE
+nl	unknown Gram-negatives	onbekende Gram-negatieven	FALSE	FALSE
+nl	unknown Gram-positives	onbekende Gram-positieven	FALSE	FALSE
+nl	unknown name	onbekende naam	FALSE	FALSE
+nl	unknown kingdom	onbekend koninkrijk	FALSE	FALSE
+nl	unknown phylum	onbekend fylum	FALSE	FALSE
+nl	unknown class	onbekende klasse	FALSE	FALSE
+nl	unknown order	onbekende orde	FALSE	FALSE
+nl	unknown family	onbekende familie	FALSE	FALSE
+nl	unknown genus	onbekend geslacht	FALSE	FALSE
+nl	unknown species	onbekende soort	FALSE	FALSE
+nl	unknown subspecies	onbekende ondersoort	FALSE	FALSE
+nl	unknown rank	onbekende rang	FALSE	FALSE
+nl	CoNS	CNS	TRUE	FALSE
+nl	CoPS	CPS	TRUE	FALSE
+nl	Gram-negative	Gram-negatief	FALSE	FALSE
+nl	Gram-positive	Gram-positief	FALSE	FALSE
+nl	Bacteria	Bacteriën	FALSE	FALSE
+nl	Fungi	Schimmels	FALSE	FALSE
+nl	Yeasts	Gisten	FALSE	FALSE
+nl	Protozoa	Protozoën	FALSE	FALSE
+nl	biogroup	biogroep	FALSE	FALSE
+nl	vegetative	vegetatief	FALSE	FALSE
+nl	([([ ]*?)group	\\1groep	FALSE	FALSE
+nl	([([ ]*?)Group	\\1Groep	FALSE	FALSE
+nl	antibiotic	antibioticum	FALSE	FALSE
+nl	Antibiotic	Antibioticum	FALSE	FALSE
+nl	Drug	Middel	FALSE	FALSE
+nl	drug	middel	FALSE	FALSE
+nl	no .*growth	geen .*groei	FALSE	TRUE
+nl	no|not	geen|niet	FALSE	TRUE
+
+es	Coagulase-negative Staphylococcus	Staphylococcus coagulasa negativo	FALSE	FALSE
+es	Coagulase-positive Staphylococcus	Staphylococcus coagulasa positivo	FALSE	FALSE
+es	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE
+es	unknown Gram-negatives	Gram negativos desconocidos	FALSE	FALSE
+es	unknown Gram-positives	Gram positivos desconocidos	FALSE	FALSE
+es	unknown name	nombre desconocido	FALSE	FALSE
+es	unknown kingdom	reino desconocido	FALSE	FALSE
+es	unknown phylum	filo desconocido	FALSE	FALSE
+es	unknown class	clase desconocida	FALSE	FALSE
+es	unknown order	orden desconocido	FALSE	FALSE
+es	unknown family	familia desconocida	FALSE	FALSE
+es	unknown genus	género desconocido	FALSE	FALSE
+es	unknown species	especie desconocida	FALSE	FALSE
+es	unknown subspecies	subespecie desconocida	FALSE	FALSE
+es	unknown rank	rango desconocido	FALSE	FALSE
+es	CoNS	SCN	TRUE	FALSE
+es	CoPS	SCP	TRUE	FALSE
+es	Gram-negative	Gram negativo	FALSE	FALSE
+es	Gram-positive	Gram positivo	FALSE	FALSE
+es	Bacteria	Bacterias	FALSE	FALSE
+es	Fungi	Hongos	FALSE	FALSE
+es	Yeasts	Levaduras	FALSE	FALSE
+es	Protozoa	Protozoarios	FALSE	FALSE
+es	biogroup	biogrupo	FALSE	FALSE
+es	biotype	biotipo	FALSE	FALSE
+es	vegetative	vegetativo	FALSE	FALSE
+es	([([ ]*?)group	\\1grupo	FALSE	FALSE
+es	([([ ]*?)Group	\\1Grupo	FALSE	FALSE
+es	no .*growth	no .*crecimientonon	FALSE	TRUE
+es	no|not	no|sin	FALSE	TRUE
+
+it	Coagulase-negative Staphylococcus	Staphylococcus negativo coagulasi	FALSE	FALSE
+it	Coagulase-positive Staphylococcus	Staphylococcus positivo coagulasi	FALSE	FALSE
+it	Beta-haemolytic Streptococcus	Streptococcus Beta-emolitico	FALSE	FALSE
+it	unknown Gram-negatives	Gram negativi sconosciuti	FALSE	FALSE
+it	unknown Gram-positives	Gram positivi sconosciuti	FALSE	FALSE
+it	unknown name	nome sconosciuto	FALSE	FALSE
+it	unknown kingdom	regno sconosciuto	FALSE	FALSE
+it	unknown phylum	phylum sconosciuto	FALSE	FALSE
+it	unknown class	classe sconosciuta	FALSE	FALSE
+it	unknown order	ordine sconosciuto	FALSE	FALSE
+it	unknown family	famiglia sconosciuta	FALSE	FALSE
+it	unknown genus	genere sconosciuto	FALSE	FALSE
+it	unknown species	specie sconosciute	FALSE	FALSE
+it	unknown subspecies	sottospecie sconosciute	FALSE	FALSE
+it	unknown rank	grado sconosciuto	FALSE	FALSE
+it	Gram-negative	Gram negativo	FALSE	FALSE
+it	Gram-positive	Gram positivo	FALSE	FALSE
+it	Bacteria	Batteri	FALSE	FALSE
+it	Fungi	Funghi	FALSE	FALSE
+it	Yeasts	Lieviti	FALSE	FALSE
+it	Protozoa	Protozoi	FALSE	FALSE
+it	biogroup	biogruppo	FALSE	FALSE
+it	biotype	biotipo	FALSE	FALSE
+it	vegetative	vegetativo	FALSE	FALSE
+it	([([ ]*?)group	\\1gruppo	FALSE	FALSE
+it	([([ ]*?)Group	\\1Gruppo	FALSE	FALSE
+it	no .*growth	sem .*crescimento	FALSE	TRUE
+it	no|not	sem	FALSE	TRUE
+
+fr	Coagulase-negative Staphylococcus	Staphylococcus à coagulase négative	FALSE	FALSE
+fr	Coagulase-positive Staphylococcus	Staphylococcus à coagulase positif	FALSE	FALSE
+fr	Beta-haemolytic Streptococcus	Streptococcus Bêta-hémolytique	FALSE	FALSE
+fr	unknown Gram-negatives	Gram négatifs inconnus	FALSE	FALSE
+fr	unknown Gram-positives	Gram positifs inconnus	FALSE	FALSE
+fr	unknown name	nom inconnu	FALSE	FALSE
+fr	unknown kingdom	règme inconnu	FALSE	FALSE
+fr	unknown phylum	embranchement inconnu	FALSE	FALSE
+fr	unknown class	classe inconnue	FALSE	FALSE
+fr	unknown order	ordre inconnu	FALSE	FALSE
+fr	unknown family	famille inconnue	FALSE	FALSE
+fr	unknown genus	genre inconnu	FALSE	FALSE
+fr	unknown species	espèce inconnue	FALSE	FALSE
+fr	unknown subspecies	sous-espèce inconnue	FALSE	FALSE
+fr	unknown rank	rang inconnu	FALSE	FALSE
+fr	Gram-negative	Gram négatif	FALSE	FALSE
+fr	Gram-positive	Gram positif	FALSE	FALSE
+fr	Bacteria	Bactéries	FALSE	FALSE
+fr	Fungi	Champignons	FALSE	FALSE
+fr	Yeasts	Levures	FALSE	FALSE
+fr	Protozoa	Protozoaires	FALSE	FALSE
+fr	biogroup	biogroupe	FALSE	FALSE
+fr	vegetative	végétatif	FALSE	FALSE
+fr	([([ ]*?)group	\\1groupe	FALSE	FALSE
+fr	([([ ]*?)Group	\\1Groupe	FALSE	FALSE
+fr	no .*growth	pas .*croissance	FALSE	TRUE
+fr	no|not	non	FALSE	TRUE
+
+pt	Coagulase-negative Staphylococcus	Staphylococcus coagulase negativo	FALSE	FALSE
+pt	Coagulase-positive Staphylococcus	Staphylococcus coagulase positivo	FALSE	FALSE
+pt	Beta-haemolytic Streptococcus	Streptococcus Beta-hemolítico	FALSE	FALSE
+pt	unknown Gram-negatives	Gram negativos desconhecidos	FALSE	FALSE
+pt	unknown Gram-positives	Gram positivos desconhecidos	FALSE	FALSE
+pt	unknown name	nome desconhecido	FALSE	FALSE
+pt	unknown kingdom	reino desconhecido	FALSE	FALSE
+pt	unknown phylum	filo desconhecido	FALSE	FALSE
+pt	unknown class	classe desconhecida	FALSE	FALSE
+pt	unknown order	ordem desconhecido	FALSE	FALSE
+pt	unknown family	família desconhecida	FALSE	FALSE
+pt	unknown genus	gênero desconhecido	FALSE	FALSE
+pt	unknown species	espécies desconhecida	FALSE	FALSE
+pt	unknown subspecies	subespécies desconhecida	FALSE	FALSE
+pt	unknown rank	classificação desconhecido	FALSE	FALSE
+pt	Gram-negative	Gram negativo	FALSE	FALSE
+pt	Gram-positive	Gram positivo	FALSE	FALSE
+pt	Bacteria	Bactérias	FALSE	FALSE
+pt	Fungi	Fungos	FALSE	FALSE
+pt	Yeasts	Leveduras	FALSE	FALSE
+pt	Protozoa	Protozoários	FALSE	FALSE
+pt	biogroup	biogrupo	FALSE	FALSE
+pt	biotype	biótipo	FALSE	FALSE
+pt	vegetative	vegetativo	FALSE	FALSE
+pt	([([ ]*?)group	\\1grupo	FALSE	FALSE
+pt	([([ ]*?)Group	\\1Grupo	FALSE	FALSE
+pt	no .*growth	sem .*crescimento	FALSE	TRUE
+pt	no|not	sem	FALSE	TRUE
+
+de	clavulanic acid	Clavulansäure	FALSE	TRUE
+
+nl	4-aminosalicylic acid	4-aminosalicylzuur
+nl	Adefovir dipivoxil	Adefovir
+nl	Aldesulfone sodium	Aldesulfon
+nl	Amikacin	Amikacine
+nl	Amoxicillin	Amoxicilline
+nl	Amoxicillin/beta-lactamase inhibitor	Amoxicilline/enzymremmer
+nl	Amphotericin B	Amfotericine B
+nl	Ampicillin	Ampicilline
+nl	Ampicillin/beta-lactamase inhibitor	Ampicilline/enzymremmer
+nl	Anidulafungin	Anidulafungine
+nl	Azidocillin	Azidocilline
+nl	Azithromycin	Azitromycine
+nl	Azlocillin	Azlocilline
+nl	Bacampicillin	Bacampicilline
+nl	Bacitracin	Bacitracine
+nl	Benzathine benzylpenicillin	Benzylpenicillinebenzathine
+nl	Benzathine phenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine
+nl	Benzylpenicillin	Benzylpenicilline
+nl	Calcium aminosalicylate	Aminosalicylzuur
+nl	Capreomycin	Capreomycine
+nl	Carbenicillin	Carbenicilline
+nl	Carindacillin	Carindacilline
+nl	Caspofungin	Caspofungine
+nl	Ce(f|ph)acetrile	Cefacetril	FALSE
+nl	Ce(f|ph)alexin	Cefalexine	FALSE	FALSE
+nl	Ce(f|ph)alotin	Cefalotine	FALSE
+nl	Ce(f|ph)amandole	Cefamandol	FALSE
+nl	Ce(f|ph)apirin	Cefapirine	FALSE
+nl	Ce(f|ph)azedone	Cefazedon	FALSE
+nl	Ce(f|ph)azolin	Cefazoline	FALSE
+nl	Ce(f|ph)alothin	Cefalotine	FALSE
+nl	Ce(f|ph)alexin	Cefalexine	FALSE
+nl	Ce(f|ph)epime	Cefepim	FALSE
+nl	Ce(f|ph)ixime	Cefixim	FALSE
+nl	Ce(f|ph)menoxime	Cefmenoxim	FALSE
+nl	Ce(f|ph)metazole	Cefmetazol	FALSE
+nl	Ce(f|ph)odizime	Cefodizim	FALSE
+nl	Ce(f|ph)onicid	Cefonicide	FALSE
+nl	Ce(f|ph)operazone	Cefoperazon	FALSE
+nl	Ce(f|ph)operazone/beta-lactamase inhibitor	Cefoperazon/enzymremmer	FALSE
+nl	Ce(f|ph)otaxime	Cefotaxim	FALSE
+nl	Ce(f|ph)oxitin	Cefoxitine	FALSE
+nl	Ce(f|ph)pirome	Cefpirom	FALSE
+nl	Ce(f|ph)podoxime	Cefpodoxim	FALSE
+nl	Ce(f|ph)radine	Cefradine	FALSE
+nl	Ce(f|ph)sulodin	Cefsulodine	FALSE
+nl	Ce(f|ph)tazidime	Ceftazidim	FALSE
+nl	Ce(f|ph)tezole	Ceftezol	FALSE
+nl	Ce(f|ph)tizoxime	Ceftizoxim	FALSE
+nl	Ce(f|ph)triaxone	Ceftriaxon	FALSE
+nl	Ce(f|ph)uroxime	Cefuroxim	FALSE
+nl	Ce(f|ph)uroxime/metronidazole	Cefuroxim/andere antibacteriele middelen	FALSE
+nl	Chloramphenicol	Chlooramfenicol
+nl	Chlortetracycline	Chloortetracycline
+nl	Cinoxacin	Cinoxacine
+nl	Ciprofloxacin	Ciprofloxacine
+nl	Clarithromycin	Claritromycine
+nl	Clavulanic acid	Clavulaanzuur
+nl	clavulanic acid	clavulaanzuur
+nl	Clindamycin	Clindamycine
+nl	Clometocillin	Clometocilline
+nl	Clotrimazole	Clotrimazol
+nl	Cloxacillin	Cloxacilline
+nl	Colistin	Colistine
+nl	Dapsone	Dapson
+nl	Daptomycin	Daptomycine
+nl	Dibekacin	Dibekacine
+nl	Dicloxacillin	Dicloxacilline
+nl	Dirithromycin	Diritromycine
+nl	Econazole	Econazol
+nl	Enoxacin	Enoxacine
+nl	Epicillin	Epicilline
+nl	Erythromycin	Erytromycine
+nl	Ethambutol/isoniazid	Ethambutol/isoniazide
+nl	Fleroxacin	Fleroxacine
+nl	Flucloxacillin	Flucloxacilline
+nl	Fluconazole	Fluconazol
+nl	Flucytosine	Fluorocytosine
+nl	Flurithromycin	Fluritromycine
+nl	Fosfomycin	Fosfomycine
+nl	Fusidic acid	Fusidinezuur
+nl	Gatifloxacin	Gatifloxacine
+nl	Gemifloxacin	Gemifloxacine
+nl	Gentamicin	Gentamicine
+nl	Grepafloxacin	Grepafloxacine
+nl	Hachimycin	Hachimycine
+nl	Hetacillin	Hetacilline
+nl	Imipenem/cilastatin	Imipenem/enzymremmer
+nl	Inosine pranobex	Inosiplex
+nl	Isepamicin	Isepamicine
+nl	Isoconazole	Isoconazol
+nl	Isoniazid	Isoniazide
+nl	Itraconazole	Itraconazol
+nl	Josamycin	Josamycine
+nl	Kanamycin	Kanamycine
+nl	Ketoconazole	Ketoconazol
+nl	Levofloxacin	Levofloxacine
+nl	Lincomycin	Lincomycine
+nl	Lomefloxacin	Lomefloxacine
+nl	Lysozyme	Lysozym
+nl	Mandelic acid	Amandelzuur
+nl	Metampicillin	Metampicilline
+nl	Meticillin	Meticilline
+nl	Metisazone	Metisazon
+nl	Metronidazole	Metronidazol
+nl	Mezlocillin	Mezlocilline
+nl	Micafungin	Micafungine
+nl	Miconazole	Miconazol
+nl	Midecamycin	Midecamycine
+nl	Miocamycin	Miocamycine
+nl	Moxifloxacin	Moxifloxacine
+nl	Mupirocin	Mupirocine
+nl	Nalidixic acid	Nalidixinezuur
+nl	Neomycin	Neomycine
+nl	Netilmicin	Netilmicine
+nl	Nitrofurantoin	Nitrofurantoine
+nl	Norfloxacin	Norfloxacine
+nl	Novobiocin	Novobiocine
+nl	Nystatin	Nystatine
+nl	Ofloxacin	Ofloxacine
+nl	Oleandomycin	Oleandomycine
+nl	Ornidazole	Ornidazol
+nl	Oxacillin	Oxacilline
+nl	Oxolinic acid	Oxolinezuur
+nl	Oxytetracycline	Oxytetracycline
+nl	Pazufloxacin	Pazufloxacine
+nl	Pefloxacin	Pefloxacine
+nl	Penamecillin	Penamecilline
+nl	Penicillin	Penicilline
+nl	Pheneticillin	Feneticilline
+nl	Phenoxymethylpenicillin	Fenoxymethylpenicilline
+nl	Pipemidic acid	Pipemidinezuur
+nl	Piperacillin	Piperacilline
+nl	Piperacillin/beta-lactamase inhibitor	Piperacilline/enzymremmer
+nl	Piromidic acid	Piromidinezuur
+nl	Pivampicillin	Pivampicilline
+nl	Polymyxin B	Polymyxine B
+nl	Posaconazole	Posaconazol
+nl	Pristinamycin	Pristinamycine
+nl	Procaine benzylpenicillin	Benzylpenicillineprocaine
+nl	Propicillin	Propicilline
+nl	Prulifloxacin	Prulifloxacine
+nl	Quinupristin/dalfopristin	Quinupristine/dalfopristine
+nl	Ribostamycin	Ribostamycine
+nl	Rifabutin	Rifabutine
+nl	Rifampicin	Rifampicine
+nl	Rifampicin/pyrazinamide/ethambutol/isoniazid	Rifampicine/pyrazinamide/ethambutol/isoniazide
+nl	Rifampicin/pyrazinamide/isoniazid	Rifampicine/pyrazinamide/isoniazide
+nl	Rifampicin/isoniazid	Rifampicine/isoniazide
+nl	Rifamycin	Rifamycine
+nl	Rifaximin	Rifaximine
+nl	Rokitamycin	Rokitamycine
+nl	Rosoxacin	Rosoxacine
+nl	Roxithromycin	Roxitromycine
+nl	Rufloxacin	Rufloxacine
+nl	Sisomicin	Sisomicine
+nl	Sodium aminosalicylate	Aminosalicylzuur
+nl	Sparfloxacin	Sparfloxacine
+nl	Spectinomycin	Spectinomycine
+nl	Spiramycin	Spiramycine
+nl	Spiramycin/metronidazole	Spiramycine/metronidazol
+nl	Staphylococcus immunoglobulin	Stafylokokkenimmunoglobuline
+nl	Streptoduocin	Streptoduocine
+nl	Streptomycin	Streptomycine
+nl	Streptomycin/isoniazid	Streptomycine/isoniazide
+nl	Sulbenicillin	Sulbenicilline
+nl	Sulfadiazine/tetroxoprim	Sulfadiazine/tetroxoprim
+nl	Sulfadiazine/trimethoprim	Sulfadiazine/trimethoprim
+nl	Sulfadimidine/trimethoprim	Sulfadimidine/trimethoprim
+nl	Sulfafurazole	Sulfafurazol
+nl	Sulfaisodimidine	Sulfisomidine
+nl	Sulfalene	Sulfaleen
+nl	Sulfamazone	Sulfamazon
+nl	Sulfamerazine/trimethoprim	Sulfamerazine/trimethoprim
+nl	Sulfamethizole	Sulfamethizol
+nl	Sulfamethoxazole	Sulfamethoxazol
+nl	Sulfamethoxazole/trimethoprim	Sulfamethoxazol/trimethoprim
+nl	Sulfametoxydiazine	Sulfamethoxydiazine
+nl	Sulfametrole/trimethoprim	Sulfametrol/trimethoprim
+nl	Sulfamoxole	Sulfamoxol
+nl	Sulfamoxole/trimethoprim	Sulfamoxol/trimethoprim
+nl	Sulfaperin	Sulfaperine
+nl	Sulfaphenazole	Sulfafenazol
+nl	Sulfathiazole	Sulfathiazol
+nl	Sulfathiourea	Sulfathioureum
+nl	Sultamicillin	Sultamicilline
+nl	Talampicillin	Talampicilline
+nl	Teicoplanin	Teicoplanine
+nl	Telithromycin	Telitromycine
+nl	Temafloxacin	Temafloxacine
+nl	Temocillin	Temocilline
+nl	Tenofovir disoproxil	Tenofovir
+nl	Terizidone	Terizidon
+nl	Thiamphenicol	Thiamfenicol
+nl	Thioacetazone/isoniazid	Thioacetazon/isoniazide
+nl	Ticarcillin	Ticarcilline
+nl	Ticarcillin/beta-lactamase inhibitor	Ticarcilline/enzymremmer
+nl	Ticarcillin/clavulanic acid	Ticarcilline/clavulaanzuur
+nl	Tinidazole	Tinidazol
+nl	Tobramycin	Tobramycine
+nl	Trimethoprim/sulfamethoxazole	Cotrimoxazol
+nl	Troleandomycin	Troleandomycine
+nl	Trovafloxacin	Trovafloxacine
+nl	Vancomycin	Vancomycine
+nl	Voriconazole	Voriconazol
+nl	Aminoglycosides	Aminoglycosiden	TRUE	FALSE
+nl	Amphenicols	Amfenicolen	TRUE	FALSE
+nl	Antifungals/antimycotics	Antifungica/antimycotica	TRUE	FALSE
+nl	Antimycobacterials	Antimycobacteriele middelen	TRUE	FALSE
+nl	Beta-lactams/penicillins	Beta-lactams/penicillines	TRUE	FALSE
+nl	Cephalosporins (1st gen.)	Cefalosporines (1e gen.)	TRUE	FALSE
+nl	Cephalosporins (2nd gen.)	Cefalosporines (2e gen.)	TRUE	FALSE
+nl	Cephalosporins (3rd gen.)	Cefalosporines (3e gen.)	TRUE	FALSE
+nl	Cephalosporins (4th gen.)	Cefalosporines (4e gen.)	TRUE	FALSE
+nl	Cephalosporins (5th gen.)	Cefalosporines (5e gen.)	TRUE	FALSE
+nl	Cephalosporins (unclassified gen.)	Cefalosporines (ongeclassificeerd)	TRUE	FALSE
+nl	Cephalosporins	Cefalosporines	TRUE	FALSE
+nl	Glycopeptides	Glycopeptiden	TRUE	FALSE
+nl	Macrolides/lincosamides	Macroliden/lincosamiden	TRUE	FALSE
+nl	Other antibacterials	Overige antibiotica	TRUE	FALSE
+nl	Polymyxins	Polymyxines	TRUE	FALSE
+nl	Quinolones	Quinolonen	TRUE	FALSE

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

docs/extra.css

@@ -88,7 +88,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
   /* adjusted colour for all real links; having href attribute */
   color: #128f76;
 }
-.ot, .dv, .fl, .cn {
+.ot, .dv {
   /* numbers and TRUE/FALSE */
   color: slategray;
 }
@@ -187,13 +187,10 @@ div[id^=last-updated] h2 {
 }
 
 /* tables, make them look like scientific ones */
-table {
+.table {
   font-size: 90%;
 }
-table * {
-  vertical-align: middle !important;
-}
-table td {
+.table td {
   padding: 4px !important;
 }
 thead {

docs/index.html

@@ -43,7 +43,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 
@@ -395,9 +395,8 @@ Since you are one of our users, we would like to know how you use the package an
 <p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
 <p>The latest and unpublished development version can be installed from GitHub using:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> 
 <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
-<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
 </div>
 </div>
 <div id="get-started" class="section level3">

docs/news/index.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 
@@ -236,13 +236,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1509020" class="section level1">
-<h1 class="page-header" data-toc-text="1.5.0.9020">
-<a href="#amr-1509020" class="anchor"></a>AMR 1.5.0.9020<small> Unreleased </small>
+    <div id="amr-1509018" class="section level1">
+<h1 class="page-header" data-toc-text="1.5.0.9018">
+<a href="#amr-1509018" class="anchor"></a>AMR 1.5.0.9018<small> Unreleased </small>
 </h1>
-<div id="last-updated-18-february-2021" class="section level2">
+<div id="last-updated-9-february-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-18-february-2021" class="anchor"></a><small>Last updated: 18 February 2021</small>
+<a href="#last-updated-9-february-2021" class="anchor"></a><small>Last updated: 9 February 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">
@@ -259,11 +259,11 @@
 <li>
 <p>Added argument <code>only_rsi_columns</code> for some functions, which defaults to <code>FALSE</code>, to indicate if the functions must only be applied to columns that are of class <code>&lt;rsi&gt;</code> (i.e., transformed with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:</p>
 <ul>
-<li>All antibiotic selector functions (<code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
-<li>All antibiotic filter functions (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
+<li>All antibiotic selector functions (<code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code>aminoglocysides()</code>, <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
+<li>All antibiotic filter functions (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code>filter_aminoglocysides()</code>, <code><a href="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
 <li><code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></li>
 <li>
-<code><a href="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code> and <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
+<code><a href="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><a href="../reference/mdro.html">brmo()</a></code>, <code>mrgn</code> and <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
 <li><code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code></li>
 </ul>
 </li>
@@ -325,7 +325,6 @@
 <li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
 </li>
 <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
-<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
 </ul>
 </div>
 <div id="other" class="section level3">
@@ -652,7 +651,7 @@
 <p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
 <p>Negative effects of this change are:</p>
 <ul>
-<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
+<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
 <li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code>&lt;ord&gt;</code>, not <code>&lt;rsi&gt;</code> anymore. This is purely a visual effect.</del></li>
 <li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
 <li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@@ -989,7 +988,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co">#&gt; invalid microorganism code, NA generated</span></code></pre></div>
 <p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
 </li>
-<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
+<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
 <li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
 </ul>
 </div>
@@ -1258,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
 <li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
 </li>
-<li>Frequency tables (<code>freq()</code>):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
 <ul>
 <li><p>speed improvement for microbial IDs</p></li>
 <li><p>fixed factor level names for R Markdown</p></li>
@@ -1268,12 +1267,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
 <span class="co"># grouped boxplots:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
@@ -1283,7 +1282,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
 </li>
 <li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
-<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
+<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
 </li>
 <li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
 <li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@@ -1524,7 +1523,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 </li>
 </ul>
 </li>
-<li>Frequency tables (<code>freq()</code> function):
+<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
 <ul>
 <li>
 <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@@ -1534,15 +1533,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <span class="co"># OLD WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
-  <span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
 <span class="co"># NEW WAY</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
 
 <span class="co"># Even supports grouping variables:</span>
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span>
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 </li>
 <li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
 <li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@@ -1625,7 +1624,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
 <li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
 <li>
-<p>Frequency tables - <code>freq()</code>:</p>
+<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
 <ul>
 <li>
 <p>Support for grouping variables, test with:</p>
@@ -1633,14 +1632,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 <li>
 <p>Support for (un)selecting columns:</p>
 <div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">septic_patients</span> <span class="op">%&gt;%</span> 
-  <span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
 </li>
 <li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@@ -1658,7 +1657,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
 <li><p>Fix for <code>mo_property</code> not working properly</p></li>
 <li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
-<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
+<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
 <li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
 <li>
 <p>AI improvements for <code>as.mo</code>:</p>
@@ -1826,13 +1825,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
-<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
+<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
 <p>For lists, subsetting is possible:</p>
 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
 <code class="sourceCode R">
 <span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
-<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
+<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
 </li>
 </ul>
 </div>
@@ -1906,13 +1905,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
 <ul>
 <li>A vignette to explain its usage</li>
 <li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
-<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
+<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
 </li>
 <li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
 </li>
 <li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
 </li>
-<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
+<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
 </li>
 <li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
 <li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-02-18T22:21Z
+last_built: 2021-02-09T11:26Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/ab_property.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/antibiotic_class_selectors.html

@@ -83,7 +83,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 
@@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># See ?example_isolates.</span>
 
 <span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
-<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
+<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
 <span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
 <span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mo"</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
 

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/filter_ab_class.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/first_isolate.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/guess_ab_col.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/index.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

docs/reference/key_antibiotics.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/mdro.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/mo_property.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/reference/resistance_predict.html

@@ -82,7 +82,7 @@
       </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">1.5.0.9019</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </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">1.5.0.9020</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
       </span>
     </div>
 

git_premaster.sh

@@ -123,8 +123,10 @@ echo
 echo "••••••••••••••••••••"
 echo "• Building package •"
 echo "••••••••••••••••••••"
-echo "• Building 'data-raw/AMR_latest.tar.gz'..."
-Rscript -e "x <- devtools::build(path = 'data-raw/AMR_latest.tar.gz', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
+echo "• Removing old build from 'data-raw/'..."
+rm data-raw/AMR_*.tar.gz
+echo "• Building 'data-raw/AMR_${new_version}.tar.gz'..."
+Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
 echo "• Installing..."
 Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
 echo

index.md

@@ -125,12 +125,10 @@ It will be downloaded and installed automatically. For RStudio, click on the men
 The latest and unpublished development version can be installed from GitHub using:
 
 ```r
-install.packages("remotes") # if you haven't already
+install.packages("remotes") 
 remotes::install_github("msberends/AMR")
 ```
 
-You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>
-
 ### Get started
 
 To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.

man/antibiotic_class_selectors.Rd

@@ -85,7 +85,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 # See ?example_isolates.
 
 # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
-example_isolates[, carbapenems()]
+example_isolates[, c(carbapenems())]
 # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
 example_isolates[, c("mo", aminoglycosides())]
 

pkgdown/extra.css

@@ -88,7 +88,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
   /* adjusted colour for all real links; having href attribute */
   color: #128f76;
 }
-.ot, .dv, .fl, .cn {
+.ot, .dv {
   /* numbers and TRUE/FALSE */
   color: slategray;
 }
@@ -187,13 +187,10 @@ div[id^=last-updated] h2 {
 }
 
 /* tables, make them look like scientific ones */
-table {
+.table {
   font-size: 90%;
 }
-table * {
-  vertical-align: middle !important;
-}
-table td {
+.table td {
   padding: 4px !important;
 }
 thead {

tests/testthat/test-mo_property.R

@@ -84,9 +84,6 @@ test_that("mo_property works", {
   expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
 
   expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
-  
-  dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
-  expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
 
   # manual property function
   expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))