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AMR
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(v1.2.0.9027) move to github

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-07-08 17:48:57 +02:00
parent 76fc8e1b14
commit 5195e0b9da
17 changed files with 77 additions and 76 deletions
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10
.github/workflows/R-CMD-check.yaml → .github/workflows/check.yaml vendored
View File

@ -28,10 +28,10 @@ on:
branches:
- master
name: R-CMD-check
name: check
jobs:
R-CMD-check:
check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@ -43,9 +43,9 @@ jobs:
- {os: windows-latest, r: 'release'}
- {os: macOS-latest, r: 'release'}
- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'oldrel'}
- {os: macOS-latest, r: 'oldrel'}
- {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: windows-latest, r: 'oldrel'}
# - {os: macOS-latest, r: 'oldrel'}
# - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'devel'}
- {os: macOS-latest, r: 'devel'}
- {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

2
.github/workflows/codecovr.yaml vendored
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@ -64,5 +64,5 @@ jobs:
shell: Rscript {0}
- name: Test coverage
run: covr::codecov()
run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"))
shell: Rscript {0}

2
.github/workflows/lintr.yaml vendored
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@ -62,5 +62,5 @@ jobs:
shell: Rscript {0}
- name: Lint
run: lintr::lint_package()
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"))
shell: Rscript {0}

37
codecov.yml → .gitlab-ci.yml
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@ -3,7 +3,7 @@
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
@ -16,27 +16,18 @@
# 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.github.io/AMR. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
codecov:
require_ci_to_pass: no # allow fail
ci:
- !appveyor # ignore CI builds by AppVeyor
comment: no
coverage:
precision: 1
round: up
range: "0...100"
status:
project: no
patch: no
changes: no
ignore:
- "R/atc_online.R"
- "R/mo_history.R"
- "R/mo_source.R"
- "R/resistance_predict.R" # gives a strange error but unit tests work
# as long as GitLab used - make sure the website will be updated
pages:
stage: website
allow_failure: true
when: always
only:
- master
script:
- mv docs public
artifacts:
paths:
- public

2
DESCRIPTION
View File

@ -1,5 +1,5 @@
Package: AMR
Version: 1.2.0.9026
Version: 1.2.0.9027
Date: 2020-07-08
Title: Antimicrobial Resistance Analysis
Authors@R: c(

5
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 1.2.0.9026
# AMR 1.2.0.9027
## <small>Last updated: 08-Jul-2020</small>
### New
@ -37,6 +37,9 @@
* Improved error handling, giving more useful info when functions return an error
* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
### Other
* Project moved to GitHub
# AMR 1.2.0
### Breaking

2
docs/404.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>

2
docs/articles/index.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>

2
docs/authors.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>

2
docs/extra.js
View File

@ -41,7 +41,7 @@ $( document ).ready(function() {
// redirect to GitLab
var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab");
var url_new = url_old.replace("gitlab", "github");
if (url_old != url_new) {
window.location.replace(url_new);
}

8
docs/index.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>
@ -235,7 +235,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
</ul>
</div>
@ -253,9 +253,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>The latest and unpublished development version can be installed with (<strong>precaution: may be unstable</strong>):</p>
<p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"remotes"</span>)
<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_gitlab.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
<span class="kw pkg">remotes</span><span class="kw ns">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span>(<span class="st">"msberends/AMR"</span>)</pre></div>
</div>
</div>
<div id="get-started" class="section level3">

63
docs/news/index.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>
@ -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-1209026" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9026">
<a href="#amr-1209026" class="anchor"></a>AMR 1.2.0.9026<small> Unreleased </small>
<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>
</h1>
<div id="last-updated-08-jul-2020" class="section level2">
<h2 class="hasAnchor">
@ -288,6 +288,13 @@
<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
</ul>
</div>
<div id="other" class="section level3">
<h3 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>Project moved to GitHub</li>
</ul>
</div>
</div>
</div>
<div id="amr-120" class="section level1">
@ -344,9 +351,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam</li>
</ul>
</div>
<div id="other" class="section level3">
<div id="other-1" class="section level3">
<h3 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h3>
<a href="#other-1" class="anchor"></a>Other</h3>
<ul>
<li>Removed previously deprecated function <code>p.symbol()</code> - it was replaced with <code><a href="../reference/p_symbol.html">p_symbol()</a></code>
</li>
@ -386,9 +393,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Added generic CLSI rules for R/SI interpretation using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for years 2010-2019 (thanks to Anthony Underwood)</li>
</ul>
</div>
<div id="other-1" class="section level3">
<div id="other-2" class="section level3">
<h3 class="hasAnchor">
<a href="#other-1" class="anchor"></a>Other</h3>
<a href="#other-2" class="anchor"></a>Other</h3>
<ul>
<li>Support for the upcoming <code>dplyr</code> version 1.0.0</li>
<li>More robust assigning for classes <code>rsi</code> and <code>mic</code>
@ -484,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="other-2" class="section level3">
<div id="other-3" class="section level3">
<h3 class="hasAnchor">
<a href="#other-2" class="anchor"></a>Other</h3>
<a href="#other-3" class="anchor"></a>Other</h3>
<ul>
<li>Add a <code>CITATION</code> file</li>
<li>Full support for the upcoming R 4.0</li>
@ -584,9 +591,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="other-3" class="section level3">
<div id="other-4" class="section level3">
<h3 class="hasAnchor">
<a href="#other-3" class="anchor"></a>Other</h3>
<a href="#other-4" class="anchor"></a>Other</h3>
<ul>
<li>Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great <a href="https://roxygen2.r-lib.org/index.html">Roxygen2</a>, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.</li>
<li>Change dependency on <code>clean</code> to <code>cleaner</code>, as this package was renamed accordingly upon CRAN request</li>
@ -738,9 +745,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>Added more MIC factor levels (<code><a href="../reference/as.mic.html">as.mic()</a></code>)</li>
</ul>
<div id="other-4" class="section level4">
<div id="other-5" class="section level4">
<h4 class="hasAnchor">
<a href="#other-4" class="anchor"></a>Other</h4>
<a href="#other-5" class="anchor"></a>Other</h4>
<ul>
<li>Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors</li>
<li>Cleaned the coding style of every single syntax line in this package with the help of the <code>lintr</code> package</li>
@ -821,9 +828,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="other-5" class="section level4">
<div id="other-6" class="section level4">
<h4 class="hasAnchor">
<a href="#other-5" class="anchor"></a>Other</h4>
<a href="#other-6" class="anchor"></a>Other</h4>
<ul>
<li>Fixed a note thrown by CRAN tests</li>
</ul>
@ -917,9 +924,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
</ul>
</div>
<div id="other-6" class="section level4">
<div id="other-7" class="section level4">
<h4 class="hasAnchor">
<a href="#other-6" class="anchor"></a>Other</h4>
<a href="#other-7" class="anchor"></a>Other</h4>
<ul>
<li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
</li>
@ -1164,9 +1171,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
</ul>
</div>
<div id="other-7" class="section level4">
<div id="other-8" class="section level4">
<h4 class="hasAnchor">
<a href="#other-7" class="anchor"></a>Other</h4>
<a href="#other-8" class="anchor"></a>Other</h4>
<ul>
<li>Updated licence text to emphasise GPL 2.0 and that this is an R package.</li>
</ul>
@ -1281,9 +1288,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Percentages will now will rounded more logically (e.g. in <code>freq</code> function)</p></li>
</ul>
</div>
<div id="other-8" class="section level4">
<div id="other-9" class="section level4">
<h4 class="hasAnchor">
<a href="#other-8" class="anchor"></a>Other</h4>
<a href="#other-9" class="anchor"></a>Other</h4>
<ul>
<li>New dependency on package <code>crayon</code>, to support formatted text in the console</li>
<li>Dependency <code>tidyr</code> is now mandatory (went to <code>Import</code> field) since <code>portion_df</code> and <code>count_df</code> rely on it</li>
@ -1416,9 +1423,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</div>
<div id="other-9" class="section level4">
<div id="other-10" class="section level4">
<h4 class="hasAnchor">
<a href="#other-9" class="anchor"></a>Other</h4>
<a href="#other-10" class="anchor"></a>Other</h4>
<ul>
<li>More unit tests to ensure better integrity of functions</li>
</ul>
@ -1545,9 +1552,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Other small fixes</li>
</ul>
</div>
<div id="other-10" class="section level4">
<div id="other-11" class="section level4">
<h4 class="hasAnchor">
<a href="#other-10" class="anchor"></a>Other</h4>
<a href="#other-11" class="anchor"></a>Other</h4>
<ul>
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
<ul>
@ -1607,9 +1614,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
</ul>
</div>
<div id="other-11" class="section level4">
<div id="other-12" class="section level4">
<h4 class="hasAnchor">
<a href="#other-11" class="anchor"></a>Other</h4>
<a href="#other-12" class="anchor"></a>Other</h4>
<ul>
<li>Expanded <code>README.md</code> with more examples</li>
<li>Added <a href="https://orcid.org">ORCID</a> of authors to DESCRIPTION file</li>

2
docs/pkgdown.yml
View File

@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-08T12:47Z
last_built: 2020-07-08T15:02Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
docs/reference/index.html
View File

@ -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">1.2.0.9026</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9027</span>
</span>
</div>

8
index.md
View File

@ -50,7 +50,7 @@ This package can be used for:
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html))
* Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html))
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
* Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
* Principal component analysis for AMR ([tutorial](./articles/PCA.html))
### Get this package
@ -69,10 +69,10 @@ It will be downloaded and installed automatically. For RStudio, click on the men
#### Latest development version
The latest and unpublished development version can be installed with (**precaution: may be unstable**):
The latest and unpublished development version can be installed from GitHub using:
```r
install.packages("remotes")
remotes::install_gitlab("msberends/AMR")
install.packages("remotes")
remotes::install_github("msberends/AMR")
```
### Get started

2
pkgdown/extra.js
View File

@ -41,7 +41,7 @@ $( document ).ready(function() {
// redirect to GitLab
var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab");
var url_new = url_old.replace("gitlab", "github");
if (url_old != url_new) {
window.location.replace(url_new);
}