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(v0.7.0.9004) pkgdown update

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dr. M.S. (Matthijs) Berends
2019-06-09 08:57:54 +02:00
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commit f6c47c8c88
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_pkgdown.yml
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@ -19,152 +19,160 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR'
title: "AMR (for R)"
url: "https://msberends.gitlab.io/AMR"
development:
mode: release # improves indexing by search engines
mode: "release" # improves indexing by search engines
version_tooltip: "Latest development version"
news:
one_page: true
navbar:
title: 'AMR (for R)'
title: "AMR (for R)"
left:
- text: 'Home'
icon: 'fa-home'
href: 'index.html'
- text: 'How to'
icon: 'fa-question-circle'
- text: "Home"
icon: "fa-home"
href: "index.html"
- text: "How to"
icon: "fa-question-circle"
menu:
- text: 'Conduct AMR analysis'
icon: 'fa-directions'
href: 'articles/AMR.html'
- text: 'Predict antimicrobial resistance'
icon: 'fa-dice'
href: 'articles/resistance_predict.html'
- text: 'Determine multi-drug resistance (MDR)'
icon: 'fa-skull-crossbones'
href: 'articles/MDR.html'
- text: 'Work with WHONET data'
icon: 'fa-globe-americas'
href: 'articles/WHONET.html'
- text: 'Import data from SPSS/SAS/Stata'
icon: 'fa-file-upload'
href: 'articles/SPSS.html'
- text: 'Apply EUCAST rules'
icon: 'fa-exchange-alt'
href: 'articles/EUCAST.html'
- text: 'Get properties of a microorganism'
icon: 'fa-bug'
href: 'reference/mo_property.html' # reference instead of article
- text: 'Get properties of an antibiotic'
icon: 'fa-capsules'
href: 'reference/ab_property.html' # reference instead of article
- text: 'Create frequency tables'
icon: 'fa-sort-amount-down'
href: 'articles/freq.html'
- text: 'Use the G-test'
icon: 'fa-clipboard-check'
href: 'reference/g.test.html' # reference instead of article
- text: 'Other: benchmarks'
icon: 'fa-shipping-fast'
href: 'articles/benchmarks.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: "Conduct AMR analysis"
icon: "fa-directions"
href: "articles/AMR.html"
- text: "Predict antimicrobial resistance"
icon: "fa-dice"
href: "articles/resistance_predict.html"
- text: "Determine multi-drug resistance (MDR)"
icon: "fa-skull-crossbones"
href: "articles/MDR.html"
- text: "Work with WHONET data"
icon: "fa-globe-americas"
href: "articles/WHONET.html"
- text: "Import data from SPSS/SAS/Stata"
icon: "fa-file-upload"
href: "articles/SPSS.html"
- text: "Apply EUCAST rules"
icon: "fa-exchange-alt"
href: "articles/EUCAST.html"
- text: "Get properties of a microorganism"
icon: "fa-bug"
href: "reference/mo_property.html" # reference instead of article
- text: "Get properties of an antibiotic"
icon: "fa-capsules"
href: "reference/ab_property.html" # reference instead of article
- text: "Create frequency tables"
icon: "fa-sort-amount-down"
href: "articles/freq.html"
# - text: "Use the G-test"
# icon: "fa-clipboard-check"
# href: "reference/g.test.html" # reference instead of article
- text: "Other: benchmarks"
icon: "fa-shipping-fast"
href: "articles/benchmarks.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/"
right:
- text: 'Source Code'
icon: 'fab fa-gitlab'
href: 'https://gitlab.com/msberends/AMR'
- text: 'Licence'
icon: 'fa-book'
href: 'LICENSE-text.html'
- text: "Source Code"
icon: "fab fa-gitlab"
href: "https://gitlab.com/msberends/AMR"
- text: "Licence"
icon: "fa-book"
href: "LICENSE-text.html"
reference:
- title: 'Background information'
- title: "Background information"
desc: >
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
for more information about how to work with functions in this package.
contents:
- '`AMR`'
- '`catalogue_of_life`'
- '`catalogue_of_life_version`'
- '`WHOCC`'
- title: 'Cleaning your data'
- "`AMR`"
- "`catalogue_of_life`"
- "`catalogue_of_life_version`"
- "`WHOCC`"
- 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](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
contents:
- starts_with("as.")
- '`mo_source`'
- '`eucast_rules`'
- '`rsi_translation`'
- '`guess_ab_col`'
- '`read.4D`'
- title: 'Adding variables to your data'
- "`mo_source`"
- "`eucast_rules`"
- "`rsi_translation`"
- "`guess_ab_col`"
- "`read.4D`"
- title: "Adding variables to your data"
desc: >
Functions to add new data to existing data, like the determination
of first isolates, multi-drug resistant microorganisms (MDRO), getting
properties of microorganisms or antibiotics and determining the age of
patients or divide ages into age groups.
contents:
- '`first_isolate`'
- '`mdro`'
- '`key_antibiotics`'
- '`mo_property`'
- '`ab_property`'
- '`age`'
- '`age_groups`'
- '`p.symbol`'
- '`join`'
- '`atc_online_property`'
- title: 'Analysing your data'
- "`first_isolate`"
- "`mdro`"
- "`key_antibiotics`"
- "`mo_property`"
- "`ab_property`"
- "`age`"
- "`age_groups`"
- "`p.symbol`"
- "`join`"
- "`atc_online_property`"
- title: "Analysing your data"
desc: >
Functions for conducting AMR analysis, like counting isolates, calculating
resistance or susceptibility, creating frequency tables or make plots.
contents:
- '`availability`'
- '`count`'
- '`portion`'
- '`filter_ab_class`'
- '`freq`'
- '`g.test`'
- '`ggplot_rsi`'
- '`kurtosis`'
- '`resistance_predict`'
- '`skewness`'
- title: 'Included data sets'
- "`availability`"
- "`count`"
- "`portion`"
- "`filter_ab_class`"
- "`freq`"
- "`g.test`"
- "`ggplot_rsi`"
- "`kurtosis`"
- "`resistance_predict`"
- "`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`'
- '`WHONET`'
- '`microorganisms.codes`'
- '`microorganisms.old`'
- "`antibiotics`"
- "`microorganisms`"
- "`septic_patients`"
- "`WHONET`"
- "`microorganisms.codes`"
- "`microorganisms.old`"
- title: Other functions
desc: >
These functions are mostly for internal use, but some of
them may also be suitable for your analysis. Especially the
'like' function can be useful: `if (x %like% y) {...}`.
contents:
- '`get_locale`'
- '`like`'
- title: Deprecated functions
- "`get_locale`"
- "`like`"
- title: Extended functions
desc: >
These functions are extensions of functions in other packages.
contents:
- "`extended-functions`"
- title: functions
desc: >
These functions are deprecated, meaning that they still
work but show a warning with every use and will be removed
in a future version.
contents:
- '`AMR-deprecated`'
- "`AMR-deprecated`"
authors:
Matthijs S. Berends:
@ -179,11 +187,11 @@ authors:
href: https://www.rug.nl/staff/b.sinha/
template:
assets: pkgdown/logos # use logos in this folder
assets: "pkgdown/logos" # use logos in this folder
params:
noindex: false
bootswatch: flatly
bootswatch: "flatly"
docsearch:
# using algolia.com
api_key: 'f737050abfd4d726c63938e18f8c496e'
index_name: 'amr'
api_key: "f737050abfd4d726c63938e18f8c496e"
index_name: "amr"