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(v0.8.0.9035) add more mo codes

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dr. M.S. (Matthijs) Berends 2019-11-24 22:48:56 +01:00
parent e53cc4990c
commit 7c28b392b1
17 changed files with 27 additions and 25 deletions
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4
DESCRIPTION
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Package: AMR
Version: 0.8.0.9034
Date: 2019-11-23
Version: 0.8.0.9035
Date: 2019-11-24
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

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NEWS.md
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# AMR 0.8.0.9034
## <small>Last updated: 23-Nov-2019</small>
# AMR 0.8.0.9035
## <small>Last updated: 24-Nov-2019</small>
### Breaking
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
@ -57,6 +57,7 @@
* Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the `antibiotics` data set
* More robust way of determining valid MIC values
* Small changed to the `example_isolates` data set to better reflect reality
* Added more microorganisms codes from laboratory systems (esp. species of *Pseudescherichia* and *Rodentibacter*)
### Other
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request

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R/data.R
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@ -133,7 +133,7 @@ catalogue_of_life <- list(
#' Translation table for common microorganism codes
#'
#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 5,006 observations and 2 variables:
#' @format A \code{\link{data.frame}} with 5,433 observations and 2 variables:
#' \describe{
#' \item{\code{code}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}

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R/mo_property.R
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#' mo_kingdom("E. coli") # "Bacteria"
#' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria"
#' mo_order("E. coli") # "Enterobacterales" ()
#' mo_order("E. coli") # "Enterobacterales"
#' mo_family("E. coli") # "Enterobacteriaceae"
#' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli"

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data/microorganisms.codes.rda
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docs/404.html
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</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

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docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

2
docs/index.html
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@ -45,7 +45,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

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docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>
@ -231,13 +231,13 @@
</div>
<div id="amr-0-8-0-9034" class="section level1">
<div id="amr-0-8-0-9035" class="section level1">
<h1 class="page-header">
<a href="#amr-0-8-0-9034" class="anchor"></a>AMR 0.8.0.9034<small> Unreleased </small>
<a href="#amr-0-8-0-9035" class="anchor"></a>AMR 0.8.0.9035<small> Unreleased </small>
</h1>
<div id="last-updated-23-nov-2019" class="section level2">
<div id="last-updated-24-nov-2019" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-23-nov-2019" class="anchor"></a><small>Last updated: 23-Nov-2019</small>
<a href="#last-updated-24-nov-2019" class="anchor"></a><small>Last updated: 24-Nov-2019</small>
</h2>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -319,6 +319,7 @@
<li>Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the <code>antibiotics</code> data set</li>
<li>More robust way of determining valid MIC values</li>
<li>Small changed to the <code>example_isolates</code> data set to better reflect reality</li>
<li>Added more microorganisms codes from laboratory systems (esp. species of <em>Pseudescherichia</em> and <em>Rodentibacter</em>)</li>
</ul>
</div>
<div id="other" class="section level3">
@ -1391,7 +1392,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9034">0.8.0.9034</a></li>
<li><a href="#amr-0-8-0-9035">0.8.0.9035</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>

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docs/reference/antibiotics.html
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@ -85,7 +85,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9034</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>

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docs/reference/microorganisms.codes.html
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@ -85,7 +85,7 @@
</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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>
@ -242,7 +242,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,006 observations and 2 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 5,433 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>code</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
<dt><code>mo</code></dt><dd><p>ID of the microorganism in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>

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docs/reference/mo_property.html
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@ -85,7 +85,7 @@
</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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9035</span>
</span>
</div>
@ -356,7 +356,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_kingdom</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gammaproteobacteria"</span>
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacterales" ()</span>
<span class='fu'>mo_order</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacterales"</span>
<span class='fu'>mo_family</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Enterobacteriaceae"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>

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man/microorganisms.codes.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for common microorganism codes}
\format{A \code{\link{data.frame}} with 5,006 observations and 2 variables:
\format{A \code{\link{data.frame}} with 5,433 observations and 2 variables:
\describe{
\item{\code{code}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}

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man/mo_property.Rd
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@ -134,7 +134,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
mo_kingdom("E. coli") # "Bacteria"
mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria"
mo_order("E. coli") # "Enterobacterales" ()
mo_order("E. coli") # "Enterobacterales"
mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"