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(v0.7.1.9071) p_symbol()

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dr. M.S. (Matthijs) Berends 2019-09-03 09:47:39 +02:00
parent 06b6266366
commit b5d2a08401
18 changed files with 363 additions and 55 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9070 Version: 0.7.1.9071
Date: 2019-09-02 Date: 2019-09-03
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

1
NAMESPACE
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@ -163,6 +163,7 @@ export(mo_year)
export(mrgn) export(mrgn)
export(n_rsi) export(n_rsi)
export(p.symbol) export(p.symbol)
export(p_symbol)
export(portion_I) export(portion_I)
export(portion_IR) export(portion_IR)
export(portion_R) export(portion_R)

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.7.1.9070 # AMR 0.7.1.9071
<small>Last updated: 02-Sep-2019</small> <small>Last updated: 03-Sep-2019</small>
### Breaking ### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@ -98,6 +98,7 @@
* Improved `filter_ab_class()` to be more reliable and to support 5th generation cephalosporins * Improved `filter_ab_class()` to be more reliable and to support 5th generation cephalosporins
* Function `availability()` now uses `portion_R()` instead of `portion_IR()`, to comply with EUCAST insights * Function `availability()` now uses `portion_R()` instead of `portion_IR()`, to comply with EUCAST insights
* Functions `age()` and `age_groups()` now have a `na.rm` parameter to remove empty values * Functions `age()` and `age_groups()` now have a `na.rm` parameter to remove empty values
* Renamed function `p.symbol()` to `p_symbol()` (the former is now deprecated and will be removed in a future version)
#### Other #### Other
* Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors * Added Prof Dr Casper Albers as doctoral advisor and Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors

7
R/deprecated.R
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@ -31,3 +31,10 @@ as.atc <- function(x) {
.Deprecated("ab_atc", package = "AMR") .Deprecated("ab_atc", package = "AMR")
AMR::ab_atc(x) AMR::ab_atc(x)
} }
#' @rdname AMR-deprecated
#' @export
p.symbol <- function(...) {
.Deprecated("p_symbol", package = "AMR")
AMR::p_symbol(...)
}

38
R/p.symbol.R → R/p_symbol.R
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@ -27,34 +27,16 @@
#' @return Text #' @return Text
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @export #' @export
p.symbol <- function(p, emptychar = " ") { p_symbol <- function(p, emptychar = " ") {
setting.bak <- options()$scipen
options(scipen = 999) p <- as.double(p)
s <- vector(mode = "character", length = length(p)) s <- rep(NA_character_, length(p))
for (i in 1:length(p)) {
if (is.na(p[i])) { s[p <= 1] <- emptychar
s[i] <- NA_character_ s[p <= 0.100] <- "."
next s[p <= 0.050] <- "*"
} s[p <= 0.010] <- "**"
if (p[i] > 1) { s[p <= 0.001] <- "***"
s[i] <- NA_character_
next
} else {
p_test <- p[i]
}
if (p_test > 0.1) {
s[i] <- emptychar
} else if (p_test > 0.05) {
s[i] <- '.'
} else if (p_test > 0.01) {
s[i] <- '*'
} else if (p_test > 0.001) {
s[i] <- '**'
} else if (p_test >= 0) {
s[i] <- '***'
}
}
options(scipen = setting.bak)
s s
} }

2
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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>

2
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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>

2
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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>

11
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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>
@ -225,11 +225,11 @@
</div> </div>
<div id="amr-0-7-1-9070" class="section level1"> <div id="amr-0-7-1-9071" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9070" class="anchor"></a>AMR 0.7.1.9070<small> Unreleased </small> <a href="#amr-0-7-1-9071" class="anchor"></a>AMR 0.7.1.9071<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 02-Sep-2019</small></p> <p><small>Last updated: 03-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3> <a href="#breaking" class="anchor"></a>Breaking</h3>
@ -341,6 +341,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>Improved <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> to be more reliable and to support 5th generation cephalosporins</li> <li>Improved <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> to be more reliable and to support 5th generation cephalosporins</li>
<li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code><a href="../reference/portion.html">portion_R()</a></code> instead of <code><a href="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</li> <li>Function <code><a href="../reference/availability.html">availability()</a></code> now uses <code><a href="../reference/portion.html">portion_R()</a></code> instead of <code><a href="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</li>
<li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> parameter to remove empty values</li> <li>Functions <code><a href="../reference/age.html">age()</a></code> and <code><a href="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> parameter to remove empty values</li>
<li>Renamed function <code><a href="../reference/AMR-deprecated.html">p.symbol()</a></code> to <code><a href="../reference/p_symbol.html">p_symbol()</a></code> (the former is now deprecated and will be removed in a future version)</li>
</ul> </ul>
<div id="other" class="section level4"> <div id="other" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
@ -1260,7 +1261,7 @@ 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-0-7-1-9070">0.7.1.9070</a></li> <li><a href="#amr-0-7-1-9071">0.7.1.9071</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>

8
docs/reference/AMR-deprecated.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">0.7.1.9055</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>
@ -234,7 +234,9 @@
</div> </div>
<pre class="usage"><span class='fu'>as.atc</span>(<span class='no'>x</span>)</pre> <pre class="usage"><span class='fu'>as.atc</span>(<span class='no'>x</span>)
<span class='fu'>p.symbol</span>(<span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2> <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -255,7 +257,7 @@
<footer> <footer>
<div class="copyright"> <div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p> <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<div class="pkgdown"> <div class="pkgdown">

8
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">0.7.1.9070</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9071</span>
</span> </span>
</div> </div>
@ -384,9 +384,9 @@
</tr><tr> </tr><tr>
<td> <td>
<p><code><a href="p.symbol.html">p.symbol()</a></code> </p> <p><code><a href="AMR-deprecated.html">as.atc()</a></code> <code><a href="AMR-deprecated.html">p.symbol()</a></code> </p>
</td> </td>
<td><p>Symbol of a p value</p></td> <td><p>Deprecated functions</p></td>
</tr><tr> </tr><tr>
<td> <td>
@ -556,7 +556,7 @@
<tr> <tr>
<td> <td>
<p><code><a href="AMR-deprecated.html">as.atc()</a></code> </p> <p><code><a href="AMR-deprecated.html">as.atc()</a></code> <code><a href="AMR-deprecated.html">p.symbol()</a></code> </p>
</td> </td>
<td><p>Deprecated functions</p></td> <td><p>Deprecated functions</p></td>
</tr> </tr>

308
docs/reference/p_symbol.html Normal file
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@ -0,0 +1,308 @@
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<h1>Symbol of a p value</h1>
<div class="hidden name"><code>p_symbol.Rd</code></div>
</div>
<div class="ref-description">
<p>Return the symbol related to the p value: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1. Values above <code>p = 1</code> will return <code>NA</code>.</p>
</div>
<pre class="usage"><span class='fu'>p_symbol</span>(<span class='no'>p</span>, <span class='kw'>emptychar</span> <span class='kw'>=</span> <span class='st'>" "</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>p</th>
<td><p>p value</p></td>
</tr>
<tr>
<th>emptychar</th>
<td><p>text to show when <code>p &gt; 0.1</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Text</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
</ul>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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2
docs/sitemap.xml
View File

@ -115,7 +115,7 @@
<loc>https://msberends.gitlab.io/AMR/reference/mo_source.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/mo_source.html</loc>
</url> </url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/p.symbol.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/p_symbol.html</loc>
</url> </url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/portion.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/portion.html</loc>

3
man/AMR-deprecated.Rd
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@ -3,9 +3,12 @@
\name{AMR-deprecated} \name{AMR-deprecated}
\alias{AMR-deprecated} \alias{AMR-deprecated}
\alias{as.atc} \alias{as.atc}
\alias{p.symbol}
\title{Deprecated functions} \title{Deprecated functions}
\usage{ \usage{
as.atc(x) as.atc(x)
p.symbol(...)
} }
\description{ \description{
These functions are so-called '\link{Deprecated}'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one). These functions are so-called '\link{Deprecated}'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).

8
man/p.symbol.Rd → man/p_symbol.Rd
View File

@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/p.symbol.R % Please edit documentation in R/p_symbol.R
\name{p.symbol} \name{p_symbol}
\alias{p.symbol} \alias{p_symbol}
\title{Symbol of a p value} \title{Symbol of a p value}
\usage{ \usage{
p.symbol(p, emptychar = " ") p_symbol(p, emptychar = " ")
} }
\arguments{ \arguments{
\item{p}{p value} \item{p}{p value}

3
tests/testthat/test-deprecated.R
View File

@ -35,4 +35,7 @@ test_that("deprecated functions work", {
AMC_ED20 = "S"), AMC_ED20 = "S"),
as.atc("augmentin"))), as.atc("augmentin"))),
"AMC_ED20") "AMC_ED20")
expect_identical(suppressWarnings(p.symbol(seq(0, 1, 0.001))),
p_symbol(seq(0, 1, 0.001)))
}) })

4
tests/testthat/test-p.symbol.R → tests/testthat/test-p_symbol.R
View File

@ -19,9 +19,9 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. # # Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== # # ==================================================================== #
context("p.symbol.R") context("p_symbol.R")
test_that("P symbol works", { test_that("P symbol works", {
expect_identical(p.symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3)), expect_identical(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3)),
c("***", "**", "*", ".", " ", NA, NA)) c("***", "**", "*", ".", " ", NA, NA))
}) })