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add all options to documentation

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dr. M.S. (Matthijs) Berends
2023-01-23 20:07:57 +01:00
parent 19fd0ef121
commit eef00069fd
31 changed files with 207 additions and 104 deletions
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34
_pkgdown.yml
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@ -72,37 +72,40 @@ navbar:
- text: "How to"
icon: "fa-question-circle"
menu:
- text: "Conduct AMR analysis"
- text: "User- Or Team-specific Package Settings"
icon: "fa-gear"
href: "reference/AMR-options.html"
- text: "Conduct AMR Analysis"
icon: "fa-directions"
href: "articles/AMR.html"
- text: "Predict antimicrobial resistance"
- text: "Predict Antimicrobial Resistance"
icon: "fa-dice"
href: "articles/resistance_predict.html"
- text: "Data sets for download / own use"
- text: "Data Sets for Download / Own Use"
icon: "fa-database"
href: "articles/datasets.html"
- text: "Conduct principal component analysis for AMR"
- text: "Conduct Principal Component Analysis for AMR"
icon: "fa-compress"
href: "articles/PCA.html"
- text: "Determine multi-drug resistance (MDR)"
- text: "Determine Multi-Drug Resistance (MDR)"
icon: "fa-skull-crossbones"
href: "articles/MDR.html"
- text: "Work with WHONET data"
- text: "Work with WHONET Data"
icon: "fa-globe-americas"
href: "articles/WHONET.html"
- text: "Import data from SPSS/SAS/Stata"
- text: "Import Data From SPSS/SAS/Stata"
icon: "fa-file-upload"
href: "articles/SPSS.html"
- text: "Apply EUCAST rules"
- text: "Apply Eucast Rules"
icon: "fa-exchange-alt"
href: "articles/EUCAST.html"
- text: "Get taxonomy of a microorganism"
- text: "Get Taxonomy of a Microorganism"
icon: "fa-bug"
href: "reference/mo_property.html" # reference instead of an article
- text: "Get properties of an antibiotic drug"
- text: "Get Properties of an Antibiotic Drug"
icon: "fa-capsules"
href: "reference/ab_property.html" # reference instead of an article
- text: "Get properties of an antiviral drug"
- text: "Get Properties of an Antiviral Drug"
icon: "fa-capsules"
href: "reference/av_property.html" # reference instead of an article
- text: "Manual"
@ -176,6 +179,15 @@ reference:
- "`resistance_predict`"
- "`guess_ab_col`"
- title: "Other: AMR-specific options"
desc: >
The AMR package is customisable, by providing settings that can be set per user or per team. For
example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported
language can be set for the whole team (system-language independent) for antibiotic names in a
foreign language.
contents:
- "`AMR-options`"
- title: "Other: antiviral drugs"
desc: >
This package also provides extensive support for antiviral agents, even though it is not the primary