P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

less deps

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-01-27 19:30:40 +01:00
parent a2d3ea280a
commit e76961a66b
27 changed files with 44 additions and 40 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
DESCRIPTION
View File

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

6
R/atc_online.R
View File

@ -19,7 +19,7 @@
# 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.}
#' @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',
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
has_internet <- function(url) {
# extract host from given url

2
R/ggplot_rsi.R
View File

@ -19,7 +19,7 @@
# 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.
#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})

2
docs/LICENSE-text.html
View File

@ -78,7 +78,7 @@
</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="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>
</div>

2
docs/articles/index.html
View File

@ -78,7 +78,7 @@
</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="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>
</div>

2
docs/authors.html
View File

@ -78,7 +78,7 @@
</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="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>
</div>

2
docs/index.html
View File

@ -42,7 +42,7 @@
</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="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>
</div>

2
docs/news/index.html
View File

@ -78,7 +78,7 @@
</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="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>
</div>

2
docs/reference/AMR-deprecated.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/AMR.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/ITIS.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/WHOCC.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/abname.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/age.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/antibiotics.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/as.atc.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/as.mo.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

8
docs/reference/atc_online.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<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 -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet">
<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." />
@ -80,7 +80,7 @@
</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="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>
</div>
@ -216,7 +216,7 @@
<div class="row">
<div class="col-md-9 contents">
<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>

2
docs/reference/atc_property.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

8
docs/reference/ggplot_rsi.html
View File

@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<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 -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet">
<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." />
@ -80,7 +80,7 @@
</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="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>
</div>
@ -216,7 +216,7 @@
<div class="row">
<div class="col-md-9 contents">
<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>

6
docs/reference/index.html
View File

@ -78,7 +78,7 @@
</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="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>
</div>
@ -349,7 +349,7 @@
<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>
</td>
<td><p>Properties of an ATC code</p></td>
<td><p>Get ATC properties from WHOCC website</p></td>
</tr><tr>
<td>
@ -417,7 +417,7 @@
<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>
</td>
<td><p>AMR bar plots with <code>ggplot</code></p></td>
<td><p>AMR plots with <code>ggplot2</code></p></td>
</tr><tr>
<td>

2
docs/reference/microorganisms.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/microorganisms.old.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/mo_property.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
docs/reference/septic_patients.html
View File

@ -80,7 +80,7 @@
</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="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>
</div>

2
man/atc_online.Rd
View File

@ -4,7 +4,7 @@
\alias{atc_online_property}
\alias{atc_online_groups}
\alias{atc_online_ddd}
\title{Properties of an ATC code}
\title{Get ATC properties from WHOCC website}
\source{
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
}

2
man/ggplot_rsi.Rd
View File

@ -8,7 +8,7 @@
\alias{scale_rsi_colours}
\alias{theme_rsi}
\alias{labels_rsi_count}
\title{AMR bar plots with \code{ggplot}}
\title{AMR plots with \code{ggplot2}}
\usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),