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(v0.7.1.9097) mdro() examples fix

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dr. M.S. (Matthijs) Berends 2019-10-07 14:57:27 +02:00
parent 4e9c4c1b4e
commit f479dfce60
12 changed files with 22 additions and 22 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9096 Version: 0.7.1.9097
Date: 2019-10-07 Date: 2019-10-07
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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# AMR 0.7.1.9096 # AMR 0.7.1.9097
<small>Last updated: 07-Oct-2019</small> <small>Last updated: 07-Oct-2019</small>
### Breaking ### Breaking

6
R/mdro.R
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@ -62,9 +62,9 @@
#' MRGN = mrgn(.)) #' MRGN = mrgn(.))
#' #'
#' example_isolates %>% #' example_isolates %>%
#' rename(PIP = TZP) # no piperacillin, so take piperacillin/tazobactam #' rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam
#' mrgn() %>% # check German guideline #' mrgn() %>% # check German guideline
#' freq() # check frequencies #' freq() # check frequencies
mdro <- function(x, mdro <- function(x,
guideline = NULL, guideline = NULL,
col_mo = NULL, col_mo = NULL,

2
docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-7-1-9096" class="section level1"> <div id="amr-0-7-1-9097" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9096" class="anchor"></a>AMR 0.7.1.9096<small> Unreleased </small> <a href="#amr-0-7-1-9097" class="anchor"></a>AMR 0.7.1.9097<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 07-Oct-2019</small></p> <p><small>Last updated: 07-Oct-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1289,7 +1289,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9096">0.7.1.9096</a></li> <li><a href="#amr-0-7-1-9097">0.7.1.9097</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>

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docs/reference/mdro.html
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@ -85,7 +85,7 @@
</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">0.7.1.9096</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9097</span>
</span> </span>
</div> </div>
@ -394,9 +394,9 @@
<span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>)) <span class='kw'>MRGN</span> <span class='kw'>=</span> <span class='fu'>mrgn</span>(<span class='no'>.</span>))
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>rename</a></span>(<span class='kw'>PIP</span> <span class='kw'>=</span> <span class='no'>TZP</span>) <span class='co'># no piperacillin, so take piperacillin/tazobactam</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>rename</a></span>(<span class='kw'>PIP</span> <span class='kw'>=</span> <span class='no'>TZP</span>) <span class='kw'>%&gt;%</span> <span class='co'># no piperacillin, so take piperacillin/tazobactam</span>
<span class='fu'>mrgn</span>() <span class='kw'>%&gt;%</span> <span class='co'># check German guideline</span> <span class='fu'>mrgn</span>() <span class='kw'>%&gt;%</span> <span class='co'># check German guideline</span>
<span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>() <span class='co'># check frequencies</span></pre> <span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>() <span class='co'># check frequencies</span></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2> <h2>Contents</h2>

6
man/mdro.Rd
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@ -154,7 +154,7 @@ example_isolates \%>\%
MRGN = mrgn(.)) MRGN = mrgn(.))
example_isolates \%>\% example_isolates \%>\%
rename(PIP = TZP) # no piperacillin, so take piperacillin/tazobactam rename(PIP = TZP) \%>\% # no piperacillin, so take piperacillin/tazobactam
mrgn() \%>\% # check German guideline mrgn() \%>\% # check German guideline
freq() # check frequencies freq() # check frequencies
} }