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@ -139,14 +139,6 @@ The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the o
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SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See \emph{Source} and the \link{microorganisms} data set for more info.
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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}
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\section{Matching Score for Microorganisms}{
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With ambiguous user input in \code{\link[=as.mo]{as.mo()}} and all the \code{\link[=mo_property]{mo_*}} functions, the returned results are chosen based on their matching score using \code{\link[=mo_matching_score]{mo_matching_score()}}. This matching score \eqn{m}, is calculated as:
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@ -198,97 +190,91 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this \code{AMR} package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find \href{https://msberends.github.io/AMR/articles/datasets.html}{all download links on our website}, which is automatically updated with every code change.
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}
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\section{Read more on Our Website!}{
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On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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# taxonomic tree -----------------------------------------------------------
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mo_kingdom("E. coli") # "Bacteria"
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mo_phylum("E. coli") # "Proteobacteria"
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mo_class("E. coli") # "Gammaproteobacteria"
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mo_order("E. coli") # "Enterobacterales"
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mo_family("E. coli") # "Enterobacteriaceae"
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mo_genus("E. coli") # "Escherichia"
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mo_species("E. coli") # "coli"
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mo_subspecies("E. coli") # ""
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mo_kingdom("Klebsiella pneumoniae")
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mo_phylum("Klebsiella pneumoniae")
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mo_class("Klebsiella pneumoniae")
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mo_order("Klebsiella pneumoniae")
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mo_family("Klebsiella pneumoniae")
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mo_genus("Klebsiella pneumoniae")
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mo_species("Klebsiella pneumoniae")
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mo_subspecies("Klebsiella pneumoniae")
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# colloquial properties ----------------------------------------------------
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mo_name("E. coli") # "Escherichia coli"
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mo_fullname("E. coli") # "Escherichia coli" - same as mo_name()
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mo_shortname("E. coli") # "E. coli"
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mo_name("Klebsiella pneumoniae")
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mo_fullname("Klebsiella pneumoniae")
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mo_shortname("Klebsiella pneumoniae")
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# other properties ---------------------------------------------------------
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mo_gramstain("E. coli") # "Gram-negative"
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mo_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes)
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mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
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mo_rank("E. coli") # "species"
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mo_url("E. coli") # get the direct url to the online database entry
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mo_synonyms("E. coli") # get previously accepted taxonomic names
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mo_gramstain("Klebsiella pneumoniae")
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mo_snomed("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_rank("Klebsiella pneumoniae")
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mo_url("Klebsiella pneumoniae")
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mo_synonyms("Klebsiella pneumoniae")
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# scientific reference -----------------------------------------------------
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mo_ref("E. coli") # "Castellani et al., 1919"
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mo_authors("E. coli") # "Castellani et al."
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mo_year("E. coli") # 1919
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mo_lpsn("E. coli") # 776057 (LPSN record ID)
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mo_ref("Klebsiella pneumoniae")
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mo_authors("Klebsiella pneumoniae")
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mo_year("Klebsiella pneumoniae")
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mo_lpsn("Klebsiella pneumoniae")
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# abbreviations known in the field -----------------------------------------
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mo_genus("MRSA") # "Staphylococcus"
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mo_species("MRSA") # "aureus"
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mo_shortname("VISA") # "S. aureus"
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mo_gramstain("VISA") # "Gram-positive"
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mo_genus("MRSA")
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mo_species("MRSA")
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mo_shortname("VISA")
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mo_gramstain("VISA")
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mo_genus("EHEC") # "Escherichia"
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mo_species("EHEC") # "coli"
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mo_genus("EHEC")
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mo_species("EHEC")
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# known subspecies ---------------------------------------------------------
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mo_name("doylei") # "Campylobacter jejuni doylei"
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mo_genus("doylei") # "Campylobacter"
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mo_species("doylei") # "jejuni"
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mo_subspecies("doylei") # "doylei"
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mo_name("doylei")
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mo_genus("doylei")
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mo_species("doylei")
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mo_subspecies("doylei")
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mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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mo_shortname("K. pneu rh") # "K. pneumoniae"
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mo_fullname("K. pneu rh")
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mo_shortname("K. pneu rh")
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\donttest{
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# Becker classification, see ?as.mo ----------------------------------------
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mo_fullname("S. epi") # "Staphylococcus epidermidis"
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mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
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mo_shortname("S. epi") # "S. epidermidis"
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mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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mo_fullname("S. epi")
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mo_fullname("S. epi", Becker = TRUE)
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mo_shortname("S. epi")
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mo_shortname("S. epi", Becker = TRUE)
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# Lancefield classification, see ?as.mo ------------------------------------
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mo_fullname("S. pyo") # "Streptococcus pyogenes"
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mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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mo_shortname("S. pyo") # "S. pyogenes"
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mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" (='Group A Streptococci')
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mo_fullname("S. pyo")
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mo_fullname("S. pyo", Lancefield = TRUE)
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mo_shortname("S. pyo")
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mo_shortname("S. pyo", Lancefield = TRUE)
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# language support --------------------------------------------------------
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mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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mo_gramstain("E. coli", language = "es") # "Gram negativo"
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mo_gramstain("Klebsiella pneumoniae", language = "de")
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mo_gramstain("Klebsiella pneumoniae", language = "nl")
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mo_gramstain("Klebsiella pneumoniae", language = "es")
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# mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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mo_kingdom("E. coli") # "Bacteria" on a German system
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mo_type("E. coli") # "Bakterien" on a German system
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mo_type("E. coli") # "Bacteria" on an English system
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mo_kingdom("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "de") # "Streptococcus Gruppe A"
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language = "de")
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mo_fullname("S. pyogenes",
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Lancefield = TRUE,
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language = "nl") # "Streptococcus groep A"
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language = "nl")
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# other --------------------------------------------------------------------
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mo_is_yeast(c("Candida", "E. coli")) # TRUE, FALSE
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mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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# gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
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\donttest{
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# gram stains and intrinsic resistance can be used as a filter in dplyr verbs
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if (require("dplyr")) {
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example_isolates \%>\%
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filter(mo_is_gram_positive())
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@ -299,11 +285,11 @@ if (require("dplyr")) {
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# get a list with the complete taxonomy (from kingdom to subspecies)
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mo_taxonomy("E. coli")
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mo_taxonomy("Klebsiella pneumoniae")
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# get a list with the taxonomy, the authors, Gram-stain,
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# SNOMED codes, and URL to the online database
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mo_info("E. coli")
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}
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# SNOMED codes, and URL to the online database
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mo_info("Klebsiella pneumoniae")
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}
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}
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\seealso{
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