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(v1.5.0.9020) translation fix

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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
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.5.0.9019
Date: 2021-02-17
Version: 1.5.0.9020
Date: 2021-02-18
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.5.0.9019
## <small>Last updated: 17 February 2021</small>
# AMR 1.5.0.9020
## <small>Last updated: 18 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.
@ -57,6 +57,7 @@
* 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

1898
R/mo.R
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7
R/mo_property.R
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@ -172,7 +172,10 @@ 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)
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
language = language,
only_unknown = FALSE,
affect_mo_name = TRUE)
}
#' @rdname mo_property
@ -214,7 +217,7 @@ 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)
translate_AMR(shortnames, language = language, only_unknown = FALSE, affect_mo_name = TRUE)
}
#' @rdname mo_property

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R/sysdata.rda
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12
R/translate.R
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@ -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) {
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, affect_mo_name = FALSE) {
if (is.null(language)) {
return(from)
@ -146,10 +146,13 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
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
@ -167,7 +170,8 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
replacement = df_trans$replacement[i],
x = from_unique_translated,
ignore.case = df_trans$ignore.case[i],
fixed = df_trans$fixed[i]))
fixed = df_trans$fixed[i],
perl = !df_trans$fixed[i]))
# force UTF-8 for diacritics
from_unique_translated <- enc2utf8(from_unique_translated)

2
README.md
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@ -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_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.

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data-raw/AMR_1.5.0.9019.tar.gz → data-raw/AMR_latest.tar.gz
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5
data-raw/reproduction_of_microorganisms.R
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@ -31,8 +31,9 @@
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
# https://doi.org/10.15468/rffz4x
#
# 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)
# And from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
# (register first) https://lpsn.dsmz.de/downloads
# download the latest CSV file.
library(dplyr)
library(AMR)

819
data-raw/translations.tsv
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@ -1,407 +1,412 @@
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
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
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

2
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

2
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

2
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

5
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</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>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>
<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>
<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">

13
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</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-1509019" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9019">
<a href="#amr-1509019" class="anchor"></a>AMR 1.5.0.9019<small> Unreleased </small>
<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>
</h1>
<div id="last-updated-17-february-2021" class="section level2">
<div id="last-updated-18-february-2021" class="section level2">
<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>
<div id="new" class="section level3">
<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>
<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">

2
docs/pkgdown.yml
View File

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

2
docs/reference/index.html
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

2
docs/survey.html
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@ -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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
</span>
</div>

6
git_premaster.sh
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@ -123,10 +123,8 @@ echo
echo "••••••••••••••••••••"
echo "• Building package •"
echo "••••••••••••••••••••"
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 "• 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 "• Installing..."
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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:
```r
install.packages("remotes")
install.packages("remotes") # if you haven't already
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.

3
tests/testthat/test-mo_property.R
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@ -84,6 +84,9 @@ 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")))