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Merge branch 'premaster' of https://gitlab.com/msberends/AMR into premaster

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dr. M.S. (Matthijs) Berends 2019-07-30 19:00:41 +02:00
commit 47920df6ca
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4
DESCRIPTION
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Package: AMR Package: AMR
Version: 0.7.1.9017 Version: 0.7.1.9018
Date: 2019-07-29 Date: 2019-07-30
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

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NEWS.md
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# AMR 0.7.1.9017 # AMR 0.7.1.9018
### 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.

4
R/eucast_rules.R
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@ -139,8 +139,6 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' } #' }
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @examples #' @examples
#' a <- eucast_rules(septic_patients)
#'
#' a <- data.frame(mo = c("Staphylococcus aureus", #' a <- data.frame(mo = c("Staphylococcus aureus",
#' "Enterococcus faecalis", #' "Enterococcus faecalis",
#' "Escherichia coli", #' "Escherichia coli",
@ -176,7 +174,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
#' # 5 Pseudomonas aeruginosa R R - - R R R #' # 5 Pseudomonas aeruginosa R R - - R R R
#' #'
#' #'
#' # do not apply EUCAST rules, but rather get a a data.frame #' # do not apply EUCAST rules, but rather get a data.frame
#' # with 18 rows, containing all details about the transformations: #' # with 18 rows, containing all details about the transformations:
#' c <- eucast_rules(a, verbose = TRUE) #' c <- eucast_rules(a, verbose = TRUE)
eucast_rules <- function(x, eucast_rules <- function(x,

1
R/like.R
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@ -48,6 +48,7 @@
#' #'
#' # get frequencies of bacteria whose name start with 'Ent' or 'ent' #' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
#' library(dplyr) #' library(dplyr)
#' library(clean)
#' septic_patients %>% #' septic_patients %>%
#' left_join_microorganisms() %>% #' left_join_microorganisms() %>%
#' filter(genus %like% '^ent') %>% #' filter(genus %like% '^ent') %>%

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docs/LICENSE-text.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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>

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docs/articles/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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>

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docs/authors.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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>

8
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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9017" class="section level1"> <div id="amr-0-7-1-9018" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9017" class="anchor"></a>AMR 0.7.1.9017<small> Unreleased </small> <a href="#amr-0-7-1-9018" class="anchor"></a>AMR 0.7.1.9018<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-0-7-1-9017">0.7.1.9017</a></li> <li><a href="#amr-0-7-1-9018">0.7.1.9018</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/eucast_rules.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">0.7.1.9018</span>
</span> </span>
</div> </div>
@ -374,8 +374,6 @@
<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='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>septic_patients</span>)
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>, <span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>, <span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>, <span class='st'>"Escherichia coli"</span>,
@ -411,7 +409,7 @@
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span> <span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
<span class='co'># do not apply EUCAST rules, but rather get a a data.frame</span> <span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span> <span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># }</span></pre> <span class='co'># }</span></pre>

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docs/reference/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">0.7.1.9017</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9018</span>
</span> </span>
</div> </div>

5
docs/reference/like.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">0.7.1.9018</span>
</span> </span>
</div> </div>
@ -299,10 +299,11 @@
<span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</span> <span class='co'># get frequencies of bacteria whose name start with 'Ent' or 'ent'</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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>clean</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span> <span class='fu'><a href='join.html'>left_join_microorganisms</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>genus</span> <span class='kw'>%like%</span> <span class='st'>'^ent'</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>freq</span>(<span class='no'>genus</span>, <span class='no'>species</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/clean/topics/freq'>freq</a></span>(<span class='no'>genus</span>, <span class='no'>species</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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man/eucast_rules.Rd
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@ -135,8 +135,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\examples{ \examples{
a <- eucast_rules(septic_patients)
a <- data.frame(mo = c("Staphylococcus aureus", a <- data.frame(mo = c("Staphylococcus aureus",
"Enterococcus faecalis", "Enterococcus faecalis",
"Escherichia coli", "Escherichia coli",
@ -172,7 +170,7 @@ b
# 5 Pseudomonas aeruginosa R R - - R R R # 5 Pseudomonas aeruginosa R R - - R R R
# do not apply EUCAST rules, but rather get a a data.frame # do not apply EUCAST rules, but rather get a data.frame
# with 18 rows, containing all details about the transformations: # with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE) c <- eucast_rules(a, verbose = TRUE)
} }

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man/like.Rd
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@ -56,6 +56,7 @@ a \%like\% b
# get frequencies of bacteria whose name start with 'Ent' or 'ent' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
library(dplyr) library(dplyr)
library(clean)
septic_patients \%>\% septic_patients \%>\%
left_join_microorganisms() \%>\% left_join_microorganisms() \%>\%
filter(genus \%like\% '^ent') \%>\% filter(genus \%like\% '^ent') \%>\%