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(v0.9.0.9027) documentation fix

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dr. M.S. (Matthijs) Berends 2020-02-17 15:07:25 +01:00
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commit c8981a563e
12 changed files with 19 additions and 16 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 0.9.0.9026 Version: 0.9.0.9027
Date: 2020-02-17 Date: 2020-02-17
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 0.9.0.9026 # AMR 0.9.0.9027
## <small>Last updated: 17-Feb-2020</small> ## <small>Last updated: 17-Feb-2020</small>
### New ### New

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R/disk.R
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#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' # transform existing disk zones to the `disk` class #' # transform existing disk zones to the `disk` class
#' library(dplyr)
#' df <- data.frame(microorganism = "E. coli", #' df <- data.frame(microorganism = "E. coli",
#' AMP = 20, #' AMP = 20,
#' CIP = 14, #' CIP = 14,
#' GEN = 18, #' GEN = 18,
#' TOB = 16) #' TOB = 16)
#' df <- df %>% mutate_at(vars(AMP:TOB, as.disk)) #' df <- df %>% mutate_at(vars(AMP:TOB), as.disk)
#' df #' df
#' #'
#' # interpret disk values, see ?as.rsi #' # interpret disk values, see ?as.rsi

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docs/404.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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docs/authors.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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docs/index.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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docs/news/index.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>
@ -219,9 +219,9 @@
</div> </div>
<div id="amr-0909026" class="section level1"> <div id="amr-0909027" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0909026" class="anchor"></a>AMR 0.9.0.9026<small> Unreleased </small> <a href="#amr-0909027" class="anchor"></a>AMR 0.9.0.9027<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-17-feb-2020" class="section level2"> <div id="last-updated-17-feb-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -1450,7 +1450,7 @@
<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-0909026">0.9.0.9026</a></li> <li><a href="#amr-0909027">0.9.0.9027</a></li>
<li><a href="#amr-090">0.9.0</a></li> <li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li> <li><a href="#amr-080">0.8.0</a></li>
<li><a href="#amr-071">0.7.1</a></li> <li><a href="#amr-071">0.7.1</a></li>

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docs/reference/as.disk.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>
@ -266,12 +266,13 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># transform existing disk zones to the `disk` class</span> <pre class="examples"><span class='co'># transform existing disk zones to the `disk` class</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>, <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>microorganism</span> <span class='kw'>=</span> <span class='st'>"E. coli"</span>,
<span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>AMP</span> <span class='kw'>=</span> <span class='fl'>20</span>,
<span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fl'>14</span>, <span class='kw'>CIP</span> <span class='kw'>=</span> <span class='fl'>14</span>,
<span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fl'>18</span>, <span class='kw'>GEN</span> <span class='kw'>=</span> <span class='fl'>18</span>,
<span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fl'>16</span>) <span class='kw'>TOB</span> <span class='kw'>=</span> <span class='fl'>16</span>)
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'>mutate_at</span>(<span class='fu'>vars</span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>, <span class='no'>as.disk</span>)) <span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>df</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>AMP</span>:<span class='no'>TOB</span>), <span class='no'>as.disk</span>)
<span class='no'>df</span> <span class='no'>df</span>
<span class='co'># interpret disk values, see ?as.rsi</span> <span class='co'># interpret disk values, see ?as.rsi</span>

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docs/reference/index.html
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</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">0.9.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9027</span>
</span> </span>
</div> </div>

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man/as.disk.Rd
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@ -39,12 +39,13 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
\examples{ \examples{
# transform existing disk zones to the `disk` class # transform existing disk zones to the `disk` class
library(dplyr)
df <- data.frame(microorganism = "E. coli", df <- data.frame(microorganism = "E. coli",
AMP = 20, AMP = 20,
CIP = 14, CIP = 14,
GEN = 18, GEN = 18,
TOB = 16) TOB = 16)
df <- df \%>\% mutate_at(vars(AMP:TOB, as.disk)) df <- df \%>\% mutate_at(vars(AMP:TOB), as.disk)
df df
# interpret disk values, see ?as.rsi # interpret disk values, see ?as.rsi