mirror of
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(v0.7.0.9004) pkgdown update
This commit is contained in:
parent
ec48f1d83b
commit
f6c47c8c88
@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.7.0.9003
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Date: 2019-06-08
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Version: 0.7.0.9004
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Date: 2019-06-09
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 0.7.0.9003
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# AMR 0.7.0.9004
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#### New
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* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
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218
_pkgdown.yml
218
_pkgdown.yml
@ -19,152 +19,160 @@
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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title: 'AMR (for R)'
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url: 'https://msberends.gitlab.io/AMR'
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title: "AMR (for R)"
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url: "https://msberends.gitlab.io/AMR"
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development:
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mode: release # improves indexing by search engines
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mode: "release" # improves indexing by search engines
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version_tooltip: "Latest development version"
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news:
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one_page: true
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navbar:
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title: 'AMR (for R)'
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title: "AMR (for R)"
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left:
|
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- text: 'Home'
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icon: 'fa-home'
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href: 'index.html'
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- text: 'How to'
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icon: 'fa-question-circle'
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- text: "Home"
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icon: "fa-home"
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href: "index.html"
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- text: "How to"
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icon: "fa-question-circle"
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menu:
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- text: 'Conduct AMR analysis'
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icon: 'fa-directions'
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href: 'articles/AMR.html'
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- text: 'Predict antimicrobial resistance'
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icon: 'fa-dice'
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href: 'articles/resistance_predict.html'
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- text: 'Determine multi-drug resistance (MDR)'
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icon: 'fa-skull-crossbones'
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href: 'articles/MDR.html'
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- text: 'Work with WHONET data'
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icon: 'fa-globe-americas'
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href: 'articles/WHONET.html'
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- text: 'Import data from SPSS/SAS/Stata'
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icon: 'fa-file-upload'
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href: 'articles/SPSS.html'
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- text: 'Apply EUCAST rules'
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icon: 'fa-exchange-alt'
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href: 'articles/EUCAST.html'
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- text: 'Get properties of a microorganism'
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icon: 'fa-bug'
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href: 'reference/mo_property.html' # reference instead of article
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- text: 'Get properties of an antibiotic'
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icon: 'fa-capsules'
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href: 'reference/ab_property.html' # reference instead of article
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- text: 'Create frequency tables'
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icon: 'fa-sort-amount-down'
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href: 'articles/freq.html'
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- text: 'Use the G-test'
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icon: 'fa-clipboard-check'
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href: 'reference/g.test.html' # reference instead of article
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- text: 'Other: benchmarks'
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icon: 'fa-shipping-fast'
|
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href: 'articles/benchmarks.html'
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- text: 'Manual'
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icon: 'fa-book-open'
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href: 'reference/'
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- text: 'Authors'
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icon: 'fa-users'
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href: 'authors.html'
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- text: 'Changelog'
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icon: 'far fa-newspaper'
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href: 'news/'
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- text: "Conduct AMR analysis"
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icon: "fa-directions"
|
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href: "articles/AMR.html"
|
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- text: "Predict antimicrobial resistance"
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icon: "fa-dice"
|
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href: "articles/resistance_predict.html"
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- text: "Determine multi-drug resistance (MDR)"
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icon: "fa-skull-crossbones"
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href: "articles/MDR.html"
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- text: "Work with WHONET data"
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icon: "fa-globe-americas"
|
||||
href: "articles/WHONET.html"
|
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- text: "Import data from SPSS/SAS/Stata"
|
||||
icon: "fa-file-upload"
|
||||
href: "articles/SPSS.html"
|
||||
- text: "Apply EUCAST rules"
|
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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
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- text: "Create frequency tables"
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||||
icon: "fa-sort-amount-down"
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href: "articles/freq.html"
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# - text: "Use the G-test"
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# icon: "fa-clipboard-check"
|
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# href: "reference/g.test.html" # reference instead of article
|
||||
- text: "Other: benchmarks"
|
||||
icon: "fa-shipping-fast"
|
||||
href: "articles/benchmarks.html"
|
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- text: "Manual"
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icon: "fa-book-open"
|
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href: "reference/"
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- text: "Authors"
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||||
icon: "fa-users"
|
||||
href: "authors.html"
|
||||
- text: "Changelog"
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icon: "far fa-newspaper"
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href: "news/"
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right:
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- text: 'Source Code'
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icon: 'fab fa-gitlab'
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href: 'https://gitlab.com/msberends/AMR'
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- text: 'Licence'
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||||
icon: 'fa-book'
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href: 'LICENSE-text.html'
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- text: "Source Code"
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||||
icon: "fab fa-gitlab"
|
||||
href: "https://gitlab.com/msberends/AMR"
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- text: "Licence"
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||||
icon: "fa-book"
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href: "LICENSE-text.html"
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reference:
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- title: 'Background information'
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- title: "Background information"
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desc: >
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Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
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for more information about how to work with functions in this package.
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contents:
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- '`AMR`'
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- '`catalogue_of_life`'
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- '`catalogue_of_life_version`'
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- '`WHOCC`'
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- title: 'Cleaning your data'
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- "`AMR`"
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- "`catalogue_of_life`"
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- "`catalogue_of_life_version`"
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- "`WHOCC`"
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- title: "Cleaning your data"
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desc: >
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Functions for cleaning and optimising your data, to be able to add
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variables later on (like taxonomic properties) or to fix and extend
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antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
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contents:
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- starts_with("as.")
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- '`mo_source`'
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- '`eucast_rules`'
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- '`rsi_translation`'
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- '`guess_ab_col`'
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- '`read.4D`'
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- title: 'Adding variables to your data'
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- "`mo_source`"
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- "`eucast_rules`"
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- "`rsi_translation`"
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- "`guess_ab_col`"
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- "`read.4D`"
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- title: "Adding variables to your data"
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desc: >
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Functions to add new data to existing data, like the determination
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of first isolates, multi-drug resistant microorganisms (MDRO), getting
|
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properties of microorganisms or antibiotics and determining the age of
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patients or divide ages into age groups.
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contents:
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- '`first_isolate`'
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- '`mdro`'
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- '`key_antibiotics`'
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||||
- '`mo_property`'
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||||
- '`ab_property`'
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||||
- '`age`'
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- '`age_groups`'
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- '`p.symbol`'
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||||
- '`join`'
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- '`atc_online_property`'
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||||
- title: 'Analysing your data'
|
||||
- "`first_isolate`"
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- "`mdro`"
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- "`key_antibiotics`"
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- "`mo_property`"
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- "`ab_property`"
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- "`age`"
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- "`age_groups`"
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||||
- "`p.symbol`"
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||||
- "`join`"
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||||
- "`atc_online_property`"
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- title: "Analysing your data"
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||||
desc: >
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||||
Functions for conducting AMR analysis, like counting isolates, calculating
|
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resistance or susceptibility, creating frequency tables or make plots.
|
||||
contents:
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||||
- '`availability`'
|
||||
- '`count`'
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||||
- '`portion`'
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||||
- '`filter_ab_class`'
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||||
- '`freq`'
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||||
- '`g.test`'
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||||
- '`ggplot_rsi`'
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||||
- '`kurtosis`'
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||||
- '`resistance_predict`'
|
||||
- '`skewness`'
|
||||
- title: 'Included data sets'
|
||||
- "`availability`"
|
||||
- "`count`"
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||||
- "`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"
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -163,13 +163,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -163,13 +163,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -163,13 +163,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
@ -42,7 +42,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -127,13 +127,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -163,13 +163,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -239,9 +232,9 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0709003" class="section level1">
|
||||
<div id="amr-0709004" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0709003" class="anchor"></a>AMR 0.7.0.9003<small> Unreleased </small>
|
||||
<a href="#amr-0709004" class="anchor"></a>AMR 0.7.0.9004<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="new" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
@ -1108,7 +1101,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0709003">0.7.0.9003</a></li>
|
||||
<li><a href="#amr-0709004">0.7.0.9004</a></li>
|
||||
<li><a href="#amr-070">0.7.0</a></li>
|
||||
<li><a href="#amr-061">0.6.1</a></li>
|
||||
<li><a href="#amr-060">0.6.0</a></li>
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9004</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -163,13 +163,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -555,7 +548,21 @@
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
|
||||
<h2 id="section-extended-functions" class="hasAnchor"><a href="#section-extended-functions" class="anchor"></a>Extended functions</h2>
|
||||
<p class="section-desc"><p>These functions are extensions of functions in other packages.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
<tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="extended-functions.html">scale_type.mo()</a></code> <code><a href="extended-functions.html">scale_type.ab()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Extended functions</p></td>
|
||||
</tr>
|
||||
</tbody><tbody>
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-functions" class="hasAnchor"><a href="#section-functions" class="anchor"></a>functions</h2>
|
||||
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
@ -579,7 +586,8 @@
|
||||
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
|
||||
<li><a href="#section-included-data-sets">Included data sets</a></li>
|
||||
<li><a href="#section-other-functions">Other functions</a></li>
|
||||
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
|
||||
<li><a href="#section-extended-functions">Extended functions</a></li>
|
||||
<li><a href="#section-functions">functions</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -52,7 +52,9 @@ echo "••••••••••••••••••••••••
|
||||
echo "• Reloading/documenting package •"
|
||||
echo "•••••••••••••••••••••••••••••••••"
|
||||
Rscript -e "devtools::load_all(quiet = TRUE)"
|
||||
echo "Documenting..."
|
||||
Rscript -e "suppressMessages(devtools::document())"
|
||||
echo "Installing..."
|
||||
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
||||
echo
|
||||
echo "••••••••••••••••••••••••••"
|
||||
|
||||
Loading…
Reference in New Issue
Block a user