P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 19:26:13 +01:00
Code Releases Activity

(v1.5.0.9020) translation fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-02-18 23:23:14 +01:00
parent 601ea7377c
commit daa12ced2c
22 changed files with 1416 additions and 1381 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.5.0.9019 Version: 1.5.0.9020
Date: 2021-02-17 Date: 2021-02-18
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 1.5.0.9019 # AMR 1.5.0.9020
## <small>Last updated: 17 February 2021</small> ## <small>Last updated: 18 February 2021</small>
### New ### 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. * 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.
@ -57,6 +57,7 @@
* Updated colours of values R, S and I in tibble printing * 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()` * 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. * 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 ### Other
* Big documentation updates * Big documentation updates

1898
R/mo.R
View File

File diff suppressed because it is too large Load Diff

7
R/mo_property.R
View File

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

BIN
R/sysdata.rda
View File

Binary file not shown.

12
R/translate.R
View File

@ -123,7 +123,7 @@ coerce_language_setting <- function(lang) {
} }
# translate strings based on inst/translations.tsv # translate strings based on inst/translations.tsv
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) { translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, affect_mo_name = FALSE) {
if (is.null(language)) { if (is.null(language)) {
return(from) return(from)
@ -146,10 +146,13 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
if (only_unknown == TRUE) { if (only_unknown == TRUE) {
df_trans <- subset(df_trans, pattern %like% "unknown") 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 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 df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
# check if text to look for is in one of the patterns # check if text to look for is in one of the patterns
@ -167,7 +170,8 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
replacement = df_trans$replacement[i], replacement = df_trans$replacement[i],
x = from_unique_translated, x = from_unique_translated,
ignore.case = df_trans$ignore.case[i], ignore.case = df_trans$ignore.case[i],
fixed = df_trans$fixed[i])) fixed = df_trans$fixed[i],
perl = !df_trans$fixed[i]))
# force UTF-8 for diacritics # force UTF-8 for diacritics
from_unique_translated <- enc2utf8(from_unique_translated) from_unique_translated <- enc2utf8(from_unique_translated)

2
README.md
View File

@ -10,7 +10,7 @@
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" /> <img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
The latest built **source package** (`AMR_x.x.x.tar.gz`) can be found in folder [/data-raw/](data-raw). The latest built **source package** (`AMR_latest.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. `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.

BIN
data-raw/AMR_1.5.0.9019.tar.gz → data-raw/AMR_latest.tar.gz
View File

Binary file not shown.

5
data-raw/reproduction_of_microorganisms.R
View File

@ -31,8 +31,9 @@
# Data retrieved from the Global Biodiversity Information Facility (GBIF): # Data retrieved from the Global Biodiversity Information Facility (GBIF):
# https://doi.org/10.15468/rffz4x # https://doi.org/10.15468/rffz4x
# #
# And from the Leibniz Institute: German Collection of Microorganisms and Cell Cultures (DSMZ) # And from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
# (register first at https://bacdive.dsmz.de/api/pnu/registration/register/ and use API as done below) # (register first) https://lpsn.dsmz.de/downloads
# download the latest CSV file.
library(dplyr) library(dplyr)
library(AMR) library(AMR)

819
data-raw/translations.tsv
View File

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

Can't render this file because it has a wrong number of fields in line 186.

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.5.0.9019</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>

5
docs/index.html
View File

@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>
@ -395,8 +395,9 @@ 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><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> <p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <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> <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>
<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> <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> </div>
<div id="get-started" class="section level3"> <div id="get-started" class="section level3">

13
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509019" class="section level1"> <div id="amr-1509020" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9019"> <h1 class="page-header" data-toc-text="1.5.0.9020">
<a href="#amr-1509019" class="anchor"></a>AMR 1.5.0.9019<small> Unreleased </small> <a href="#amr-1509020" class="anchor"></a>AMR 1.5.0.9020<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-17-february-2021" class="section level2"> <div id="last-updated-18-february-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-17-february-2021" class="anchor"></a><small>Last updated: 17 February 2021</small> <a href="#last-updated-18-february-2021" class="anchor"></a><small>Last updated: 18 February 2021</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -325,6 +325,7 @@
<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>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>
<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>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> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-02-17T09:58Z last_built: 2021-02-18T22:21Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.5.0.9020</span>
</span> </span>
</div> </div>

6
git_premaster.sh
View File

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

4
index.md
View File

@ -125,10 +125,12 @@ 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: The latest and unpublished development version can be installed from GitHub using:
```r ```r
install.packages("remotes") install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR") 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 ### 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. 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.

3
tests/testthat/test-mo_property.R
View File

@ -84,6 +84,9 @@ test_that("mo_property works", {
expect_output(print(mo_gramstain("Escherichia coli", language = "fr"))) expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN")) 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 # manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname"))) expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))