diff --git a/DESCRIPTION b/DESCRIPTION index d5546329..701cda35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9006 +Version: 1.8.2.9007 Date: 2022-10-06 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index fa62c76d..a4955a2a 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9006 +# AMR 1.8.2.9007 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/mo_property.R b/R/mo_property.R index 34ddcb36..abbf519b 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -115,10 +115,10 @@ #' #' \donttest{ #' # Becker classification, see ?as.mo ---------------------------------------- -#' mo_fullname("Staph. epi") -#' mo_fullname("Staph. epi", Becker = TRUE) -#' mo_shortname("Staph. epi") -#' mo_shortname("Staph. epi", Becker = TRUE) +#' mo_fullname("Staph. epidermidis") +#' mo_fullname("Staph. epidermidis", Becker = TRUE) +#' mo_shortname("Staph. epidermidis") +#' mo_shortname("Staph. epidermidis", Becker = TRUE) #' #' # Lancefield classification, see ?as.mo ------------------------------------ #' mo_fullname("S. pyo") @@ -137,7 +137,8 @@ #' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official #' mo_kingdom("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae") -#' mo_type("Klebsiella pneumoniae", language = "nl") +#' mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect +#' mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated #' #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de") #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk") @@ -151,12 +152,12 @@ #' if (require("dplyr")) { #' example_isolates %>% #' filter(mo_is_gram_positive()) %>% -#' count(mo_genus(), count = TRUE) +#' count(mo_genus(), sort = TRUE) #' } #' if (require("dplyr")) { #' example_isolates %>% #' filter(mo_is_intrinsic_resistant(ab = "vanco")) %>% -#' count(mo_genus(), count = TRUE) +#' count(mo_genus(), sort = TRUE) #' } #' #' diff --git a/R/sysdata.rda b/R/sysdata.rda index e5fdc7f0..7ba4e2f7 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/translations.tsv b/data-raw/translations.tsv index ba195d10..3039c88c 100644 --- a/data-raw/translations.tsv +++ b/data-raw/translations.tsv @@ -23,10 +23,10 @@ CoNS FALSE TRUE FALSE TRUE KNS CNS KNS CoNS グラム陰性 CoNS КОС SCN CoPS FALSE TRUE FALSE TRUE KPS CPS KPS CoPS グラム陽性 CoPS КПС SCP KPS KPS КПС Gram-negative TRUE TRUE FALSE FALSE 革兰氏阴性 Gram-negativ Gram-negatief Gram négatif Gramnegativ Αρνητικό κατά Gram Gram negativo ^細菌$ Gram-ujemne Gram negativo Грамотрицательные Gram negativo Gram-negativ Gram-negatif Грамнегативні Gram-positive TRUE TRUE FALSE FALSE 革兰氏阳性 Gram-positiv Gram-positief Gram positif Grampositiv Θετικό κατά Gram Gram positivo ^真菌$ Gram-dodatnie Gram positivo Грамположительные Gram positivo Gram-positiv Gram-pozitif Грампозитивні -^Bacteria$ TRUE TRUE FALSE FALSE ^细菌$ Bakterier Bacteriën Bactéries Bakterien ^Βακτήρια$ Batteri ^酵母$ ^Bakterie$ Bactérias Бактерии Bacterias Bakterier ^Bakteri$ Бактерії -^Fungi$ TRUE TRUE FALSE FALSE ^真菌$ Støbeforme Schimmels Champignons Pilze ^Μύκητες$ Funghi ^原生動物$ ^Grzyby$ Fungos Грибы Hongos Svampar ^Mantarlar$ Гриби -^Yeasts$ TRUE TRUE FALSE FALSE ^酵母菌$ Gær Gisten Levures Hefen ^Ζυμομύκητες$ Lieviti バイオグループ ^Drożdże$ Leveduras Животные Levaduras Jästdjur ^Mayalar$ Дріжджі -^Protozoa$ TRUE TRUE FALSE FALSE ^原生动物$ Protozoer Protozoën Protozoaires Protozoen ^Πρωτόζωα$ Protozoi 生物型 ^Protozoa$ Protozoários Протозоа Protozoarios Protozoer ^Protozoa$ Найпростіші +^Bacteria$ TRUE TRUE FALSE FALSE 细菌 Bakterier Bacteriën Bactéries Bakterien Βακτήρια Batteri 酵母 Bakterie Bactérias Бактерии Bacterias Bakterier Bakteri Бактерії +^Fungi$ TRUE TRUE FALSE FALSE 真菌 Støbeforme Schimmels Champignons Pilze Μύκητες Funghi 原生動物 Grzyby Fungos Грибы Hongos Svampar Mantarlar Гриби +^Yeasts$ TRUE TRUE FALSE FALSE 酵母菌 Gær Gisten Levures Hefen Ζυμομύκητες Lieviti バイオグループ Drożdże Leveduras Животные Levaduras Jästdjur Mayalar Дріжджі +^Protozoa$ TRUE TRUE FALSE FALSE ^原生动物$ Protozoer Protozoën Protozoaires Protozoen Πρωτόζωα Protozoi 生物型 Protozoa Protozoários Протозоа Protozoarios Protozoer Protozoa Найпростіші biogroup TRUE TRUE FALSE FALSE 生物群 biogruppe biogroep biogroupe Biogruppe βιοομάδα biogruppo 植物型 biogrupa biogrupo биогруппа biogrupo biogrupp biyogrup біогрупа biotype TRUE TRUE FALSE FALSE 生物型 biotype Biotyp βιότυπος biotipo ([([ ]*?))) グループ biotyp biótipo биотип biotipo biotyp biyotip біотип vegetative TRUE TRUE FALSE FALSE 无性系 vegetativ vegetatief végétatif vegetativ βλαστικός vegetativo ([[ ]*?)グループ wegetatywna vegetativo вегетативный vegetativo vegetativ vejetatif вегетативний diff --git a/man/mo_property.Rd b/man/mo_property.Rd index afe1cd5e..2721cb20 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -400,10 +400,10 @@ mo_shortname("K. pneu rh") \donttest{ # Becker classification, see ?as.mo ---------------------------------------- -mo_fullname("Staph. epi") -mo_fullname("Staph. epi", Becker = TRUE) -mo_shortname("Staph. epi") -mo_shortname("Staph. epi", Becker = TRUE) +mo_fullname("Staph. epidermidis") +mo_fullname("Staph. epidermidis", Becker = TRUE) +mo_shortname("Staph. epidermidis") +mo_shortname("Staph. epidermidis", Becker = TRUE) # Lancefield classification, see ?as.mo ------------------------------------ mo_fullname("S. pyo") @@ -422,7 +422,8 @@ mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian # mo_type is equal to mo_kingdom, but mo_kingdom will remain official mo_kingdom("Klebsiella pneumoniae") mo_type("Klebsiella pneumoniae") -mo_type("Klebsiella pneumoniae", language = "nl") +mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect +mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de") mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk") @@ -436,12 +437,12 @@ mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) if (require("dplyr")) { example_isolates \%>\% filter(mo_is_gram_positive()) \%>\% - count(mo_genus(), count = TRUE) + count(mo_genus(), sort = TRUE) } if (require("dplyr")) { example_isolates \%>\% filter(mo_is_intrinsic_resistant(ab = "vanco")) \%>\% - count(mo_genus(), count = TRUE) + count(mo_genus(), sort = TRUE) }