ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid

man/ab_property.Rd

@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ab_property.R
+\name{ab_property}
+\alias{ab_property}
+\alias{ab_atc}
+\alias{ab_official}
+\alias{ab_official_nl}
+\alias{ab_trivial_nl}
+\alias{ab_certe}
+\alias{ab_umcg}
+\title{Property of an antibiotic}
+\usage{
+ab_property(x, property = "official")
+
+ab_atc(x)
+
+ab_official(x)
+
+ab_official_nl(x)
+
+ab_trivial_nl(x)
+
+ab_certe(x)
+
+ab_umcg(x)
+}
+\arguments{
+\item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}}
+
+\item{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}}
+}
+\description{
+Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
+}
+\examples{
+ab_atc("amcl")         # J01CR02
+ab_official("amcl")    # Amoxicillin and beta-lactamase inhibitor
+ab_official_nl("amcl") # Amoxicilline met enzymremmer
+ab_trivial_nl("amcl")  # Amoxicilline/clavulaanzuur
+ab_certe("amcl")       # amcl
+ab_umcg("amcl")        # AMCL
+}
+\seealso{
+\code{\link{antibiotics}}
+}

man/antibiotics.Rd

@@ -9,11 +9,11 @@
   \item{\code{atc}}{ATC code, like \code{J01CR02}}
   \item{\code{certe}}{Certe code, like \code{amcl}}
   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
-  \item{\code{abbr}}{Abbreviation as used by many countries, to be used for \code{\link{guess_atc}}}
-  \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and enzyme inhibitor"}}
+  \item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
+  \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and beta-lactamase inhibitor"}}
   \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
   \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
-  \item{\code{trade_name}}{Trade name as used by many countries, to be used for \code{\link{guess_atc}}}
+  \item{\code{trade_name}}{Trade name as used by many countries, used internally by \code{\link{as.atc}}}
   \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
   \item{\code{oral_units}}{Units of \code{ddd_units}}
   \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}

man/as.atc.Rd

@@ -23,6 +23,8 @@ Character (vector) with class \code{"act"}. Unknown values will return \code{NA}
 Use this function to determine the ATC code of one or more antibiotics. The dataset \code{\link{antibiotics}} will be searched for abbreviations, official names and trade names.
 }
 \details{
+Use the \code{\link{ab_property}} functions to get properties based on the returned ATC code, see Examples.
+
 In the ATC classification system, the active substances are classified in a hierarchy with five different levels.  The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups.  The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance.  The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
   Source: \url{https://www.whocc.no/atc/structure_and_principles/}
 }
@@ -36,6 +38,11 @@ as.atc("ERY")
 as.atc("Erythrocin") # Trade name
 as.atc("Eryzole")    # Trade name
 as.atc("Pediamycin") # Trade name
+
+# Use ab_* functions to get a specific property based on an ATC code
+Cipro <- as.atc("cipro") # returns `J01MA02`
+ab_official(Cipro)       # returns "Ciprofloxacin"
+ab_umcg(Cipro)           # returns "CIPR", the code used in the UMCG
 }
 \seealso{
 \code{\link{antibiotics}} for the dataframe that is being used to determine ATC's.

man/as.bactid.Rd

@@ -2,6 +2,7 @@
 % Please edit documentation in R/bactid.R
 \name{as.bactid}
 \alias{as.bactid}
+\alias{bactid}
 \alias{guess_bactid}
 \alias{is.bactid}
 \title{Transform to bacteria ID}
@@ -34,6 +35,8 @@ Use this function to determine a valid ID based on a genus (and species). This i
 \details{
 \code{guess_bactid} is an alias of \code{as.bactid}.
 
+Use the \code{\link{mo_property}} functions to get properties based on the returned bactid, see Examples.
+
 Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
 \itemize{
   \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
@@ -56,12 +59,18 @@ as.bactid("MRSA") # Methicillin Resistant S. aureus
 as.bactid("VISA") # Vancomycin Intermediate S. aureus
 as.bactid("VRSA") # Vancomycin Resistant S. aureus
 
+# guess_bactid is an alias of as.bactid and works the same
 guess_bactid("S. epidermidis")                 # will remain species: STAEPI
 guess_bactid("S. epidermidis", Becker = TRUE)  # will not remain species: STACNS
 
 guess_bactid("S. pyogenes")                    # will remain species: STCAGA
 guess_bactid("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
 
+# Use mo_* functions to get a specific property based on a bactid
+Ecoli <- as.bactid("E. coli") # returns `ESCCOL`
+mo_genus(Ecoli)               # returns "Escherichia"
+mo_gramstain(Ecoli)           # returns "Negative rods"
+
 \dontrun{
 df$bactid <- as.bactid(df$microorganism_name)
 

man/atc.property.Rd

@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/atc.R
-\name{atc.property}
-\alias{atc.property}
-\alias{atc.official}
-\alias{atc.official_nl}
-\alias{atc.trivial_nl}
-\alias{atc.certe}
-\alias{atc.umcg}
-\title{Get antibiotic property based on ATC}
-\usage{
-atc.official(atc)
-
-atc.official_nl(atc)
-
-atc.trivial_nl(atc)
-
-atc.certe(atc)
-
-atc.umcg(atc)
-}
-\arguments{
-\item{atc}{a valid ATC code, created with \code{\link{as.atc}}}
-}
-\description{
-Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code.
-}

man/bactid.property.Rd

@@ -1,42 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/bactid.R
-\name{bactid.property}
-\alias{bactid.property}
-\alias{bactid.family}
-\alias{bactid.genus}
-\alias{bactid.species}
-\alias{bactid.subspecies}
-\alias{bactid.fullname}
-\alias{bactid.type}
-\alias{bactid.gramstain}
-\alias{bactid.aerobic}
-\alias{bactid.type_nl}
-\alias{bactid.gramstain_nl}
-\title{Get microbial property based on `bactid`}
-\usage{
-bactid.family(bactid)
-
-bactid.genus(bactid)
-
-bactid.species(bactid)
-
-bactid.subspecies(bactid)
-
-bactid.fullname(bactid)
-
-bactid.type(bactid)
-
-bactid.gramstain(bactid)
-
-bactid.aerobic(bactid)
-
-bactid.type_nl(bactid)
-
-bactid.gramstain_nl(bactid)
-}
-\arguments{
-\item{bactid}{a valid bactid code, created with \code{\link{as.bactid}}}
-}
-\description{
-Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
-}

man/microorganisms.Rd

@@ -3,8 +3,8 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Dataset with ~2500 microorganisms}
-\format{A data.frame with 2464 observations and 12 variables:
+\title{Dataset with ~2650 microorganisms}
+\format{A data.frame with 2,646 observations and 12 variables:
 \describe{
   \item{\code{bactid}}{ID of microorganism}
   \item{\code{bactsys}}{Bactsyscode of microorganism}
@@ -23,7 +23,7 @@
 microorganisms
 }
 \description{
-A dataset containing 2464 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
+A dataset containing 2,646 microorganisms. MO codes of the UMCG can be looked up using \code{\link{microorganisms.umcg}}.
 }
 \seealso{
 \code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}

man/mo_property.Rd

@@ -0,0 +1,88 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mo_property.R
+\name{mo_property}
+\alias{mo_property}
+\alias{mo_family}
+\alias{mo_genus}
+\alias{mo_species}
+\alias{mo_subspecies}
+\alias{mo_fullname}
+\alias{mo_type}
+\alias{mo_gramstain}
+\alias{mo_aerobic}
+\alias{mo_type_nl}
+\alias{mo_gramstain_nl}
+\title{Property of a microorganism}
+\usage{
+mo_property(x, property = "fullname")
+
+mo_family(x)
+
+mo_genus(x)
+
+mo_species(x)
+
+mo_subspecies(x)
+
+mo_fullname(x)
+
+mo_type(x)
+
+mo_gramstain(x)
+
+mo_aerobic(x)
+
+mo_type_nl(x)
+
+mo_gramstain_nl(x)
+}
+\arguments{
+\item{x}{a (vector of a) valid \code{\link{bactid}} or any text that can be coerced to a valid bactid with \code{\link{as.bactid}}}
+
+\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"bactid"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
+}
+\description{
+Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
+}
+\examples{
+# All properties
+mo_family("E. coli")       # Enterobacteriaceae
+mo_genus("E. coli")        # Escherichia
+mo_species("E. coli")      # coli
+mo_subspecies("E. coli")   # <NA>
+mo_fullname("E. coli")     # Escherichia coli
+mo_type("E. coli")         # Bacteria
+mo_gramstain("E. coli")    # Negative rods
+mo_aerobic("E. coli")      # TRUE
+mo_type_nl("E. coli")      # Bacterie
+mo_gramstain_nl("E. coli") # Negatieve staven
+
+
+# Abbreviations known in the field
+mo_genus("EHEC")           # Escherichia
+mo_species("EHEC")         # coli
+mo_subspecies("EHEC")      # EHEC
+mo_fullname("EHEC")        # Escherichia coli (EHEC)
+
+mo_genus("MRSA")           # Staphylococcus
+mo_species("MRSA")         # aureus
+mo_gramstain("MRSA")       # Positive cocci
+
+mo_genus("VISA")           # Staphylococcus
+mo_species("VISA")         # aureus
+
+
+# Known subspecies
+mo_genus("doylei")         # Campylobacter
+mo_species("doylei")       # jejuni
+mo_fullname("doylei")      # Campylobacter jejuni (doylei)
+
+
+# Anaerobic bacteria
+mo_genus("B. fragilis")    # Bacteroides
+mo_species("B. fragilis")  # fragilis
+mo_aerobic("B. fragilis")  # FALSE
+}
+\seealso{
+\code{\link{microorganisms}}
+}