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dr. M.S. (Matthijs) Berends 2020-07-08 20:43:25 +02:00
parent 5195e0b9da
commit d39d32448b
15 changed files with 30 additions and 26 deletions
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4
.github/workflows/check.yaml vendored
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@ -28,10 +28,10 @@ on:
branches: branches:
- master - master
name: check name: R-code-check
jobs: jobs:
check: R-code-check:
runs-on: ${{ matrix.config.os }} runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) name: ${{ matrix.config.os }} (${{ matrix.config.r }})

4
.github/workflows/codecovr.yaml vendored
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@ -28,10 +28,10 @@ on:
branches: branches:
- master - master
name: test-coverage name: code-tested
jobs: jobs:
test-coverage: code-tested:
runs-on: macOS-latest runs-on: macOS-latest
env: env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

7
.github/workflows/lintr.yaml vendored
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@ -26,12 +26,13 @@ on:
- master - master
pull_request: pull_request:
branches: branches:
- premaster
- master - master
name: lint name: lintr
jobs: jobs:
lint: lintr:
runs-on: macOS-latest runs-on: macOS-latest
env: env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@ -62,5 +63,5 @@ jobs:
shell: Rscript {0} shell: Rscript {0}
- name: Lint - 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} shell: Rscript {0}

9
.gitlab-ci.yml
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis # # Antimicrobial Resistance (AMR) Analysis #
# # # #
# SOURCE # # SOURCE #
# https://gitlab.com/msberends/AMR # # https://github.com/msberends/AMR #
# # # #
# LICENCE # # LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. # # (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,12 +16,15 @@
# We created this package for both routine data analysis and academic # # We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be # # research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # 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 # as long as GitLab used - make sure the website will be updated
stages:
- deploy
pages: pages:
stage: website stage: deploy
allow_failure: true allow_failure: true
when: always when: always
only: only:

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.2.0.9027 Version: 1.2.0.9028
Date: 2020-07-08 Date: 2020-07-08
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.2.0.9027 # AMR 1.2.0.9028
## <small>Last updated: 08-Jul-2020</small> ## <small>Last updated: 08-Jul-2020</small>
### New ### New

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209027" class="section level1"> <div id="amr-1209028" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9027"> <h1 class="page-header" data-toc-text="1.2.0.9028">
<a href="#amr-1209027" class="anchor"></a>AMR 1.2.0.9027<small> Unreleased </small> <a href="#amr-1209028" class="anchor"></a>AMR 1.2.0.9028<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-08-jul-2020" class="section level2"> <div id="last-updated-08-jul-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-07-08T15:02Z last_built: 2020-07-08T18:41Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

6
vignettes/SPSS.Rmd
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@ -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.** * **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. 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
To import a data file, just click *Import Dataset* in the Environment tab: 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. 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: 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()`. If you want named variables to be imported as factors so it resembles SPSS more, use `as_factor()`.