mirror of https://github.com/msberends/AMR.git
111 lines
2.5 KiB
YAML
111 lines
2.5 KiB
YAML
|
url: https://msberends.gitlab.io
|
||
|
|
||
|
title: 'AMR (for R)'
|
||
|
|
||
|
navbar:
|
||
|
title: 'AMR (for R)'
|
||
|
left:
|
||
|
- text: 'Home'
|
||
|
icon: 'fa-home'
|
||
|
href: 'index.html'
|
||
|
- text: 'Get Started'
|
||
|
icon: 'fa-directions'
|
||
|
href: 'articles/AMR.html'
|
||
|
- text: 'Manual'
|
||
|
icon: 'fa-book-open'
|
||
|
href: 'reference/'
|
||
|
- text: 'Authors'
|
||
|
icon: 'fa-users'
|
||
|
href: 'authors.html'
|
||
|
- text: 'Changelog'
|
||
|
icon: 'far fa-newspaper'
|
||
|
href: 'news/'
|
||
|
- text: 'Source Code'
|
||
|
icon: 'fab fa-gitlab'
|
||
|
href: 'https://gitlab.com/msberends/AMR'
|
||
|
right:
|
||
|
- text: 'Licence'
|
||
|
icon: 'fa-book'
|
||
|
href: 'LICENSE-text.html'
|
||
|
|
||
|
reference:
|
||
|
- title: Cleaning your data
|
||
|
desc: >
|
||
|
Functions for cleaning and optimising your data, to be able
|
||
|
to add variables later on (like taxonomic properties) or to
|
||
|
fix and extend antibiotic interpretations by applying EUCAST rules.
|
||
|
contents:
|
||
|
- starts_with("as.")
|
||
|
- '`eucast_rules`'
|
||
|
- '`read.4D`'
|
||
|
- title: Adding variables to your data
|
||
|
desc: >
|
||
|
Functions to add new data to existing data, like the determination
|
||
|
of first isolates,
|
||
|
contents:
|
||
|
- '`first_isolate`'
|
||
|
- '`mdro`'
|
||
|
- '`key_antibiotics`'
|
||
|
- '`mo_property`'
|
||
|
- '`ab_property`'
|
||
|
- '`atc_property`'
|
||
|
- '`abname`'
|
||
|
- '`age`'
|
||
|
- '`age_groups`'
|
||
|
- '`p.symbol`'
|
||
|
- '`join`'
|
||
|
- title: Analysing your data
|
||
|
desc: >
|
||
|
Functions for conducting AMR analysis
|
||
|
contents:
|
||
|
- '`count`'
|
||
|
- '`portion`'
|
||
|
- '`freq`'
|
||
|
- '`g.test`'
|
||
|
- '`ggplot_rsi`'
|
||
|
- '`kurtosis`'
|
||
|
- '`resistance_predict`'
|
||
|
- '`rsi`'
|
||
|
- '`skewness`'
|
||
|
- title: Included data sets
|
||
|
desc: >
|
||
|
References for microorganisms and antibiotics, and even a
|
||
|
genuine data set with isolates from septic patients.
|
||
|
contents:
|
||
|
- '`antibiotics`'
|
||
|
- '`microorganisms`'
|
||
|
- '`septic_patients`'
|
||
|
- '`microorganisms.certe`'
|
||
|
- '`microorganisms.old`'
|
||
|
- '`microorganisms.umcg`'
|
||
|
- '`supplementary_data`'
|
||
|
- title: Other
|
||
|
desc: ~
|
||
|
contents:
|
||
|
- '`get_locale`'
|
||
|
- '`like`'
|
||
|
- '`mo_failures`'
|
||
|
- '`mo_renamed`'
|
||
|
|
||
|
authors:
|
||
|
Matthijs S. Berends:
|
||
|
href: https://www.rug.nl/staff/m.s.berends/
|
||
|
Christian F. Luz:
|
||
|
href: https://www.rug.nl/staff/c.f.luz/
|
||
|
Corinna Glasner:
|
||
|
href: https://www.rug.nl/staff/c.glasner/
|
||
|
Alex W. Friedrich:
|
||
|
href: https://www.rug.nl/staff/a.w.friedrich/
|
||
|
Bhanu N. M. Sinha:
|
||
|
href: https://www.rug.nl/staff/b.sinha/
|
||
|
|
||
|
template:
|
||
|
assets: pkgdown/logos
|
||
|
params:
|
||
|
noindex: false
|
||
|
bootswatch: flatly
|
||
|
docsearch:
|
||
|
# using algolia.com
|
||
|
api_key: 'f737050abfd4d726c63938e18f8c496e'
|
||
|
index_name: 'amr'
|