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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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man/microorganisms.codes.Rd
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@ -5,7 +5,7 @@
\alias{microorganisms.codes}
\title{Data Set with 5,604 Common Microorganism Codes}
\format{
A \link{data.frame} with 5,604 observations and 2 variables:
A [tibble\link[tibble:tibble]{tibble::tibble} with 5,604 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
@ -17,11 +17,9 @@ microorganisms.codes
\description{
A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link[=set_mo_source]{set_mo_source()}}. They will all be searched when using \code{\link[=as.mo]{as.mo()}} and consequently all the \code{\link[=mo_property]{mo_*}} functions.
}
\section{Reference Data Publicly Available}{
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.
\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
@ -31,7 +29,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
}
\examples{
head(microorganisms.codes)
microorganisms.codes
}
\seealso{
\code{\link[=as.mo]{as.mo()}} \link{microorganisms}