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(v0.7.1.9032) eucast_rules() improvements
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@ -9,11 +9,13 @@ All antimicrobial drugs and their official names, ATC codes, ATC groups and defi
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
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\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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}
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\section{Read more on our website!}{
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@ -41,11 +41,13 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
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\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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}
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\section{Read more on our website!}{
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@ -35,11 +35,13 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}). \strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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This package contains \strong{all ~450 antimicrobial 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{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
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\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See \url{https://www.whocc.no/copyright_disclaimer/}.}
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}
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\section{Read more on our website!}{
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@ -33,7 +33,7 @@ eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
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\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
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\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a \code{data.frame} with extensive info about which rows and columns would be effected and in which way.}
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\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.}
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\item{...}{column name of an antibiotic, see section Antibiotics}
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}
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@ -53,7 +53,7 @@ The file containing all EUCAST rules is located here: \url{https://gitlab.com/ms
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To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
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The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
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\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
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\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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@ -170,10 +170,12 @@ b
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# 5 Pseudomonas aeruginosa R R - - R R R
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\donttest{
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# do not apply EUCAST rules, but rather get a data.frame
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# with 18 rows, containing all details about the transformations:
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c <- eucast_rules(a, verbose = TRUE)
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}
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}
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\keyword{eucast}
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\keyword{interpretive}
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\keyword{reading}
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@ -9,7 +9,7 @@ guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE)
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\arguments{
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\item{x}{a \code{data.frame}}
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\item{search_string}{a text to search \code{x} for}
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\item{search_string}{a text to search \code{x} for, will be checked with \code{\link{as.ab}} if this value is not a column in \code{x}}
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\item{verbose}{a logical to indicate whether additional info should be printed}
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}
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@ -20,7 +20,7 @@ A column name of \code{x}, or \code{NULL} when no result is found.
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This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations.
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}
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\details{
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You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or ATC code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
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You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \code{\link{antibiotics}} data set for any column containing a name or code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
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}
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\section{Read more on our website!}{
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@ -62,7 +62,7 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
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To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
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The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown below in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
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\strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
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\strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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@ -89,7 +89,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
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}
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}
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\description{
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Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
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Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
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}
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\details{
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All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
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@ -130,7 +130,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
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}
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\examples{
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## taxonomic tree
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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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@ -140,35 +140,33 @@ 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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## colloquial properties
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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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## other properties
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# other properties ---------------------------------------------------------
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mo_gramstain("E. coli") # "Gram-negative"
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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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## scientific reference
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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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# Abbreviations known in the field
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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("MRSA") # "S. aureus"
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mo_gramstain("MRSA") # "Gram-positive"
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mo_shortname("VISA") # "S. aureus"
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mo_gramstain("VISA") # "Gram-positive"
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mo_genus("VISA") # "Staphylococcus"
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mo_species("VISA") # "aureus"
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mo_genus("EHEC") # "Escherichia"
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mo_species("EHEC") # "coli"
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# Known subspecies
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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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@ -177,14 +175,14 @@ mo_subspecies("doylei") # "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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# Becker classification, see ?as.mo
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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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# Lancefield classification, see ?as.mo
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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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@ -214,6 +212,7 @@ mo_taxonomy("E. coli")
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# get a list with the taxonomy, the authors and the URL to the online database
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mo_info("E. coli")
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}
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}
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\seealso{
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\code{\link{microorganisms}}
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}
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