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(v0.9.0.9024) global vars fix

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dr. M.S. (Matthijs) Berends 2020-02-14 20:03:43 +01:00
parent 9b8b02960e
commit c7a93af3d0
15 changed files with 24 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.9.0.9023 Version: 0.9.0.9024
Date: 2020-02-14 Date: 2020-02-14
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 0.9.0.9023 # AMR 0.9.0.9024
## <small>Last updated: 14-Feb-2020</small> ## <small>Last updated: 14-Feb-2020</small>
### New ### New

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R/data.R
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@ -196,7 +196,7 @@ catalogue_of_life <- list(
#' Data set for R/SI interpretation #' Data set for R/SI interpretation
#' #'
#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. #' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values.
#' @format A [`data.frame`] with 13,975 observations and 9 variables: #' @format A [`data.frame`] with 13,975 observations and 9 variables:
#' - `guideline`\cr Name of the guideline #' - `guideline`\cr Name of the guideline
#' - `method`\cr Either "MIC" or "DISK" #' - `method`\cr Either "MIC" or "DISK"

3
R/globals.R
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@ -25,6 +25,7 @@ globalVariables(c(".",
"ab_txt", "ab_txt",
"abbreviations", "abbreviations",
"antibiotic", "antibiotic",
"antibiotics",
"CNS_CPS", "CNS_CPS",
"col_id", "col_id",
"count", "count",
@ -57,6 +58,7 @@ globalVariables(c(".",
"median", "median",
"microorganisms", "microorganisms",
"microorganisms.codes", "microorganisms.codes",
"microorganisms.old",
"missing_names", "missing_names",
"mo", "mo",
"mono_count", "mono_count",
@ -82,6 +84,7 @@ globalVariables(c(".",
"R", "R",
"real_first_isolate", "real_first_isolate",
"ref", "ref",
"rsi_translation",
"rule_group", "rule_group",
"rule_name", "rule_name",
"S", "S",

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docs/404.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>

4
docs/index.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>
@ -240,7 +240,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li> <li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li> <li>Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li> <li>Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li> <li>Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (<a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt">link</a>)</li>
</ul> </ul>
<p>This package is ready-to-use for specialists in many fields:</p> <p>This package is ready-to-use for specialists in many fields:</p>
<ul> <ul>

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docs/news/index.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>
@ -231,9 +231,9 @@
</div> </div>
<div id="amr-0909023" class="section level1"> <div id="amr-0909024" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0909023" class="anchor"></a>AMR 0.9.0.9023<small> Unreleased </small> <a href="#amr-0909024" class="anchor"></a>AMR 0.9.0.9024<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-14-feb-2020" class="section level2"> <div id="last-updated-14-feb-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -1462,7 +1462,7 @@
<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-0909023">0.9.0.9023</a></li> <li><a href="#amr-0909024">0.9.0.9024</a></li>
<li><a href="#amr-090">0.9.0</a></li> <li><a href="#amr-090">0.9.0</a></li>
<li><a href="#amr-080">0.8.0</a></li> <li><a href="#amr-080">0.8.0</a></li>
<li><a href="#amr-071">0.7.1</a></li> <li><a href="#amr-071">0.7.1</a></li>

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docs/reference/index.html
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@ -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">0.9.0.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>

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docs/reference/rsi_translation.html
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@ -51,7 +51,7 @@
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" /> <meta property="og:title" content="Data set for R/SI interpretation — rsi_translation" />
<meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use as.rsi() to transform MICs or disks measurements to R/SI values." /> <meta property="og:description" content="Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi() to transform MICs or disks measurements to R/SI values." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" /> <meta name="twitter:card" content="summary" />
@ -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">0.9.0.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9024</span>
</span> </span>
</div> </div>
@ -234,7 +234,7 @@
</div> </div>
<div class="ref-description"> <div class="ref-description">
<p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p> <p>Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div> </div>
<pre class="usage"><span class='no'>rsi_translation</span></pre> <pre class="usage"><span class='no'>rsi_translation</span></pre>

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index.md
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@ -50,7 +50,7 @@ This package can be used for:
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html)) * Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html))
* Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code ([manual](./reference/ab_property.html)) * Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code ([manual](./reference/ab_property.html))
* Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt)) * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
This package is ready-to-use for specialists in many fields: This package is ready-to-use for specialists in many fields:

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man/rsi_translation.Rd
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@ -20,7 +20,7 @@
rsi_translation rsi_translation
} }
\description{ \description{
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values. Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
} }
\details{ \details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically. The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.

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tests/testthat/test-ggplot_rsi.R
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@ -23,6 +23,8 @@ context("ggplot_rsi.R")
test_that("ggplot_rsi works", { test_that("ggplot_rsi works", {
skip_on_cran()
skip_if_not("ggplot2" %in% rownames(installed.packages())) skip_if_not("ggplot2" %in% rownames(installed.packages()))
library(dplyr) library(dplyr)