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(v0.7.1.9056) mo and ab subsetting

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dr. M.S. (Matthijs) Berends
2019-08-14 14:57:06 +02:00
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@ -100,16 +100,12 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
#### Microbial (taxonomic) reference data
<img src="man/figures/logo_col.png">
This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, [www.catalogueoflife.org](http://www.catalogueoflife.org)). With `catalogue_of_life_version()` can be checked which version of the CoL is included in this package.
Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
#### Antimicrobial reference data
<div><img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p></div>
This package contains **all ~450 antimicrobial drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD, oral and IV) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the [Pharmaceuticals Community Register of the European Commission](http://ec.europa.eu/health/documents/community-register/html/atc.htm).
**NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/.**
@ -118,8 +114,6 @@ Read more about the data from WHOCC [in our manual](./reference/WHOCC.html).
#### WHONET / EARS-Net
<img src="./whonet.png">
We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an [example data set `WHONET`](./reference/WHONET.html) with the exact same structure as a WHONET export file. Furthermore, this package also contains a [data set `antibiotics`](./reference/antibiotics.html) with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.
Read our tutorial about [how to work with WHONET data here](./articles/WHONET.html).