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(v1.0.0.9007) small doc fix

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dr. M.S. (Matthijs) Berends
2020-02-22 17:03:47 +01:00
parent 0595af2801
commit 0d5e78b2cf
21 changed files with 48 additions and 60 deletions
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2
man/example_isolates_unclean.Rd
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@ -16,7 +16,7 @@
example_isolates_unclean
}
\description{
A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
}
\section{Read more on our website!}{

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man/filter_ab_class.Rd
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@ -54,7 +54,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
}
\description{
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
}
\details{
The \code{group} column in \link{antibiotics} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \link{antibiotics} data set.

8
man/first_isolate.Rd
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@ -125,6 +125,14 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
}
}
\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}.