mirror of https://github.com/msberends/AMR.git
(v1.4.0.9014) bugfix
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Package: AMR
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Package: AMR
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Version: 1.4.0.9013
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Version: 1.4.0.9014
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Date: 2020-11-09
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Date: 2020-11-09
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.4.0.9013
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# AMR 1.4.0.9014
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## <small>Last updated: 9 November 2020</small>
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## <small>Last updated: 9 November 2020</small>
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### New
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### New
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2
R/mo.R
2
R/mo.R
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@ -1417,7 +1417,7 @@ exec_as.mo <- function(x,
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2020, PMID 32056452
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# - Becker et al. 2020, PMID 32056452
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post_Becker <- c("") # 2020-10-20 currently all are mentioned in above papers
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post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers
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if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
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if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
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warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
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warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
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@ -140,8 +140,10 @@
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#' language = "nl") # "Streptococcus groep A"
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#' language = "nl") # "Streptococcus groep A"
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#'
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#'
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#' # gram stains can be used as a filter
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#' # gram stains can be used as a filter
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' example_isolates %>%
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#' filter(is_gram_positive())
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#' filter(is_gram_positive())
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#' }
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#'
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#'
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#' # other --------------------------------------------------------------------
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#' # other --------------------------------------------------------------------
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.github.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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -43,7 +43,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1409013" class="section level1">
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<div id="amr-1409014" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9013">
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<h1 class="page-header" data-toc-text="1.4.0.9014">
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<a href="#amr-1409013" class="anchor"></a>AMR 1.4.0.9013<small> Unreleased </small>
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<a href="#amr-1409014" class="anchor"></a>AMR 1.4.0.9014<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-9-november-2020" class="section level2">
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<div id="last-updated-9-november-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<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>
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<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>
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<div class="sourceCode" id="cb1"><pre class="downlit">
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<div class="sourceCode" id="cb1"><pre class="downlit">
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<span class="va">example_isolates</span> <span class="op">%>%</span>
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<span class="va">example_isolates</span> <span class="op">%>%</span>
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<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>
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<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>
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<span class="co">#> NOTE: Using column `mo` as input for 'x'</span></pre></div>
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<span class="co">#> NOTE: Using column `mo` as input for 'x'</span></pre></div>
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</li>
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</li>
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<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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<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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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-11-09T12:06Z
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last_built: 2020-11-09T14:18Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR//reference
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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article: https://msberends.github.io/AMR//articles
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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</div>
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@ -479,8 +479,10 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Streptococcus groep A"</span>
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language <span class='op'>=</span> <span class='st'>"nl"</span><span class='op'>)</span> <span class='co'># "Streptococcus groep A"</span>
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<span class='co'># gram stains can be used as a filter</span>
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<span class='co'># gram stains can be used as a filter</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<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>
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<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>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<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>
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<span class='op'>}</span>
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<span class='co'># other --------------------------------------------------------------------</span>
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<span class='co'># other --------------------------------------------------------------------</span>
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<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
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<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
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</span>
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</span>
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</div>
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@ -259,8 +259,10 @@ mo_fullname("S. pyogenes",
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language = "nl") # "Streptococcus groep A"
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language = "nl") # "Streptococcus groep A"
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# gram stains can be used as a filter
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# gram stains can be used as a filter
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example_isolates \%>\%
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if (require("dplyr")) {
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example_isolates \%>\%
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filter(is_gram_positive())
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filter(is_gram_positive())
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}
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# other --------------------------------------------------------------------
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# other --------------------------------------------------------------------
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# get a list with the complete taxonomy (from kingdom to subspecies)
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# get a list with the complete taxonomy (from kingdom to subspecies)
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