(v1.1.0.9000) CLSI as.rsi() fix, better vctrs support, new CI

man/AMR-vctrs.Rd

@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vctrs.R
+\name{AMR-vctrs}
+\alias{AMR-vctrs}
+\alias{vec_ptype2.mo}
+\alias{vec_cast.mo}
+\alias{vec_ptype2.ab}
+\alias{vec_cast.ab}
+\title{\code{vctrs} methods}
+\usage{
+vec_ptype2.mo(x, y, ...)
+
+vec_cast.mo(x, to, ...)
+
+vec_ptype2.ab(x, y, ...)
+
+vec_cast.ab(x, to, ...)
+}
+\description{
+These methods are needed to support methods used by the tidyverse, like joining and transforming data, with new classes that come with this package.
+}
+\section{Stable lifecycle}{
+
+\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
+The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, we are largely happy with the unlying code, and major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; we will avoid removing arguments or changing the meaning of existing arguments.
+
+If the unlying code needs breaking changes, they will occur gradually. To begin with, the function or argument will be deprecated; it will continue to work but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+}
+
+\section{Read more on our website!}{
+
+On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
+}
+
+\keyword{internal}

man/antibiotics.Rd

@@ -68,7 +68,7 @@ These data sets are available as 'flat files' for use even without R - you can f
 \item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
 }
 
-Files in R format (which data structure) can be found here:
+Files in R format (with preserved data structure) can be found here:
 \itemize{
 \item \url{https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda}
 \item \url{https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda}

man/microorganisms.Rd

@@ -48,7 +48,7 @@ This data set is available as 'flat file' for use even without R - you can find
 \item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
 }
 
-The file in R format (which data structure) can be found here:
+The file in R format (with preserved data structure) can be found here:
 \itemize{
 \item \url{https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda}
 }

man/mo_property.Rd

@@ -103,6 +103,8 @@ All functions will return the most recently known taxonomic property according t
 \item \code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)
 }
 
+The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always returns the first character of the genus and the full species, like \emph{"E. coli"}. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like \emph{"CoNS"} (Coagulase-Negative Staphylococci) and \emph{"GBS"} (Group B Streptococci).
+
 The Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
 
 All output will be \link{translate}d where possible.