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AMR
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(v1.2.0.9032) Permanently move to GitHub

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pull/67/head
dr. M.S. (Matthijs) Berends 3 years ago
parent a438dcc884
commit 1d66b5c43c
75 changed files with 92 additions and 128 deletions
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.gitlab-ci.yml
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# 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. #
# ==================================================================== #
# as long as GitLab used - make sure the website will be updated
stages:
- deploy
pages:
stage: deploy
allow_failure: true
when: always
only:
- master
script:
- mv docs public
artifacts:
paths:
- public

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DESCRIPTION
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Package: AMR
Version: 1.2.0.9031
Version: 1.2.0.9032
Date: 2020-07-09
Title: Antimicrobial Resistance Analysis
Authors@R: c(

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NEWS.md
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# AMR 1.2.0.9031
# AMR 1.2.0.9032
## <small>Last updated: 09-Jul-2020</small>
### New
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* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
### Other
* Project moved to GitHub
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
# AMR 1.2.0

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R/translate.R
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@ -126,7 +126,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
# check if text to look for is in one of the patterns
any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")),
error = function(e) {
warning("Translation not possible. Please open an issue on GitLab (https://github.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
warning("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE)
return(FALSE)
})
if (NROW(df_trans) == 0 | !any_form_in_patterns) {

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README.md
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% AMR (for R)
# `AMR` (for R)
<img src="man/figures/logo.png" align="right" height="120px" />
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR](https://msberends.github.io/AMR) to read about this package.
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR) and GitLab (https://gitlab.com/msberends/AMR).*
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*
### How to get this package
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
### Copyright
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://gitlab.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
- May be used for commercial purposes

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data-raw/country_analysis.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# Read and format data ----------------------------------------------------

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data-raw/internals.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# Run this file to update the package using: -------------------------------

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data-raw/loinc.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# last updated: 20 January 2020 - Loinc_2.67

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data-raw/poorman_prepend.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# ------------------------------------------------

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data-raw/read_EUCAST.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
library(openxlsx)

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data-raw/reproduction_of_antibiotics.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
library(dplyr)

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data-raw/reproduction_of_antivirals.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# get all data from the WHOCC website

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data-raw/reproduction_of_example_isolates_unclean.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
patients <- unlist(lapply(LETTERS, paste0, 1:10))

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data-raw/reproduction_of_microorganisms.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
# Reproduction of the `microorganisms` data set

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data-raw/snomed.R
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# 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. #
@ -16,7 +16,7 @@
# 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. #
# ==================================================================== #
library(AMR)

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docs/404.html
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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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docs/LICENSE-text.html
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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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docs/articles/SPSS.html
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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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docs/articles/WHONET.html
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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>
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<p>An example syntax could look like this:</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">readxl</span>)
<span class="no">data</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="kw">path</span> <span class="kw">=</span> <span class="st">"path/to/your/file.xlsx"</span>)</pre></body></html></div>
<p>This package comes with an <a href="https://msberends.gitlab.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
<p>This package comes with an <a href="https://msberends.github.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level3">
<h3 class="hasAnchor">
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<span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">cleaner</span>) <span class="co"># to create frequency tables</span></pre></body></html></div>
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.gitlab.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.github.io/AMR/reference/catalogue_of_life">our Catalogue of Life reference data set</a>, which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="co"># transform variables</span>

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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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docs/index.html
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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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docs/news/index.html
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</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">1.2.0.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209031" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9031">
<a href="#amr-1209031" class="anchor"></a>AMR 1.2.0.9031<small> Unreleased </small>
<div id="amr-1209032" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9032">
<a href="#amr-1209032" class="anchor"></a>AMR 1.2.0.9032<small> Unreleased </small>
</h1>
<div id="last-updated-09-jul-2020" class="section level2">
<h2 class="hasAnchor">
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<h3 class="hasAnchor">
<a href="#other" class="anchor"></a>Other</h3>
<ul>
<li>Project moved to GitHub</li>
<li>Moved primary location of this project from GitLab to <a href="https://github.com/msberends/AMR">GitHub</a>, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.</li>
</ul>
</div>
</div>

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WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-09T14:11Z
last_built: 2020-07-09T18:06Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</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">1.2.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9032</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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data <- read_excel(path = "path/to/your/file.xlsx")
```
This package comes with an [example data set `WHONET`](https://msberends.gitlab.io/AMR/reference/WHONET.html). We will use it for this analysis.
This package comes with an [example data set `WHONET`](https://msberends.github.io/AMR/reference/WHONET.html). We will use it for this analysis.
### Preparation
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We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.gitlab.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
```{r}

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