P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 11:01:57 +02:00
Code Releases Activity

EUCAST update, as.mo bugfix for empty vlaues

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

1
vignettes/AMR.Rmd
View File

@ -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
View File

@ -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)*

3
vignettes/G_test.Rmd
View File

@ -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))*

1
vignettes/Predict.Rmd
View File

@ -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

1
vignettes/ab_property.Rmd
View File

@ -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

1
vignettes/freq.Rmd
View File

@ -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

1
vignettes/mo_property.Rmd
View File

@ -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