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(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
parent f553a08a7b
commit e2aa4f996b
53 changed files with 636 additions and 475 deletions
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34
man/as.mo.Rd
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@ -34,7 +34,7 @@ clear_mo_history(...)
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
\item{allow_uncertain}{a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details}
\item{allow_uncertain}{a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less probable results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
@ -50,16 +50,16 @@ Use this function to determine a valid microorganism ID (\code{mo}). Determinati
\strong{General info} \cr
A microorganism ID from this package (class: \code{mo}) typically looks like these examples:\cr
\preformatted{
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNE Klebsiella pneumoniae
B_KLBSL_PNE_RHI Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ----> subspecies, a 3-4 letter acronym
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---> subspecies, a 4-5 letter acronym
| | ----> species, a 4-5 letter acronym
| ----> genus, a 5-7 letter acronym
----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
}
@ -105,7 +105,7 @@ You can also use e.g. \code{as.mo(..., allow_uncertain = 1)} to only allow up to
Examples:
\itemize{
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRB}) needs review.}
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRPB}) needs review.}
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GON}) needs review.}
}
@ -154,7 +154,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
\examples{
\donttest{
# These examples all return "B_STPHY_AUR", the ID of S. aureus:
# These examples all return "B_STPHY_AURS", the ID of S. aureus:
as.mo("sau") # WHONET code
as.mo("stau")
as.mo("STAU")
@ -179,11 +179,11 @@ as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
as.mo("GBS") # Group B Streptococci
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. epidermidis") # will remain species: B_STPHY_EPDR
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CONS
as.mo("S. pyogenes") # will remain species: B_STRPT_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
as.mo("S. pyogenes") # will remain species: B_STRPT_PYGN
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA
# All mo_* functions use as.mo() internally too (see ?mo_property):
mo_genus("E. coli") # returns "Escherichia"

6
man/example_isolates.Rd
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@ -3,7 +3,7 @@
\docType{data}
\name{example_isolates}
\alias{example_isolates}
\title{Data set with 2,000 blood culture isolates from septic patients}
\title{Data set with 2,000 blood culture isolates}
\format{A \code{\link{data.frame}} with 2,000 observations and 49 variables:
\describe{
\item{\code{date}}{date of receipt at the laboratory}
@ -15,13 +15,13 @@
\item{\code{gender}}{gender of the patient}
\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
\item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
\item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{ab_name}}}
\item{\code{PEN:RIF}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{ab_name}}}
}}
\usage{
example_isolates
}
\description{
An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found 4 different hospitals in the Netherlands, between 2001 and 2017. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
}
\section{Read more on our website!}{

4
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 69,855 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,460 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -34,7 +34,7 @@ Manually added were:
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
\item{22,654 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) overwriting records from the Catalogue of Life, since the DSMZ contain the latest taxonomic information based on recent publications}
}
}
\section{About the records from DSMZ (see source)}{

6
man/microorganisms.codes.Rd
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@ -3,10 +3,10 @@
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for microorganism codes}
\format{A \code{\link{data.frame}} with 4,965 observations and 2 variables:
\title{Translation table for common microorganism codes}
\format{A \code{\link{data.frame}} with 4,927 observations and 2 variables:
\describe{
\item{\code{certe}}{Commonly used code of a microorganism}
\item{\code{code}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}
}}
\usage{

2
man/microorganisms.old.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 22,932 observations and 4 variables:
\format{A \code{\link{data.frame}} with 24,246 observations and 4 variables:
\describe{
\item{\code{col_id}}{Catalogue of Life ID that was originally given}
\item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}