mirror of https://github.com/msberends/AMR.git
(v1.4.0.9014) bugfix
This commit is contained in:
parent
d3b1d33210
commit
dd5a0319ef
|
@ -1,5 +1,5 @@
|
|||
Package: AMR
|
||||
Version: 1.4.0.9013
|
||||
Version: 1.4.0.9014
|
||||
Date: 2020-11-09
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
|
|
2
NEWS.md
2
NEWS.md
|
@ -1,4 +1,4 @@
|
|||
# AMR 1.4.0.9013
|
||||
# AMR 1.4.0.9014
|
||||
## <small>Last updated: 9 November 2020</small>
|
||||
|
||||
### New
|
||||
|
|
2
R/mo.R
2
R/mo.R
|
@ -1417,7 +1417,7 @@ exec_as.mo <- function(x,
|
|||
# - Becker et al. 2014, PMID 25278577
|
||||
# - Becker et al. 2019, PMID 30872103
|
||||
# - 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])) {
|
||||
|
||||
warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
|
||||
|
|
|
@ -140,9 +140,11 @@
|
|||
#' language = "nl") # "Streptococcus groep A"
|
||||
#'
|
||||
#' # gram stains can be used as a filter
|
||||
#' example_isolates %>%
|
||||
#' filter(is_gram_positive())
|
||||
#'
|
||||
#' if (require("dplyr")) {
|
||||
#' example_isolates %>%
|
||||
#' filter(is_gram_positive())
|
||||
#' }
|
||||
#'
|
||||
#' # other --------------------------------------------------------------------
|
||||
#' # get a list with the complete taxonomy (from kingdom to subspecies)
|
||||
#' mo_taxonomy("E. coli")
|
||||
|
|
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -236,9 +236,9 @@
|
|||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1409013" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9013">
|
||||
<a href="#amr-1409013" class="anchor"></a>AMR 1.4.0.9013<small> Unreleased </small>
|
||||
<div id="amr-1409014" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9014">
|
||||
<a href="#amr-1409014" class="anchor"></a>AMR 1.4.0.9014<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-9-november-2020" class="section level2">
|
||||
<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>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit">
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</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">#> NOTE: Using column `mo` as input for 'x'</span></pre></div>
|
||||
</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>
|
||||
|
|
|
@ -12,7 +12,7 @@ articles:
|
|||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2020-11-09T12:06Z
|
||||
last_built: 2020-11-09T14:18Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</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>
|
||||
|
||||
<span class='co'># gram stains can be used as a filter</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</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='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'>%>%</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'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
|
|
|
@ -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">1.4.0.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
@ -259,8 +259,10 @@ mo_fullname("S. pyogenes",
|
|||
language = "nl") # "Streptococcus groep A"
|
||||
|
||||
# gram stains can be used as a filter
|
||||
example_isolates \%>\%
|
||||
filter(is_gram_positive())
|
||||
if (require("dplyr")) {
|
||||
example_isolates \%>\%
|
||||
filter(is_gram_positive())
|
||||
}
|
||||
|
||||
# other --------------------------------------------------------------------
|
||||
# get a list with the complete taxonomy (from kingdom to subspecies)
|
||||
|
|
Loading…
Reference in New Issue