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(v0.7.0.9003) scale fix
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 0.7.0.9002
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Version: 0.7.0.9003
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Date: 2019-06-08
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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@ -173,6 +173,8 @@ export(resistance_predict)
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export(right_join_microorganisms)
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export(rsi_predict)
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export(scale_rsi_colours)
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export(scale_type.ab)
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export(scale_type.mo)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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export(set_mo_source)
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4
NEWS.md
4
NEWS.md
@ -1,4 +1,4 @@
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# AMR 0.7.0.9002
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# AMR 0.7.0.9003
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#### New
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* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
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@ -12,7 +12,7 @@
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#### Changed
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* Fixed bug in translation of microorganism names
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* Fixed bug in determining taxonomic kingdoms
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* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severe misspelled input
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* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
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* Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab`
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* Added names of object in the header in frequency tables, even when using pipes
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* Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP)
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9
R/ab.R
9
R/ab.R
@ -258,12 +258,3 @@ as.data.frame.ab <- function (x, ...) {
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pull.ab <- function(.data, ...) {
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pull(as.data.frame(.data), ...)
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}
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#' @exportMethod scale_type.ab
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#' @noRd
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scale_type.ab <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type ab. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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48
R/extended.R
Normal file
48
R/extended.R
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@ -0,0 +1,48 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Extended functions
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#'
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#' These functions are extensions of functions in other packages.
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#' @inheritSection AMR Read more on our website!
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#' @export
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#' @keywords internal
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#' @name extended-functions
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#' @rdname extended-functions
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#' @exportMethod scale_type.mo
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#' @export
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scale_type.mo <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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#' @rdname extended-functions
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#' @exportMethod scale_type.ab
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#' @export
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scale_type.ab <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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10
R/mo.R
10
R/mo.R
@ -1484,13 +1484,3 @@ translate_allow_uncertain <- function(allow_uncertain) {
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}
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allow_uncertain
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}
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#' @exportMethod scale_type.mo
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# @export
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#' @noRd
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scale_type.mo <- function(x) {
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# fix for:
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# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
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# "Error: Discrete value supplied to continuous scale"
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"discrete"
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}
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@ -78,7 +78,7 @@
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</button>
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||||
<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
|
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
|
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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</span>
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</div>
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@ -239,9 +239,9 @@
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</div>
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<div id="amr-0709002" class="section level1">
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<div id="amr-0709003" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0709002" class="anchor"></a>AMR 0.7.0.9002<small> Unreleased </small>
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<a href="#amr-0709003" class="anchor"></a>AMR 0.7.0.9003<small> Unreleased </small>
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</h1>
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<div id="new" class="section level4">
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<h4 class="hasAnchor">
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@ -262,7 +262,7 @@
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<ul>
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<li>Fixed bug in translation of microorganism names</li>
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<li>Fixed bug in determining taxonomic kingdoms</li>
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<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severe misspelled input</li>
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<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
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<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
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</li>
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<li>Added names of object in the header in frequency tables, even when using pipes</li>
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@ -1108,7 +1108,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0709002">0.7.0.9002</a></li>
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<li><a href="#amr-0709003">0.7.0.9003</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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304
docs/reference/extended-functions.html
Normal file
304
docs/reference/extended-functions.html
Normal file
@ -0,0 +1,304 @@
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Source Code
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<div class="row">
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<div class="col-md-9 contents">
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||||
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|
||||
<h1>Extended functions</h1>
|
||||
|
||||
<div class="hidden name"><code>extended-functions.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>These functions are extensions of functions in other packages.</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
|
||||
|
||||
<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
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||||
@ -78,7 +78,7 @@
|
||||
</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="Released version">0.7.0.9002</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
|
||||
</span>
|
||||
</div>
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||||
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||||
|
||||
@ -63,6 +63,9 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/eucast_rules.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/extended-functions.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/filter_ab_class.html</loc>
|
||||
</url>
|
||||
|
||||
21
man/extended-functions.Rd
Normal file
21
man/extended-functions.Rd
Normal file
@ -0,0 +1,21 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/extended.R
|
||||
\name{extended-functions}
|
||||
\alias{extended-functions}
|
||||
\alias{scale_type.mo}
|
||||
\alias{scale_type.ab}
|
||||
\title{Extended functions}
|
||||
\usage{
|
||||
scale_type.mo(x)
|
||||
|
||||
scale_type.ab(x)
|
||||
}
|
||||
\description{
|
||||
These functions are extensions of functions in other packages.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{internal}
|
||||
@ -62,4 +62,16 @@ test_that("ggplot_rsi works", {
|
||||
expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
|
||||
expect_error(geom_rsi(septic_patients, fun = "invalid"))
|
||||
|
||||
# support for scale_type ab and mo
|
||||
expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")),
|
||||
n = c(40, 100)) %>%
|
||||
ggplot(aes(x = mo, y = n)) +
|
||||
geom_col())$data),
|
||||
"data.frame")
|
||||
expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
|
||||
n = c(40, 100)) %>%
|
||||
ggplot(aes(x = ab, y = n)) +
|
||||
geom_col())$data),
|
||||
"data.frame")
|
||||
|
||||
})
|
||||
|
||||
Loading…
Reference in New Issue
Block a user