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(v0.7.1.9017) deps

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dr. M.S. (Matthijs) Berends 2019-07-29 21:20:26 +02:00
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commit ec0ca20dee
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DESCRIPTION
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Package: AMR Package: AMR
Version: 0.7.1.9016 Version: 0.7.1.9017
Date: 2019-07-29 Date: 2019-07-29
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 0.7.1.9016 # AMR 0.7.1.9017
### Breaking ### 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. We decided to create a new package 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. * 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. We decided to create a new package 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/catalogue_of_life.R
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@ -90,6 +90,7 @@ NULL
#' @export #' @export
#' @examples #' @examples
#' library(dplyr) #' library(dplyr)
#' library(clean)
#' microorganisms %>% freq(kingdom) #' microorganisms %>% freq(kingdom)
#' microorganisms %>% group_by(kingdom) %>% freq(phylum, nmax = NULL) #' microorganisms %>% group_by(kingdom) %>% freq(phylum, nmax = NULL)
catalogue_of_life_version <- function() { catalogue_of_life_version <- function() {

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docs/LICENSE-text.html
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</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>

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docs/authors.html
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</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>

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docs/index.html
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</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9016" class="section level1"> <div id="amr-0-7-1-9017" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9016" class="anchor"></a>AMR 0.7.1.9016<small> Unreleased </small> <a href="#amr-0-7-1-9017" class="anchor"></a>AMR 0.7.1.9017<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -1198,7 +1198,7 @@ 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-0-7-1-9016">0.7.1.9016</a></li> <li><a href="#amr-0-7-1-9017">0.7.1.9017</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>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/catalogue_of_life_version.html
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@ -80,7 +80,7 @@
</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">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>
@ -264,8 +264,9 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span> <pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>kingdom</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>clean</span>)
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'>freq</span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>) <span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>kingdom</span>)
<span class='no'>microorganisms</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>kingdom</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>phylum</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

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docs/reference/index.html
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</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">0.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9017</span>
</span> </span>
</div> </div>

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man/catalogue_of_life_version.Rd
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@ -30,6 +30,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
\examples{ \examples{
library(dplyr) library(dplyr)
library(clean)
microorganisms \%>\% freq(kingdom) microorganisms \%>\% freq(kingdom)
microorganisms \%>\% group_by(kingdom) \%>\% freq(phylum, nmax = NULL) microorganisms \%>\% group_by(kingdom) \%>\% freq(phylum, nmax = NULL)
} }