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EUCAST update, as.mo bugfix for empty vlaues

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dr. M.S. (Matthijs) Berends
2019-01-08 16:23:45 +01:00
parent a0055c7efe
commit 193a2d2863
54 changed files with 1504 additions and 972 deletions
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1
vignettes/AMR.Rmd
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@ -1,6 +1,7 @@
---
title: "How to conduct AMR analysis"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true

3
vignettes/EUCAST.Rmd
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@ -1,6 +1,7 @@
---
title: "How to apply EUCAST rules"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true
@ -30,7 +31,7 @@ What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Te
> *EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.*
In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the `eucast_rules()` function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.
In Europe, a lot of medical microbiological laboratories already apply these rules ([Brown *et al.*, 2015](https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008)). Our package features their latest insights on intrinsic resistance and exceptional phenotypes (version 9.0, 2019). Moreover, the `eucast_rules()` function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.
*(more will be available soon)*

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vignettes/G_test.Rmd
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@ -1,6 +1,7 @@
---
title: "How to use the *G*-test"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true
@ -21,4 +22,4 @@ knitr::opts_chunk$set(
Sys.setlocale(locale = "C")
```
*(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./reference/g.test.html))*
*(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./../reference/g.test.html))*

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vignettes/Predict.Rmd
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@ -1,6 +1,7 @@
---
title: "How to predict antimicrobial resistance"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true

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vignettes/ab_property.Rmd
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@ -1,6 +1,7 @@
---
title: "How to get properties of an antibiotic"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true

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vignettes/freq.Rmd
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@ -1,6 +1,7 @@
---
title: "How to create frequency tables"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true

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vignettes/mo_property.Rmd
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@ -1,6 +1,7 @@
---
title: "How to get properties of a microorganism"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true