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(v0.6.1.9044) first_isolate fix for species

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dr. M.S. (Matthijs) Berends
2019-05-31 14:25:11 +02:00
parent 1f8ee3ec3e
commit 493ae2ba0c
121 changed files with 586 additions and 521 deletions
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man/AMR.Rd
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@ -13,16 +13,17 @@ We created this package for both academic research and routine analysis at the F
This package can be used for:
\itemize{
\item{Reference for microorganisms, since it contains almost all 60,000 microbial (sub)species from the Catalogue of Life}
\item{Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life}
\item{Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines}
\item{Calculating antimicrobial resistance}
\item{Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)}
\item{Calculating empirical susceptibility of both mono therapy and combination therapy}
\item{Predicting future antimicrobial resistance using regression models}
\item{Getting properties for any microorganism (like Gram stain, species, genus or family)}
\item{Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)}
\item{Plotting antimicrobial resistance}
\item{Determining first isolates to be used for AMR analysis}
\item{Applying EUCAST expert rules (not the translation from MIC to RSI values)}
\item{Determining multi-drug resistant organisms (MDRO)}
\item{Applying EUCAST expert rules}
\item{Descriptive statistics: frequency tables, kurtosis and skewness}
}
}
@ -36,7 +37,7 @@ Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Gl
\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}.
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a 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}.
}
\section{Contact us}{