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(v1.0.1.9009) prepare for next release

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dr. M.S. (Matthijs) Berends 2020-04-15 11:30:28 +02:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.0.1.9008
Date: 2020-04-14
Version: 1.0.1.9009
Date: 2020-04-15
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.0.1.9008
## <small>Last updated: 14-Apr-2020</small>
# AMR 1.0.1.9009
## <small>Last updated: 15-Apr-2020</small>
### New
* Support for easy principal component analysis for AMR, using the new `pca()` function

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R/first_isolate.R
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@ -90,18 +90,8 @@
#' library(dplyr)
#' # Filter on first isolates:
#' example_isolates %>%
#' mutate(first_isolate = first_isolate(.,
#' col_date = "date",
#' col_patient_id = "patient_id",
#' col_mo = "mo")) %>%
#' mutate(first_isolate = first_isolate(.)) %>%
#' filter(first_isolate == TRUE)
#'
#' # Which can be shortened to:
#' example_isolates %>%
#' filter_first_isolate()
#' # or for first weighted isolates:
#' example_isolates %>%
#' filter_first_weighted_isolate()
#'
#' # Now let's see if first isolates matter:
#' A <- example_isolates %>%
@ -116,14 +106,22 @@
#' resistance = resistance(GEN)) # gentamicin resistance
#'
#' # Have a look at A and B.
#' # B is more reliable because every isolate is only counted once.
#' # Gentamicin resitance in hospital D appears to be 3.1% higher than
#' # B is more reliable because every isolate is counted only once.
#' # Gentamicin resitance in hospital D appears to be 3.7% higher than
#' # when you (erroneously) would have used all isolates for analysis.
#'
#'
#' ## OTHER EXAMPLES:
#'
#' \dontrun{
#'
#' # Short-hand versions:
#' example_isolates %>%
#' filter_first_isolate()
#'
#' example_isolates %>%
#' filter_first_weighted_isolate()
#'
#'
#' # set key antibiotics to a new variable
#' x$keyab <- key_antibiotics(x)

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

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docs/LICENSE-text.html
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</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

4
docs/articles/PCA.html
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@ -39,7 +39,7 @@
</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">1.0.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">13 April 2020</h4>
<h4 class="date">15 April 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>

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docs/articles/index.html
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</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

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docs/index.html
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@ -43,7 +43,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1019008" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1.9008">
<a href="#amr-1019008" class="anchor"></a>AMR 1.0.1.9008<small> Unreleased </small>
<div id="amr-1019009" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1.9009">
<a href="#amr-1019009" class="anchor"></a>AMR 1.0.1.9009<small> Unreleased </small>
</h1>
<div id="last-updated-14-apr-2020" class="section level2">
<div id="last-updated-15-apr-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-14-apr-2020" class="anchor"></a><small>Last updated: 14-Apr-2020</small>
<a href="#last-updated-15-apr-2020" class="anchor"></a><small>Last updated: 15-Apr-2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-04-14T18:36Z
last_built: 2020-04-15T09:25Z
urls:
reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles

2
docs/reference/WHONET.html
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@ -82,7 +82,7 @@
</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">1.0.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@ -82,7 +82,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

64
docs/reference/first_isolate.html
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@ -24,16 +24,20 @@
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<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.1/css/all.min.css" integrity="sha256-PbSmjxuVAzJ6FPvNYsrXygfGhNJYyZ2GktDbkMBqQZg=" crossorigin="anonymous" />
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<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
@ -46,7 +50,7 @@
<meta property="og:title" content="Determine first (weighted) isolates — first_isolate" />
<meta property="og:description" content="Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type." />
<meta property="og:image" content="/logo.svg" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -64,7 +68,7 @@
</head>
<body>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -78,7 +82,7 @@
</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">1.0.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>
@ -223,7 +227,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Determine first (weighted) isolates</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/first_isolate.R'><code>R/first_isolate.R</code></a></small>
<div class="hidden name"><code>first_isolate.Rd</code></div>
</div>
@ -404,19 +408,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># Filter on first isolates:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
<span class='co'># Which can be shortened to:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span>()
<span class='co'># or for first weighted isolates:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>()
<span class='co'># Now let's see if first isolates matter:</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>
@ -430,8 +424,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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'># B is more reliable because every isolate is only counted once.</span>
<span class='co'># Gentamicin resitance in hospital D appears to be 3.1% higher than</span>
<span class='co'># B is more reliable because every isolate is counted only once.</span>
<span class='co'># Gentamicin resitance in hospital D appears to be 3.7% higher than</span>
<span class='co'># when you (erroneously) would have used all isolates for analysis.</span>
@ -439,6 +433,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># Short-hand versions:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_isolate</span>()
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'>filter_first_weighted_isolate</span>()
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>x</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>x</span>)
@ -450,19 +452,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#key-antibiotics">Key antibiotics</a></li>
<li><a href="#stable-lifecycle">Stable lifecycle</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
@ -473,7 +465,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
</div>
</footer>

2
docs/reference/ggplot_pca.html
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@ -82,7 +82,7 @@
</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">1.0.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/like.html
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@ -82,7 +82,7 @@
</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">1.0.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
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@ -82,7 +82,7 @@
</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">1.0.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@ -82,7 +82,7 @@
</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">1.0.1.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
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@ -82,7 +82,7 @@
</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">1.0.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

2
docs/reference/rsi_translation.html
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@ -82,7 +82,7 @@
</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">1.0.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9009</span>
</span>
</div>

24
man/first_isolate.Rd
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@ -145,19 +145,9 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
library(dplyr)
# Filter on first isolates:
example_isolates \%>\%
mutate(first_isolate = first_isolate(.,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo")) \%>\%
mutate(first_isolate = first_isolate(.)) \%>\%
filter(first_isolate == TRUE)
# Which can be shortened to:
example_isolates \%>\%
filter_first_isolate()
# or for first weighted isolates:
example_isolates \%>\%
filter_first_weighted_isolate()
# Now let's see if first isolates matter:
A <- example_isolates \%>\%
group_by(hospital_id) \%>\%
@ -171,8 +161,8 @@ B <- example_isolates \%>\%
resistance = resistance(GEN)) # gentamicin resistance
# Have a look at A and B.
# B is more reliable because every isolate is only counted once.
# Gentamicin resitance in hospital D appears to be 3.1\% higher than
# B is more reliable because every isolate is counted only once.
# Gentamicin resitance in hospital D appears to be 3.7\% higher than
# when you (erroneously) would have used all isolates for analysis.
@ -180,6 +170,14 @@ B <- example_isolates \%>\%
\dontrun{
# Short-hand versions:
example_isolates \%>\%
filter_first_isolate()
example_isolates \%>\%
filter_first_weighted_isolate()
# set key antibiotics to a new variable
x$keyab <- key_antibiotics(x)

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