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(v1.2.0.9028) GitHub actions

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  1. 4
      .github/workflows/check.yaml
  2. 4
      .github/workflows/codecovr.yaml
  3. 7
      .github/workflows/lintr.yaml
  4. 9
      .gitlab-ci.yml
  5. 2
      DESCRIPTION
  6. 2
      NEWS.md
  7. 2
      docs/404.html
  8. 2
      docs/LICENSE-text.html
  9. 2
      docs/articles/index.html
  10. 2
      docs/authors.html
  11. 2
      docs/index.html
  12. 8
      docs/news/index.html
  13. 2
      docs/pkgdown.yml
  14. 2
      docs/reference/index.html
  15. 6
      vignettes/SPSS.Rmd

4
.github/workflows/check.yaml

@ -28,10 +28,10 @@ on: @@ -28,10 +28,10 @@ on:
branches:
- master
name: check
name: R-code-check
jobs:
check:
R-code-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})

4
.github/workflows/codecovr.yaml

@ -28,10 +28,10 @@ on: @@ -28,10 +28,10 @@ on:
branches:
- master
name: test-coverage
name: code-tested
jobs:
test-coverage:
code-tested:
runs-on: macOS-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

7
.github/workflows/lintr.yaml

@ -26,12 +26,13 @@ on: @@ -26,12 +26,13 @@ on:
- master
pull_request:
branches:
- premaster
- master
name: lint
name: lintr
jobs:
lint:
lintr:
runs-on: macOS-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@ -62,5 +63,5 @@ jobs: @@ -62,5 +63,5 @@ jobs:
shell: Rscript {0}
- name: Lint
run: lint_package(linters = with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R"))
run: lintr::lint_package(linters = with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R"))
shell: Rscript {0}

9
.gitlab-ci.yml

@ -3,7 +3,7 @@ @@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,12 +16,15 @@ @@ -16,12 +16,15 @@
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
# as long as GitLab used - make sure the website will be updated
stages:
- deploy
pages:
stage: website
stage: deploy
allow_failure: true
when: always
only:

2
DESCRIPTION

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
Package: AMR
Version: 1.2.0.9027
Version: 1.2.0.9028
Date: 2020-07-08
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md

@ -1,4 +1,4 @@ @@ -1,4 +1,4 @@
# AMR 1.2.0.9027
# AMR 1.2.0.9028
## <small>Last updated: 08-Jul-2020</small>
### New

2
docs/404.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

2
docs/articles/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

2
docs/authors.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

2
docs/index.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

8
docs/news/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>
@ -229,9 +229,9 @@ @@ -229,9 +229,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209027" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9027">
<a href="#amr-1209027" class="anchor"></a>AMR 1.2.0.9027<small> Unreleased </small>
<div id="amr-1209028" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9028">
<a href="#amr-1209028" class="anchor"></a>AMR 1.2.0.9028<small> Unreleased </small>
</h1>
<div id="last-updated-08-jul-2020" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml

@ -10,7 +10,7 @@ articles: @@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-08T15:02Z
last_built: 2020-07-08T18:41Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
docs/reference/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</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="Latest development version">1.2.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9028</span>
</span>
</div>

6
vignettes/SPSS.Rmd vendored

@ -33,7 +33,7 @@ As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major @@ -33,7 +33,7 @@ As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major
* **R is highly modular.**
The [official R network (CRAN)](https://cran.r-project.org/) features almost 14,000 packages at the time of writing, our `AMR` package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitLab or GitHub. So there may even be a lot more than 14,000 packages out there.
The [official R network (CRAN)](https://cran.r-project.org/) features almost 14,000 packages at the time of writing, our `AMR` package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there.
Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our `AMR` package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of *E. coli* is. Or that all species of *Klebiella* are resistant to amoxicillin and that Floxapen^&reg;^ is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration.
@ -99,13 +99,13 @@ To work with R, probably the best option is to use [RStudio](https://www.rstudio @@ -99,13 +99,13 @@ To work with R, probably the best option is to use [RStudio](https://www.rstudio
To import a data file, just click *Import Dataset* in the Environment tab:
![](https://gitlab.com/msberends/AMR/raw/master/docs/import1.png)
![](https://github.com/msberends/AMR/raw/master/docs/import1.png)
If additional packages are needed, RStudio will ask you if they should be installed on beforehand.
In the the window that opens, you can define all options (parameters) that should be used for import and you're ready to go:
![](https://gitlab.com/msberends/AMR/raw/master/docs/import2.png)
![](https://github.com/msberends/AMR/raw/master/docs/import2.png)
If you want named variables to be imported as factors so it resembles SPSS more, use `as_factor()`.

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