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(v1.0.0.9005) info printing only in interactive mode

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-21 21:13:38 +01:00
parent 47fe8b7820
commit ea32e9916a
28 changed files with 52 additions and 36 deletions
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2
docs/reference/as.rsi.html
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@ -79,7 +79,7 @@
</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">1.0.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>

4
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>
@ -230,7 +230,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<pre class="usage"><span class='fu'>eucast_rules</span>(
<span class='no'>x</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>

2
docs/reference/example_isolates_unclean.html
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@ -79,7 +79,7 @@
</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">1.0.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>

4
docs/reference/first_isolate.html
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@ -79,7 +79,7 @@
</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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>
@ -241,7 +241,7 @@
<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"keyantibiotics"</span>,
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>include_unknown</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
)

8
docs/reference/index.html
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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="Latest development version">1.0.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>
@ -451,6 +451,12 @@
<td><p>Data set with 2,000 example isolates</p></td>
</tr><tr>
<td>
<p><code><a href="example_isolates_unclean.html">example_isolates_unclean</a></code> </p>
</td>
<td><p>Data set with unclean data</p></td>
</tr><tr>
<td>
<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td>

4
docs/reference/mdro.html
View File

@ -79,7 +79,7 @@
</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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>
@ -229,7 +229,7 @@
<span class='no'>x</span>,
<span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"CMI2012"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>pct_required_classes</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,

6
docs/reference/resistance_predict.html
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@ -79,7 +79,7 @@
</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">0.9.0.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.0.9005</span>
</span>
</div>
@ -236,7 +236,7 @@
<span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='no'>...</span>
)
@ -251,7 +251,7 @@
<span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>I_as_S</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>preserve_measurements</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='no'>...</span>
)