diff --git a/DESCRIPTION b/DESCRIPTION index 622c7c90..d7818f26 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.8.2.9060 -Date: 2022-12-10 +Version: 1.8.2.9061 +Date: 2022-12-11 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 4c7460e7..6ffe563b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9060 +# AMR 1.8.2.9061 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index 875a5f80..dd28fe2d 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -52,7 +52,7 @@ #' #' **Group 1** (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacterales. #' -#' **Group 2** consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`. +#' **Group 2** consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`. #' #' **Group 3** consists of all other microorganisms. #' diff --git a/R/sysdata.rda b/R/sysdata.rda index 9f1b5c32..f0f13911 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/translate.R b/R/translate.R index 08108d99..d1c11d36 100755 --- a/R/translate.R +++ b/R/translate.R @@ -32,9 +32,9 @@ #' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()]. #' @param x text to translate #' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. -#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names. +#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_and(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names. #' -#' To permanently silence the once-per-session language notes on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this: +#' To permanently silence the once-per-session language note on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this: #' #' ```r #' # Open .Rprofile file diff --git a/R/whocc.R b/R/whocc.R index cf6c1b13..2ce47d17 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -31,7 +31,6 @@ #' #' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology. #' @section WHOCC: -#' \if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr} #' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, ) and the Pharmaceuticals Community Register of the European Commission (). #' #' These have become the gold standard for international drug utilisation monitoring and research. diff --git a/_pkgdown.yml b/_pkgdown.yml index e74a4857..04b6b3a9 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -56,8 +56,8 @@ footer: left: [devtext] right: [logo] components: - devtext: 'AMR (for R). Developed at the University of Groningen in collaboration with non-profit organisations
Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.' - logo: '' + devtext: 'AMR (for R). Free and open-source, licenced under the GNU General Public License version 2.0 (GPL-2).
Developed at the University of Groningen and University Medical Center Groningen in The Netherlands.' + logo: '' home: sidebar: diff --git a/data-raw/_pre_commit_hook.R b/data-raw/_pre_commit_hook.R index 89bf5cf4..5da95045 100644 --- a/data-raw/_pre_commit_hook.R +++ b/data-raw/_pre_commit_hook.R @@ -171,7 +171,7 @@ MO_PREVALENT_GENERA <- c( "Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus", "Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella", "Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium", - "Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium", + "Chlamydia", "Chlamydophila", "Christensenella", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex", "Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia", "Empedobacter", "Entamoeba", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea", diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index c5ed5133..e65878e4 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_microorganisms.R @@ -740,7 +740,6 @@ taxonomy <- taxonomy %>% "Pseudomonadota", "Actinobacteria", # old, now Actinomycetota "Actinomycetota" - ) | genus %in% MO_PREVALENT_GENERA) ~ 2, diff --git a/index.md b/index.md index e3d45add..efa9d17a 100644 --- a/index.md +++ b/index.md @@ -188,12 +188,12 @@ To find out how to conduct AMR data analysis, please [continue reading here to g ### Partners -The development of this package is part of, related to, or made possible by: +The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:
- - + +
diff --git a/man/WHOCC.Rd b/man/WHOCC.Rd index d3610eeb..d78d0396 100644 --- a/man/WHOCC.Rd +++ b/man/WHOCC.Rd @@ -8,7 +8,6 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi } \section{WHOCC}{ -\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr} This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). These have become the gold standard for international drug utilisation monitoring and research. diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index 5522e73e..835f1421 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -69,7 +69,6 @@ Like all data sets in this package, these data sets are publicly available for d } \section{WHOCC}{ -\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr} This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). These have become the gold standard for international drug utilisation monitoring and research. diff --git a/man/as.ab.Rd b/man/as.ab.Rd index b2f28f5c..0e9462a5 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -51,7 +51,6 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt \section{WHOCC}{ -\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr} This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). These have become the gold standard for international drug utilisation monitoring and research. diff --git a/man/as.av.Rd b/man/as.av.Rd index 1028e3f6..8a096781 100644 --- a/man/as.av.Rd +++ b/man/as.av.Rd @@ -49,7 +49,6 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt \section{WHOCC}{ -\if{html}{\figure{logo_who.png}{options: height="60" style=margin-bottom:"5"} \cr} This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}). These have become the gold standard for international drug utilisation monitoring and research. diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 5f237447..2279a1fb 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -146,7 +146,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. -\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. +\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Christensenella}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. \strong{Group 3} consists of all other microorganisms. diff --git a/man/figures/logo_certe.png b/man/figures/logo_certe.png deleted file mode 100755 index 001925f1..00000000 Binary files a/man/figures/logo_certe.png and /dev/null differ diff --git a/man/figures/logo_eh1h.png b/man/figures/logo_eh1h.png deleted file mode 100755 index 0efc8e83..00000000 Binary files a/man/figures/logo_eh1h.png and /dev/null differ diff --git a/man/figures/logo_interreg.png b/man/figures/logo_interreg.png deleted file mode 100755 index 723a9aea..00000000 Binary files a/man/figures/logo_interreg.png and /dev/null differ diff --git a/man/figures/logo_rug.svg b/man/figures/logo_rug.svg deleted file mode 100644 index 37d19c79..00000000 --- a/man/figures/logo_rug.svg +++ /dev/null @@ -1,274 +0,0 @@ - - - - - - - - - - - - - diff --git a/man/figures/logo_umcg.png b/man/figures/logo_umcg.png deleted file mode 100755 index d562a34e..00000000 Binary files a/man/figures/logo_umcg.png and /dev/null differ diff --git a/man/figures/logo_who.png b/man/figures/logo_who.png deleted file mode 100755 index 39d33ccb..00000000 Binary files a/man/figures/logo_who.png and /dev/null differ diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index 6203c8ad..f108ec0b 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -37,7 +37,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. -\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. +\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Christensenella}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. \strong{Group 3} consists of all other microorganisms. diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 60b63b01..d4059436 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -330,7 +330,7 @@ The grouping into human pathogenic prevalence (\eqn{p}) is based on experience f \strong{Group 1} (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is \emph{Enterococcus}, \emph{Staphylococcus} or \emph{Streptococcus}. This group consequently contains all common Gram-negative bacteria, such as \emph{Pseudomonas} and \emph{Legionella} and all species within the order Enterobacterales. -\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. +\strong{Group 2} consists of all microorganisms where the taxonomic phylum is Pseudomonadota (previously named Proteobacteria), Bacillota (previously named Firmicutes), Actinomycetota (previously named Actinobacteria) or Sarcomastigophora, or where the taxonomic genus is \emph{Absidia}, \emph{Acanthamoeba}, \emph{Acholeplasma}, \emph{Acremonium}, \emph{Actinotignum}, \emph{Aedes}, \emph{Alistipes}, \emph{Alloprevotella}, \emph{Alternaria}, \emph{Amoeba}, \emph{Anaerosalibacter}, \emph{Ancylostoma}, \emph{Angiostrongylus}, \emph{Anisakis}, \emph{Anopheles}, \emph{Apophysomyces}, \emph{Arachnia}, \emph{Aspergillus}, \emph{Aureobasidium}, \emph{Bacteroides}, \emph{Basidiobolus}, \emph{Beauveria}, \emph{Bergeyella}, \emph{Blastocystis}, \emph{Blastomyces}, \emph{Borrelia}, \emph{Brachyspira}, \emph{Branhamella}, \emph{Butyricimonas}, \emph{Candida}, \emph{Capillaria}, \emph{Capnocytophaga}, \emph{Catabacter}, \emph{Cetobacterium}, \emph{Chaetomium}, \emph{Chlamydia}, \emph{Chlamydophila}, \emph{Christensenella}, \emph{Chryseobacterium}, \emph{Chrysonilia}, \emph{Cladophialophora}, \emph{Cladosporium}, \emph{Conidiobolus}, \emph{Contracaecum}, \emph{Cordylobia}, \emph{Cryptococcus}, \emph{Curvularia}, \emph{Deinococcus}, \emph{Demodex}, \emph{Dermatobia}, \emph{Dientamoeba}, \emph{Diphyllobothrium}, \emph{Dirofilaria}, \emph{Dysgonomonas}, \emph{Echinostoma}, \emph{Elizabethkingia}, \emph{Empedobacter}, \emph{Entamoeba}, \emph{Enterobius}, \emph{Exophiala}, \emph{Exserohilum}, \emph{Fasciola}, \emph{Flavobacterium}, \emph{Fonsecaea}, \emph{Fusarium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Haloarcula}, \emph{Halobacterium}, \emph{Halococcus}, \emph{Hendersonula}, \emph{Heterophyes}, \emph{Histomonas}, \emph{Histoplasma}, \emph{Hymenolepis}, \emph{Hypomyces}, \emph{Hysterothylacium}, \emph{Leishmania}, \emph{Lelliottia}, \emph{Leptosphaeria}, \emph{Leptotrichia}, \emph{Lucilia}, \emph{Lumbricus}, \emph{Malassezia}, \emph{Malbranchea}, \emph{Metagonimus}, \emph{Meyerozyma}, \emph{Microsporidium}, \emph{Microsporum}, \emph{Mortierella}, \emph{Mucor}, \emph{Mycocentrospora}, \emph{Mycoplasma}, \emph{Myroides}, \emph{Necator}, \emph{Nectria}, \emph{Ochroconis}, \emph{Odoribacter}, \emph{Oesophagostomum}, \emph{Oidiodendron}, \emph{Opisthorchis}, \emph{Ornithobacterium}, \emph{Parabacteroides}, \emph{Pediculus}, \emph{Pedobacter}, \emph{Phlebotomus}, \emph{Phocaeicola}, \emph{Phocanema}, \emph{Phoma}, \emph{Pichia}, \emph{Piedraia}, \emph{Pithomyces}, \emph{Pityrosporum}, \emph{Pneumocystis}, \emph{Porphyromonas}, \emph{Prevotella}, \emph{Pseudallescheria}, \emph{Pseudoterranova}, \emph{Pulex}, \emph{Rhizomucor}, \emph{Rhizopus}, \emph{Rhodotorula}, \emph{Riemerella}, \emph{Saccharomyces}, \emph{Sarcoptes}, \emph{Scolecobasidium}, \emph{Scopulariopsis}, \emph{Scytalidium}, \emph{Sphingobacterium}, \emph{Spirometra}, \emph{Spiroplasma}, \emph{Sporobolomyces}, \emph{Stachybotrys}, \emph{Streptobacillus}, \emph{Strongyloides}, \emph{Syngamus}, \emph{Taenia}, \emph{Tannerella}, \emph{Tenacibaculum}, \emph{Terrimonas}, \emph{Toxocara}, \emph{Treponema}, \emph{Trichinella}, \emph{Trichobilharzia}, \emph{Trichoderma}, \emph{Trichomonas}, \emph{Trichophyton}, \emph{Trichosporon}, \emph{Trichostrongylus}, \emph{Trichuris}, \emph{Tritirachium}, \emph{Trombicula}, \emph{Trypanosoma}, \emph{Tunga}, \emph{Ureaplasma}, \emph{Victivallis}, \emph{Wautersiella}, \emph{Weeksella} or \emph{Wuchereria}. \strong{Group 3} consists of all other microorganisms. diff --git a/man/translate.Rd b/man/translate.Rd index 3f413a96..731bbc9a 100644 --- a/man/translate.Rd +++ b/man/translate.Rd @@ -25,9 +25,9 @@ translate_AMR(x, language = get_AMR_locale()) For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}. } \details{ -The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names. +The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names. -To permanently silence the once-per-session language notes on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this: +To permanently silence the once-per-session language note on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this: \if{html}{\out{
}}\preformatted{# Open .Rprofile file utils::file.edit("~/.Rprofile") diff --git a/pkgdown/logos/logo_certe.png b/pkgdown/logos/logo_certe.png deleted file mode 100755 index 001925f1..00000000 Binary files a/pkgdown/logos/logo_certe.png and /dev/null differ diff --git a/pkgdown/logos/logo_certe.svg b/pkgdown/logos/logo_certe.svg new file mode 100644 index 00000000..0466bd3b --- /dev/null +++ b/pkgdown/logos/logo_certe.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/pkgdown/logos/logo_umcg.png b/pkgdown/logos/logo_umcg.png deleted file mode 100755 index d562a34e..00000000 Binary files a/pkgdown/logos/logo_umcg.png and /dev/null differ diff --git a/pkgdown/logos/logo_umcg.svg b/pkgdown/logos/logo_umcg.svg new file mode 100644 index 00000000..dda994e7 --- /dev/null +++ b/pkgdown/logos/logo_umcg.svg @@ -0,0 +1 @@ + \ No newline at end of file