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(v0.8.0.9028) examples fix

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dr. M.S. (Matthijs) Berends 2019-11-10 13:17:20 +01:00
parent 59ededa8dc
commit 54b6322056
12 changed files with 19 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.8.0.9027 Version: 0.8.0.9028
Date: 2019-11-10 Date: 2019-11-10
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 0.8.0.9027 # AMR 0.8.0.9028
<small>Last updated: 10-Nov-2019</small> <small>Last updated: 10-Nov-2019</small>
### New ### New

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R/first_isolate.R
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@ -102,13 +102,13 @@
#' A <- example_isolates %>% #' A <- example_isolates %>%
#' group_by(hospital_id) %>% #' group_by(hospital_id) %>%
#' summarise(count = n_rsi(GEN), # gentamicin availability #' summarise(count = n_rsi(GEN), # gentamicin availability
#' resistance = portion_IR(GEN)) # gentamicin resistance #' resistance = resistance(GEN)) # gentamicin resistance
#' #'
#' B <- example_isolates %>% #' B <- example_isolates %>%
#' filter_first_weighted_isolate() %>% # the 1st isolate filter #' filter_first_weighted_isolate() %>% # the 1st isolate filter
#' group_by(hospital_id) %>% #' group_by(hospital_id) %>%
#' summarise(count = n_rsi(GEN), # gentamicin availability #' summarise(count = n_rsi(GEN), # gentamicin availability
#' resistance = portion_IR(GEN)) # gentamicin resistance #' resistance = resistance(GEN)) # gentamicin resistance
#' #'
#' # Have a look at A and B. #' # Have a look at A and B.
#' # B is more reliable because every isolate is only counted once. #' # B is more reliable because every isolate is only counted once.

2
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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>

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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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>

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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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -45,7 +45,7 @@
</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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>

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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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0-8-0-9027" class="section level1"> <div id="amr-0-8-0-9028" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-8-0-9027" class="anchor"></a>AMR 0.8.0.9027<small> Unreleased </small> <a href="#amr-0-8-0-9028" class="anchor"></a>AMR 0.8.0.9028<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 10-Nov-2019</small></p> <p><small>Last updated: 10-Nov-2019</small></p>
<div id="new" class="section level3"> <div id="new" class="section level3">
@ -1337,7 +1337,7 @@ 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-0-8-0-9027">0.8.0.9027</a></li> <li><a href="#amr-0-8-0-9028">0.8.0.9028</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li> <li><a href="#amr-0-8-0">0.8.0</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>

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docs/reference/first_isolate.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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>
@ -395,13 +395,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='no'>A</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span> <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='no'>B</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span> <span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%&gt;%</span> <span class='co'># the 1st isolate filter</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>GEN</span>), <span class='co'># gentamicin availability</span>
<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='AMR-deprecated.html'>portion_IR</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span> <span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='proportion.html'>resistance</a></span>(<span class='no'>GEN</span>)) <span class='co'># gentamicin resistance</span>
<span class='co'># Have a look at A and B.</span> <span class='co'># Have a look at A and B.</span>
<span class='co'># B is more reliable because every isolate is only counted once.</span> <span class='co'># B is more reliable because every isolate is only counted once.</span>

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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">0.8.0.9027</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
</span> </span>
</div> </div>

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man/first_isolate.Rd
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@ -129,13 +129,13 @@ example_isolates \%>\%
A <- example_isolates \%>\% A <- example_isolates \%>\%
group_by(hospital_id) \%>\% group_by(hospital_id) \%>\%
summarise(count = n_rsi(GEN), # gentamicin availability summarise(count = n_rsi(GEN), # gentamicin availability
resistance = portion_IR(GEN)) # gentamicin resistance resistance = resistance(GEN)) # gentamicin resistance
B <- example_isolates \%>\% B <- example_isolates \%>\%
filter_first_weighted_isolate() \%>\% # the 1st isolate filter filter_first_weighted_isolate() \%>\% # the 1st isolate filter
group_by(hospital_id) \%>\% group_by(hospital_id) \%>\%
summarise(count = n_rsi(GEN), # gentamicin availability summarise(count = n_rsi(GEN), # gentamicin availability
resistance = portion_IR(GEN)) # gentamicin resistance resistance = resistance(GEN)) # gentamicin resistance
# Have a look at A and B. # Have a look at A and B.
# B is more reliable because every isolate is only counted once. # B is more reliable because every isolate is only counted once.