From f6c47c8c88a774e03ffa4781aa5f2ed0ec39ad6d Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Sun, 9 Jun 2019 08:57:54 +0200 Subject: [PATCH] (v0.7.0.9004) pkgdown update --- DESCRIPTION | 4 +- NEWS.md | 2 +- _pkgdown.yml | 218 ++++++++++++++++++++------------------ docs/LICENSE-text.html | 9 +- docs/articles/index.html | 9 +- docs/authors.html | 9 +- docs/index.html | 9 +- docs/news/index.html | 15 +-- docs/reference/index.html | 28 +++-- git_premaster.sh | 2 + 10 files changed, 144 insertions(+), 161 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7d5f5ad4..59700dea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.7.0.9003 -Date: 2019-06-08 +Version: 0.7.0.9004 +Date: 2019-06-09 Title: Antimicrobial Resistance Analysis Authors@R: c( person( diff --git a/NEWS.md b/NEWS.md index f0dcc7c0..ddba2af4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.0.9003 +# AMR 0.7.0.9004 #### New * 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*: diff --git a/_pkgdown.yml b/_pkgdown.yml index 53aa7e2b..380e5f53 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -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" diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index fcea131b..220fe472 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004 @@ -163,13 +163,6 @@ Create frequency tables -
  • - - - - Use the G-test - -
  • diff --git a/docs/articles/index.html b/docs/articles/index.html index bdfda45d..d656272b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004 @@ -163,13 +163,6 @@ Create frequency tables
    • -
  • - - - - Use the G-test - -
  • diff --git a/docs/authors.html b/docs/authors.html index e36fa274..da65d3e6 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004 @@ -163,13 +163,6 @@ Create frequency tables
    • -
  • - - - - Use the G-test - -
  • diff --git a/docs/index.html b/docs/index.html index 6d5dc0e9..4b64e58d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004 @@ -127,13 +127,6 @@ Create frequency tables
    • -
  • - - - - Use the G-test - -
  • diff --git a/docs/news/index.html b/docs/news/index.html index cb18f148..cc8feea5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004 @@ -163,13 +163,6 @@ Create frequency tables
    • -
  • - - - - Use the G-test - -
  • @@ -239,9 +232,9 @@ -
    +

    -AMR 0.7.0.9003 Unreleased +AMR 0.7.0.9004 Unreleased

    @@ -1108,7 +1101,7 @@ Using as.mo(..., allow_uncertain = 3)

    Contents

      -
    • 0.7.0.9003
      • +
    • 0.7.0.9004
    • 0.7.0
    • 0.6.1
    • 0.6.0
      • diff --git a/docs/reference/index.html b/docs/reference/index.html index 9cf82bba..1d6d5810 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.0.9003 + 0.7.0.9004

    @@ -163,13 +163,6 @@ Create frequency tables
    • -
  • - - - - Use the G-test - -
  • @@ -555,7 +548,21 @@ -

    Deprecated functions

    +

    Extended functions

    +

    These functions are extensions of functions in other packages.

    + + + + + +

    scale_type.mo() scale_type.ab()

    + +

    Extended functions

    + + + + +

    functions

    These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.

    @@ -579,7 +586,8 @@
  • Analysing your data
  • Included data sets
  • Other functions
    • -
  • Deprecated functions
    • +
  • Extended functions
    • +
  • functions
    • diff --git a/git_premaster.sh b/git_premaster.sh index f763cb6b..d65c5491 100755 --- a/git_premaster.sh +++ b/git_premaster.sh @@ -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 "••••••••••••••••••••••••••"