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(v0.9.0.9016) Support SNOMED codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-01-27 19:14:23 +01:00
parent 42b079cdb7
commit a13c62e6e8
31 changed files with 456 additions and 342 deletions
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9
man/as.mo.Rd
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@ -175,10 +175,11 @@ as.mo("S aureus")
as.mo("Staphylococcus aureus")
as.mo("Staphylococcus aureus (MRSA)")
as.mo("Zthafilokkoockus oureuz") # handles incorrect spelling
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(22242419) # Catalogue of Life ID
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(22242419) # Catalogue of Life ID
as.mo(115329001) # SNOMED CT code
# Dyslexia is no problem - these all work:
as.mo("Ureaplasma urealyticum")

2
man/example_isolates.Rd
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@ -15,7 +15,7 @@
\item \code{gender}\cr gender of the patient
\item \code{patient_id}\cr ID of the patient
\item \code{mo}\cr ID of microorganism created with \code{\link[=as.mo]{as.mo()}}, see also \link{microorganisms}
\item \code{PEN:RIF}\cr 40 different antibiotics with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}}); these column names occur in \link{antibiotics} data set and can be translated with \code{\link[=ab_name]{ab_name()}}
\item \code{PEN:RIF}\cr 40 different antibiotics with class \code{\link{rsi}} (see \code{\link[=as.rsi]{as.rsi()}}); these column names occur in the \link{antibiotics} data set and can be translated with \code{\link[=ab_name]{ab_name()}}
}}
\usage{
example_isolates

3
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,447 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,447 observations and 17 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{col_id}\cr Catalogue of Life ID
@ -15,6 +15,7 @@
\item \code{species_id}\cr ID of the species as used by the Catalogue of Life
\item \code{source}\cr Either "CoL", "DSMZ" (see Source) or "manually added"
\item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
\item \code{snomed}\cr SNOMED code of the microorganism. Use \code{\link[=mo_snomed]{mo_snomed()}} to retrieve it quickly, see \code{\link[=mo_property]{mo_property()}}.
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).

7
man/mo_property.Rd
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@ -15,6 +15,7 @@
\alias{mo_kingdom}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_snomed}
\alias{mo_ref}
\alias{mo_authors}
\alias{mo_year}
@ -51,6 +52,8 @@ mo_type(x, language = get_locale(), ...)
mo_gramstain(x, language = get_locale(), ...)
mo_snomed(x, ...)
mo_ref(x, ...)
mo_authors(x, ...)
@ -85,6 +88,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\item An \code{\link{integer}} in case of \code{\link[=mo_year]{mo_year()}}
\item A \code{\link{list}} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
\item A named \code{\link{character}} in case of \code{\link[=mo_url]{mo_url()}}
\item A \code{\link{double}} in case of \code{\link[=mo_snomed]{mo_snomed()}}
\item A \code{\link{character}} in all other cases
}
}
@ -141,11 +145,12 @@ mo_subspecies("E. coli") # ""
# colloquial properties ----------------------------------------------------
mo_name("E. coli") # "Escherichia coli"
mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
mo_fullname("E. coli") # "Escherichia coli" - same as mo_name()
mo_shortname("E. coli") # "E. coli"
# other properties ---------------------------------------------------------
mo_gramstain("E. coli") # "Gram-negative"
mo_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes)
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
mo_rank("E. coli") # "species"
mo_url("E. coli") # get the direct url to the online database entry

7
man/rsi_translation.Rd
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@ -3,7 +3,7 @@
\docType{data}
\name{rsi_translation}
\alias{rsi_translation}
\title{Data set for RSI interpretation}
\title{Data set for R/SI interpretation}
\format{A \code{\link{data.frame}} with 13,975 observations and 9 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
@ -20,7 +20,10 @@
rsi_translation
}
\description{
Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to RSI values.
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \link{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
}
\section{Read more on our website!}{