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(v0.8.0.9028) examples fix
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Package: AMR
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Version: 0.8.0.9027
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Version: 0.8.0.9028
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Date: 2019-11-10
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.8.0.9027
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# AMR 0.8.0.9028
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<small>Last updated: 10-Nov-2019</small>
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### New
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#' A <- example_isolates %>%
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#' group_by(hospital_id) %>%
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#' summarise(count = n_rsi(GEN), # gentamicin availability
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#' resistance = portion_IR(GEN)) # gentamicin resistance
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#' resistance = resistance(GEN)) # gentamicin resistance
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#'
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#' B <- example_isolates %>%
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#' filter_first_weighted_isolate() %>% # the 1st isolate filter
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#' group_by(hospital_id) %>%
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#' summarise(count = n_rsi(GEN), # gentamicin availability
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#' resistance = portion_IR(GEN)) # gentamicin resistance
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#' resistance = resistance(GEN)) # gentamicin resistance
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#'
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#' # Have a look at A and B.
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#' # B is more reliable because every isolate is only counted once.
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -45,7 +45,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -231,9 +231,9 @@
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</div>
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<div id="amr-0-8-0-9027" class="section level1">
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<div id="amr-0-8-0-9028" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-8-0-9027" class="anchor"></a>AMR 0.8.0.9027<small> Unreleased </small>
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<a href="#amr-0-8-0-9028" class="anchor"></a>AMR 0.8.0.9028<small> Unreleased </small>
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</h1>
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<p><small>Last updated: 10-Nov-2019</small></p>
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<div id="new" class="section level3">
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@ -1337,7 +1337,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-8-0-9027">0.8.0.9027</a></li>
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<li><a href="#amr-0-8-0-9028">0.8.0.9028</a></li>
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<li><a href="#amr-0-8-0">0.8.0</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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<li><a href="#amr-0-7-0">0.7.0</a></li>
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@ -85,7 +85,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -395,13 +395,13 @@ To conduct an analysis of antimicrobial resistance, you should only include the
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<span class='no'>A</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<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'>%>%</span>
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<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>
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<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>
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<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>
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<span class='no'>B</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
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<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'>%>%</span>
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<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>
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<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>
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<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>
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<span class='co'># Have a look at A and B.</span>
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<span class='co'># B is more reliable because every isolate is only counted once.</span>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9027</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9028</span>
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</span>
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</div>
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@ -129,13 +129,13 @@ example_isolates \%>\%
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A <- example_isolates \%>\%
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group_by(hospital_id) \%>\%
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summarise(count = n_rsi(GEN), # gentamicin availability
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resistance = portion_IR(GEN)) # gentamicin resistance
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resistance = resistance(GEN)) # gentamicin resistance
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B <- example_isolates \%>\%
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filter_first_weighted_isolate() \%>\% # the 1st isolate filter
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group_by(hospital_id) \%>\%
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summarise(count = n_rsi(GEN), # gentamicin availability
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resistance = portion_IR(GEN)) # gentamicin resistance
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resistance = resistance(GEN)) # gentamicin resistance
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# Have a look at A and B.
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# B is more reliable because every isolate is only counted once.
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