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website update

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dr. M.S. (Matthijs) Berends
2022-12-11 11:44:29 +01:00
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commit eed1c14b96
28 changed files with 19 additions and 297 deletions
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2
R/mo_matching_score.R
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#'
#' **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.
#'

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R/sysdata.rda
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R/translate.R
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#' 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

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R/whocc.R
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#'
#' 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, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<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.