P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 06:46:11 +01:00
Code Releases Activity

(v0.8.0.9035) add more mo codes

Browse Source
This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
DESCRIPTION
View File

@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.8.0.9034 Version: 0.8.0.9035
Date: 2019-11-23 Date: 2019-11-24
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 0.8.0.9034 # AMR 0.8.0.9035
## <small>Last updated: 23-Nov-2019</small> ## <small>Last updated: 24-Nov-2019</small>
### Breaking ### 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. * 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 * 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 * More robust way of determining valid MIC values
* Small changed to the `example_isolates` data set to better reflect reality * 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 ### Other
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request

2
R/data.R
View File

@ -133,7 +133,7 @@ catalogue_of_life <- list(
#' Translation table for common microorganism codes #' 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}}. #' 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{ #' \describe{
#' \item{\code{code}}{Commonly used code of a microorganism} #' \item{\code{code}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set} #' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}

2
R/mo_property.R
View File

@ -57,7 +57,7 @@
#' mo_kingdom("E. coli") # "Bacteria" #' mo_kingdom("E. coli") # "Bacteria"
#' mo_phylum("E. coli") # "Proteobacteria" #' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria" #' mo_class("E. coli") # "Gammaproteobacteria"
#' mo_order("E. coli") # "Enterobacterales" () #' mo_order("E. coli") # "Enterobacterales"
#' mo_family("E. coli") # "Enterobacteriaceae" #' mo_family("E. coli") # "Enterobacteriaceae"
#' mo_genus("E. coli") # "Escherichia" #' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli" #' mo_species("E. coli") # "coli"

BIN
data/microorganisms.codes.rda
View File

Binary file not shown.

2
docs/404.html
View File

@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/LICENSE-text.html
View File

@ -84,7 +84,7 @@
</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">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> </span>
</div> </div>

2
docs/articles/index.html
View File

@ -84,7 +84,7 @@
</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">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> </span>
</div> </div>

2
docs/authors.html
View File

@ -84,7 +84,7 @@
</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">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> </span>
</div> </div>

2
docs/index.html
View File

@ -45,7 +45,7 @@
</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">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> </span>
</div> </div>

13
docs/news/index.html
View File

@ -84,7 +84,7 @@
</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">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> </span>
</div> </div>
@ -231,13 +231,13 @@
</div> </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"> <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> </h1>
<div id="last-updated-23-nov-2019" class="section level2"> <div id="last-updated-24-nov-2019" class="section level2">
<h2 class="hasAnchor"> <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> </h2>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <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>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>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>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> </ul>
</div> </div>
<div id="other" class="section level3"> <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"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <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-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>

2
docs/reference/antibiotics.html
View File

@ -85,7 +85,7 @@
</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">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> </span>
</div> </div>

2
docs/reference/index.html
View File

@ -84,7 +84,7 @@
</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">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> </span>
</div> </div>

4
docs/reference/microorganisms.codes.html
View File

@ -85,7 +85,7 @@
</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">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> </span>
</div> </div>
@ -242,7 +242,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <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>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> <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>

4
docs/reference/mo_property.html
View File

@ -85,7 +85,7 @@
</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">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> </span>
</div> </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_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_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_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_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_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> <span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>

2
man/microorganisms.codes.Rd
View File

@ -4,7 +4,7 @@
\name{microorganisms.codes} \name{microorganisms.codes}
\alias{microorganisms.codes} \alias{microorganisms.codes}
\title{Translation table for common microorganism 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{ \describe{
\item{\code{code}}{Commonly used code of a microorganism} \item{\code{code}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set} \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}

2
man/mo_property.Rd
View File

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