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(v0.7.1.9034) mo.codes fix for Dracunculus spp.

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dr. M.S. (Matthijs) Berends 2019-08-09 23:45:26 +02:00
parent 6598c5615d
commit 3f5828e74a
13 changed files with 17 additions and 15 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.7.1.9033
Version: 0.7.1.9034
Date: 2019-08-09
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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# AMR 0.7.1.9033
# AMR 0.7.1.9034
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.

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R/data.R
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@ -113,7 +113,7 @@ catalogue_of_life <- list(
#' Translation table for 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 4,969 observations and 2 variables:
#' @format A \code{\link{data.frame}} with 4,965 observations and 2 variables:
#' \describe{
#' \item{\code{certe}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}

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data-raw/reproduction_of_microorganisms.R
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@ -538,6 +538,8 @@ MOs %>%
filter(mo_new != mo_old) %>%
select(mo_old, mo_new, everything()) %>%
View()
# and these codes are now missing (which will throw a unit test error):
AMR::microorganisms.codes %>% filter(!mo %in% AMR::microorganisms$mo)
# set prevalence per species
MOs <- MOs %>%

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data/microorganisms.codes.rda
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docs/LICENSE-text.html
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</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>

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docs/articles/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>

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docs/authors.html
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@ -78,7 +78,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>

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docs/index.html
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@ -42,7 +42,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>

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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9033" class="section level1">
<div id="amr-0-7-1-9034" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9033" class="anchor"></a>AMR 0.7.1.9033<small> Unreleased </small>
<a href="#amr-0-7-1-9034" class="anchor"></a>AMR 0.7.1.9034<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -1233,7 +1233,7 @@ 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-0-7-1-9033">0.7.1.9033</a></li>
<li><a href="#amr-0-7-1-9034">0.7.1.9034</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-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>

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docs/reference/microorganisms.codes.html
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@ -80,7 +80,7 @@
</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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9034</span>
</span>
</div>
@ -238,7 +238,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 4,969 observations and 2 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 4,965 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>certe</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>
</dl>

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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 microorganism codes}
\format{A \code{\link{data.frame}} with 4,969 observations and 2 variables:
\format{A \code{\link{data.frame}} with 4,965 observations and 2 variables:
\describe{
\item{\code{certe}}{Commonly used code of a microorganism}
\item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}