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(v1.4.0.9014) bugfix

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dr. M.S. (Matthijs) Berends 2020-11-09 15:18:36 +01:00
parent d3b1d33210
commit dd5a0319ef
16 changed files with 30 additions and 24 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9013 Version: 1.4.0.9014
Date: 2020-11-09 Date: 2020-11-09
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9013 # AMR 1.4.0.9014
## <small>Last updated: 9 November 2020</small> ## <small>Last updated: 9 November 2020</small>
### New ### New

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R/mo.R
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@ -1417,7 +1417,7 @@ exec_as.mo <- function(x,
# - Becker et al. 2014, PMID 25278577 # - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103 # - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452 # - Becker et al. 2020, PMID 32056452
post_Becker <- c("") # 2020-10-20 currently all are mentioned in above papers post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) { if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ", warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",

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R/mo_property.R
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@ -140,8 +140,10 @@
#' language = "nl") # "Streptococcus groep A" #' language = "nl") # "Streptococcus groep A"
#' #'
#' # gram stains can be used as a filter #' # gram stains can be used as a filter
#' if (require("dplyr")) {
#' example_isolates %>% #' example_isolates %>%
#' filter(is_gram_positive()) #' filter(is_gram_positive())
#' }
#' #'
#' # other -------------------------------------------------------------------- #' # other --------------------------------------------------------------------
#' # get a list with the complete taxonomy (from kingdom to subspecies) #' # get a list with the complete taxonomy (from kingdom to subspecies)

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R/sysdata.rda
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docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409013" class="section level1"> <div id="amr-1409014" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9013"> <h1 class="page-header" data-toc-text="1.4.0.9014">
<a href="#amr-1409013" class="anchor"></a>AMR 1.4.0.9013<small> Unreleased </small> <a href="#amr-1409014" class="anchor"></a>AMR 1.4.0.9014<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-9-november-2020" class="section level2"> <div id="last-updated-9-november-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -252,7 +252,7 @@
<p>Functions <code><a href="../reference/mo_property.html">is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves inside <code>dplyr</code> functions:</p> <p>Functions <code><a href="../reference/mo_property.html">is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves inside <code>dplyr</code> functions:</p>
<div class="sourceCode" id="cb1"><pre class="downlit"> <div class="sourceCode" id="cb1"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for 'x'</span></pre></div> <span class="co">#&gt; NOTE: Using column `mo` as input for 'x'</span></pre></div>
</li> </li>
<li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li> <li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-11-09T12:06Z last_built: 2020-11-09T14:18Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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docs/reference/mo_property.html
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@ -82,7 +82,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>
@ -479,8 +479,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Streptococcus groep A"</span> language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Streptococcus groep A"</span>
<span class='co'># gram stains can be used as a filter</span> <span class='co'># gram stains can be used as a filter</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>is_gram_positive</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>is_gram_positive</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># other --------------------------------------------------------------------</span> <span class='co'># other --------------------------------------------------------------------</span>
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span> <span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>

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docs/survey.html
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@ -81,7 +81,7 @@
</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">1.4.0.9013</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
</span> </span>
</div> </div>

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man/mo_property.Rd
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@ -259,8 +259,10 @@ mo_fullname("S. pyogenes",
language = "nl") # "Streptococcus groep A" language = "nl") # "Streptococcus groep A"
# gram stains can be used as a filter # gram stains can be used as a filter
if (require("dplyr")) {
example_isolates \%>\% example_isolates \%>\%
filter(is_gram_positive()) filter(is_gram_positive())
}
# other -------------------------------------------------------------------- # other --------------------------------------------------------------------
# get a list with the complete taxonomy (from kingdom to subspecies) # get a list with the complete taxonomy (from kingdom to subspecies)