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(v1.2.0.9040) conserve_capped_values for as.rsi()

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dr. M.S. (Matthijs) Berends 2020-07-29 12:47:58 +02:00
parent e7def0aa4c
commit de0f7b8950
16 changed files with 17 additions and 18 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.2.0.9039 Version: 1.2.0.9040
Date: 2020-07-29 Date: 2020-07-29
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.2.0.9039 # AMR 1.2.0.9040
## <small>Last updated: 29 July 2020</small> ## <small>Last updated: 29 July 2020</small>
### New ### New

1
R/rsi.R
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@ -261,7 +261,6 @@ as.rsi.disk <- function(x,
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
conserve_capped_values = FALSE,
...) { ...) {
stop_if(missing(mo), stop_if(missing(mo),
'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n', 'No information was supplied about the microorganisms (missing parameter "mo"). See ?as.rsi.\n\n',

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

1
docs/extra.js
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@ -93,6 +93,7 @@ $(document).ready(function() {
$('.template-citation-authors h1').eq(0).text('How to cite'); $('.template-citation-authors h1').eq(0).text('How to cite');
$('.template-citation-authors h1').eq(1).text('All contributors'); $('.template-citation-authors h1').eq(1).text('All contributors');
$(".developers").html(doct_tit($(".developers").html())); $(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors...");
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209039" class="section level1"> <div id="amr-1209040" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9039"> <h1 class="page-header" data-toc-text="1.2.0.9040">
<a href="#amr-1209039" class="anchor"></a>AMR 1.2.0.9039<small> Unreleased </small> <a href="#amr-1209040" class="anchor"></a>AMR 1.2.0.9040<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-29-july-2020" class="section level2"> <div id="last-updated-29-july-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-07-29T09:46Z last_built: 2020-07-29T10:44Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

3
docs/reference/as.rsi.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>
@ -255,7 +255,6 @@
<span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)), <span class='kw'>ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='no'>x</span>)),
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>,
<span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>uti</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>conserve_capped_values</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span> <span class='no'>...</span>
) )

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9039</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9040</span>
</span> </span>
</div> </div>

1
man/as.rsi.Rd
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@ -28,7 +28,6 @@ as.rsi(x, ...)
ab = deparse(substitute(x)), ab = deparse(substitute(x)),
guideline = "EUCAST", guideline = "EUCAST",
uti = FALSE, uti = FALSE,
conserve_capped_values = FALSE,
... ...
) )

1
pkgdown/extra.js
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@ -93,6 +93,7 @@ $(document).ready(function() {
$('.template-citation-authors h1').eq(0).text('How to cite'); $('.template-citation-authors h1').eq(0).text('How to cite');
$('.template-citation-authors h1').eq(1).text('All contributors'); $('.template-citation-authors h1').eq(1).text('All contributors');
$(".developers").html(doct_tit($(".developers").html())); $(".developers").html(doct_tit($(".developers").html()));
$(".developers a[href='authors.html']").text("All contributors...");
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');