P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 21:41:55 +02:00
Code Releases Activity

(v0.8.0.9027) adding susceptibility() and resistance()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-10 12:16:56 +01:00
parent 228a4245cb
commit 59ededa8dc
85 changed files with 1526 additions and 932 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
man/AMR.Rd
View File

@ -13,28 +13,19 @@ 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 all microbial (sub)species from the Catalogue of Life}
\item{Reference for the taxonomy of microorganisms, since the package 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{Determining first isolates to be used for AMR analysis}
\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{Calculating (empirical) susceptibility of both mono therapy and combination therapies}
\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{Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem 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}
\item{Descriptive statistics: frequency tables, kurtosis and skewness}
}
}
\section{Authors}{
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
}
\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 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}.