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dr. M.S. (Matthijs) Berends 2019-01-27 19:30:40 +01:00
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12
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.5.0.9012 Version: 0.5.0.9013
Date: 2019-01-27 Date: 2019-01-27
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
@ -45,23 +45,23 @@ Depends:
R (>= 3.1.0) R (>= 3.1.0)
Imports: Imports:
backports, backports,
curl,
crayon (>= 1.3.0), crayon (>= 1.3.0),
data.table (>= 1.9.0), data.table (>= 1.9.0),
dplyr (>= 0.7.0), dplyr (>= 0.7.0),
hms, hms,
knitr (>= 1.0.0), knitr (>= 1.0.0),
rlang (>= 0.2.0), rlang (>= 0.2.0),
rvest (>= 0.3.2), tidyr (>= 0.7.0)
tidyr (>= 0.7.0),
xml2 (>= 1.0.0)
Suggests: Suggests:
covr (>= 3.0.1), covr (>= 3.0.1),
curl,
ggplot2, ggplot2,
readxl, readxl,
rmarkdown, rmarkdown,
rstudioapi, rstudioapi,
testthat (>= 1.0.2) rvest (>= 0.3.2),
testthat (>= 1.0.2),
xml2 (>= 1.0.0)
VignetteBuilder: knitr VignetteBuilder: knitr
URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
BugReports: https://gitlab.com/msberends/AMR/issues BugReports: https://gitlab.com/msberends/AMR/issues

6
R/atc_online.R
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# Visit our website for more info: https://msberends.gitab.io/AMR. # # Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== # # ==================================================================== #
#' Properties of an ATC code #' Get ATC properties from WHOCC website
#' #'
#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \cr \strong{This function requires an internet connection.} #' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \cr \strong{This function requires an internet connection.}
#' @param atc_code a character or character vector with ATC code(s) of antibiotic(s) #' @param atc_code a character or character vector with ATC code(s) of antibiotic(s)
@ -78,6 +78,10 @@ atc_online_property <- function(atc_code,
administration = 'O', administration = 'O',
url = 'https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no') { url = 'https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no') {
if (!all(c("curl", "rvest", "xml2") %in% rownames(installed.packages()))) {
stop("Packages 'xml2', 'rvest' and 'curl' are required for this function")
}
# check active network interface, from https://stackoverflow.com/a/5078002/4575331 # check active network interface, from https://stackoverflow.com/a/5078002/4575331
has_internet <- function(url) { has_internet <- function(url) {
# extract host from given url # extract host from given url

2
R/ggplot_rsi.R
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@ -19,7 +19,7 @@
# Visit our website for more info: https://msberends.gitab.io/AMR. # # Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== # # ==================================================================== #
#' AMR bar plots with \code{ggplot} #' AMR plots with \code{ggplot2}
#' #'
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions. #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}}) #' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})

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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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/news/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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/AMR-deprecated.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/AMR.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/ITIS.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/WHOCC.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/abname.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/age.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

2
docs/reference/antibiotics.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

2
docs/reference/as.atc.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

2
docs/reference/as.mo.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/atc_online.html
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Properties of an ATC code — atc_online_property • AMR (for R)</title> <title>Get ATC properties from WHOCC website — atc_online_property • AMR (for R)</title>
<!-- favicons --> <!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet"> <link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="Properties of an ATC code — atc_online_property" /> <meta property="og:title" content="Get ATC properties from WHOCC website — atc_online_property" />
<meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. This function requires an internet connection." /> <meta property="og:description" content="Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. This function requires an internet connection." />
@ -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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>
@ -216,7 +216,7 @@
<div class="row"> <div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>Properties of an ATC code</h1> <h1>Get ATC properties from WHOCC website</h1>
<div class="hidden name"><code>atc_online.Rd</code></div> <div class="hidden name"><code>atc_online.Rd</code></div>
</div> </div>

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docs/reference/atc_property.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/ggplot_rsi.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>AMR bar plots with <code>ggplot</code> — ggplot_rsi • AMR (for R)</title> <title>AMR plots with <code>ggplot2</code> — ggplot_rsi • AMR (for R)</title>
<!-- favicons --> <!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet"> <link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script> <script src="../extra.js"></script>
<meta property="og:title" content="AMR bar plots with <code>ggplot</code> — ggplot_rsi" /> <meta property="og:title" content="AMR plots with <code>ggplot2</code> — ggplot_rsi" />
<meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot functions." /> <meta property="og:description" content="Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal ggplot functions." />
@ -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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>
@ -216,7 +216,7 @@
<div class="row"> <div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<div class="page-header"> <div class="page-header">
<h1>AMR bar plots with <code>ggplot</code></h1> <h1>AMR plots with <code>ggplot2</code></h1>
<div class="hidden name"><code>ggplot_rsi.Rd</code></div> <div class="hidden name"><code>ggplot_rsi.Rd</code></div>
</div> </div>

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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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>
@ -349,7 +349,7 @@
<td> <td>
<p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p> <p><code><a href="atc_online.html">atc_online_property()</a></code> <code><a href="atc_online.html">atc_online_groups()</a></code> <code><a href="atc_online.html">atc_online_ddd()</a></code> </p>
</td> </td>
<td><p>Properties of an ATC code</p></td> <td><p>Get ATC properties from WHOCC website</p></td>
</tr><tr> </tr><tr>
<td> <td>
@ -417,7 +417,7 @@
<td> <td>
<p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p> <p><code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code> </p>
</td> </td>
<td><p>AMR bar plots with <code>ggplot</code></p></td> <td><p>AMR plots with <code>ggplot2</code></p></td>
</tr><tr> </tr><tr>
<td> <td>

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docs/reference/microorganisms.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/microorganisms.old.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

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docs/reference/mo_property.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

2
docs/reference/septic_patients.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="Released version">0.5.0.9012</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9013</span>
</span> </span>
</div> </div>

2
man/atc_online.Rd
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\alias{atc_online_property} \alias{atc_online_property}
\alias{atc_online_groups} \alias{atc_online_groups}
\alias{atc_online_ddd} \alias{atc_online_ddd}
\title{Properties of an ATC code} \title{Get ATC properties from WHOCC website}
\source{ \source{
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/} \url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
} }

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man/ggplot_rsi.Rd
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\alias{scale_rsi_colours} \alias{scale_rsi_colours}
\alias{theme_rsi} \alias{theme_rsi}
\alias{labels_rsi_count} \alias{labels_rsi_count}
\title{AMR bar plots with \code{ggplot}} \title{AMR plots with \code{ggplot2}}
\usage{ \usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic", ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1), fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),