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(v0.8.0.9009) unit test

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dr. M.S. (Matthijs) Berends 2019-11-03 22:41:29 +01:00
parent 29e448883d
commit 0bb531f3e0
18 changed files with 35 additions and 33 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.8.0.9008
Version: 0.8.0.9009
Date: 2019-11-03
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.8.0.9008
# AMR 0.8.0.9009
<small>Last updated: 03-Nov-2019</small>
### New

2
R/age.R
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@ -133,6 +133,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
#' # same:
#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
#'
#' \dontrun{
#' # resistance of ciprofloxacine per age group
#' library(dplyr)
#' example_isolates %>%
@ -141,6 +142,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group, CIP) %>%
#' ggplot_rsi(x = "age_group")
#' }
age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
if (!is.numeric(x)) {
stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")

7
R/ggplot_rsi.R
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@ -99,7 +99,9 @@
#' example_isolates %>%
#' select(AMX) %>%
#' ggplot_rsi(colours = c(SI = "yellow"))
#'
#'
#' \dontrun{
#'
#' # resistance of ciprofloxacine per age group
#' example_isolates %>%
#' mutate(first_isolate = first_isolate(.)) %>%
@ -110,8 +112,7 @@
#' select(age_group,
#' CIP) %>%
#' ggplot_rsi(x = "age_group")
#' \donttest{
#'
#'
#' # for colourblind mode, use divergent colours from the viridis package:
#' example_isolates %>%
#' select(AMX, NIT, FOS, TMP, CIP) %>%

1
R/mdro.R
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@ -25,7 +25,6 @@
#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details.
#' @param info print progress
#' @inheritParams eucast_rules
#' @param verbose print additional info: missing antibiotic columns per parameter
#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.
#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @inheritSection eucast_rules Antibiotics

2
docs/404.html
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@ -84,7 +84,7 @@
</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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>

2
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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>

2
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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>

8
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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>
@ -231,9 +231,9 @@
</div>
<div id="amr-0-8-0-9008" class="section level1">
<div id="amr-0-8-0-9009" class="section level1">
<h1 class="page-header">
<a href="#amr-0-8-0-9008" class="anchor"></a>AMR 0.8.0.9008<small> Unreleased </small>
<a href="#amr-0-8-0-9009" class="anchor"></a>AMR 0.8.0.9009<small> Unreleased </small>
</h1>
<p><small>Last updated: 03-Nov-2019</small></p>
<div id="new" class="section level3">
@ -1332,7 +1332,7 @@ 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-0-8-0-9008">0.8.0.9008</a></li>
<li><a href="#amr-0-8-0-9009">0.8.0.9009</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>

6
docs/reference/age_groups.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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>
@ -303,6 +303,7 @@
<span class='co'># same:</span>
<span class='fu'>age_groups</span>(<span class='no'>ages</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>6</span>, <span class='fl'>13</span>, <span class='fl'>17</span>))
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -310,7 +311,8 @@
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</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='kw'>age_group</span> <span class='kw'>=</span> <span class='fu'>age_groups</span>(<span class='no'>age</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)</pre>
<span class='fu'><a href='ggplot_rsi.html'>ggplot_rsi</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>

9
docs/reference/ggplot_rsi.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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>
@ -415,6 +415,8 @@
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"yellow"</span>))
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolate</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>)) <span class='kw'>%&gt;%</span>
@ -425,7 +427,6 @@
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>age_group</span>,
<span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"age_group"</span>)
<span class='co'># \donttest{</span>
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
@ -453,7 +454,7 @@
<span class='co'># create new bacterial ID's, with all CoNS under the same group (Becker et al.)</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='no'>mo</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on top three bacterial ID's</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'>top_freq</span>(<span class='fu'><a href='https://rdrr.io/pkg/clean/man/freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>%in%</span> <span class='fu'>top_freq</span>(<span class='fu'><a href='https://rdrr.io/pkg/cleaner/man/freq.html'>freq</a></span>(<span class='no'>.</span>$<span class='no'>mo</span>), <span class='fl'>3</span>)) <span class='kw'>%&gt;%</span>
<span class='co'># filter on first isolates</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span>() <span class='kw'>%&gt;%</span>
<span class='co'># get short MO names (like "E. coli")</span>
@ -471,7 +472,7 @@
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/expression.html'>expression</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Only First Isolates, CoNS grouped according to Becker "</span>,
<span class='fu'><a href='https://rdrr.io/r/grDevices/plotmath.html'>italic</a></span>(<span class='st'>"et al."</span>), <span class='st'>" (2014)"</span>)),
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Antibiotic (EARS-Net code)"</span>)
<span class='co'># }</span></pre>
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>

2
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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>

8
docs/reference/mdro.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">0.8.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9009</span>
</span>
</div>
@ -271,7 +271,7 @@
</tr>
<tr>
<th>verbose</th>
<td><p>print additional info: missing antibiotic columns per parameter</p></td>
<td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></td>
</tr>
<tr>
<th>pct_required_classes</th>
@ -281,10 +281,6 @@
<th>...</th>
<td><p>column name of an antibiotic, see section Antibiotics</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

2
man/age_groups.Rd
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@ -60,6 +60,7 @@ age_groups(ages, "children")
# same:
age_groups(ages, c(1, 2, 4, 6, 13, 17))
\dontrun{
# resistance of ciprofloxacine per age group
library(dplyr)
example_isolates \%>\%
@ -69,6 +70,7 @@ example_isolates \%>\%
select(age_group, CIP) \%>\%
ggplot_rsi(x = "age_group")
}
}
\seealso{
To determine ages, based on one or more reference dates, use the \code{\link{age}} function.
}

5
man/ggplot_rsi.Rd
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@ -148,6 +148,8 @@ example_isolates \%>\%
example_isolates \%>\%
select(AMX) \%>\%
ggplot_rsi(colours = c(SI = "yellow"))
\dontrun{
# resistance of ciprofloxacine per age group
example_isolates \%>\%
@ -159,8 +161,7 @@ example_isolates \%>\%
select(age_group,
CIP) \%>\%
ggplot_rsi(x = "age_group")
\donttest{
# for colourblind mode, use divergent colours from the viridis package:
example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%

4
man/mdro.Rd
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@ -34,13 +34,11 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{info}{print progress}
\item{verbose}{print additional info: missing antibiotic columns per parameter}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}
\item{...}{column name of an antibiotic, see section Antibiotics}
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
}
\value{
\itemize{