mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
(v1.2.0.9027) move to github
This commit is contained in:
parent
76fc8e1b14
commit
5195e0b9da
@ -28,10 +28,10 @@ on:
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branches:
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- master
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name: R-CMD-check
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name: check
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jobs:
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R-CMD-check:
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check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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@ -43,9 +43,9 @@ jobs:
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: windows-latest, r: 'oldrel'}
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- {os: macOS-latest, r: 'oldrel'}
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- {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: windows-latest, r: 'oldrel'}
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# - {os: macOS-latest, r: 'oldrel'}
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# - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: windows-latest, r: 'devel'}
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- {os: macOS-latest, r: 'devel'}
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- {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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2
.github/workflows/codecovr.yaml
vendored
2
.github/workflows/codecovr.yaml
vendored
@ -64,5 +64,5 @@ jobs:
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R"))
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shell: Rscript {0}
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2
.github/workflows/lintr.yaml
vendored
2
.github/workflows/lintr.yaml
vendored
@ -62,5 +62,5 @@ jobs:
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shell: Rscript {0}
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- name: Lint
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run: lintr::lint_package()
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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"))
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shell: Rscript {0}
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@ -3,7 +3,7 @@
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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@ -16,27 +16,18 @@
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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codecov:
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require_ci_to_pass: no # allow fail
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ci:
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- !appveyor # ignore CI builds by AppVeyor
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comment: no
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coverage:
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precision: 1
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round: up
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range: "0...100"
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status:
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project: no
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patch: no
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changes: no
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||||
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ignore:
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- "R/atc_online.R"
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- "R/mo_history.R"
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- "R/mo_source.R"
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- "R/resistance_predict.R" # gives a strange error but unit tests work
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# as long as GitLab used - make sure the website will be updated
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pages:
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stage: website
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allow_failure: true
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when: always
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only:
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||||
- master
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script:
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- mv docs public
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artifacts:
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paths:
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||||
- public
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.2.0.9026
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Version: 1.2.0.9027
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Date: 2020-07-08
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Title: Antimicrobial Resistance Analysis
|
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Authors@R: c(
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5
NEWS.md
5
NEWS.md
@ -1,4 +1,4 @@
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||||
# AMR 1.2.0.9026
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||||
# AMR 1.2.0.9027
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## <small>Last updated: 08-Jul-2020</small>
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### 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
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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>
|
||||
|
||||
|
||||
@ -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);
|
||||
}
|
||||
|
||||
@ -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">
|
||||
|
||||
@ -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>
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
8
index.md
@ -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
|
||||
|
||||
@ -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);
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user