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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

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dr. M.S. (Matthijs) Berends
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@ -9,7 +9,7 @@
### What is `AMR` (for R)?
*(To find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html).)*
*(To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html).)*
`AMR` is a free, open-source and independent [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
@ -87,7 +87,7 @@ This package can be used for:
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org) and [List of Prokaryotic names with Standing in Nomenclature](https://lpsn.dsmz.de) ([manual](./reference/mo_property.html))
* Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines ([manual](./reference/as.rsi.html))
* Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records ([manual](./reference/ab_from_text.html))
* Determining first isolates to be used for AMR analysis ([manual](./reference/first_isolate.html))
* Determining first isolates to be used for AMR data analysis ([manual](./reference/first_isolate.html))
* Calculating antimicrobial resistance ([tutorial](./articles/AMR.html))
* Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) ([tutorial](./articles/MDR.html))
* Calculating (empirical) susceptibility of both mono therapy and combination therapies ([tutorial](./articles/AMR.html))
@ -131,7 +131,7 @@ remotes::install_github("msberends/AMR")
### Get started
To find out how to conduct AMR analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
### Short introduction
@ -185,7 +185,7 @@ The `AMR` package basically does four important things:
* Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.
* The package also contains example data sets:
* The [`example_isolates` data set](./reference/example_isolates.html). This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR analysis.
* The [`example_isolates` data set](./reference/example_isolates.html). This data set contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis.
* The [`WHONET` data set](./reference/WHONET.html). This data set only contains fake data, but with the exact same structure as files exported by WHONET. Read more about WHONET [on its tutorial page](./articles/WHONET.html).
### Copyright