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

(v1.3.0.9039) lifecycle updates, added excess kurtosis

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-10-04 21:02:16 +02:00
parent baf510183c
commit c04dc852cf
30 changed files with 120 additions and 87 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9038
Version: 1.3.0.9039
Date: 2020-10-04
Title: Antimicrobial Resistance Analysis
Authors@R: c(

5
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 1.3.0.9038
## <small>Last updated: 4 October 2020</small>
# AMR 1.3.0.9039
## <small>Last updated: 4 October 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt about this package to. We are those reviewers very grateful for going through our code so thoroughly!
@ -65,6 +65,7 @@ Note: some changes in this version were suggested by anonymous reviewers from th
* 'Penicillin V' (for oral use, code `PNV`) was removed, since its actual entry 'Phenoxymethylpenicillin' (code `PHN`) already existed
* The group name (`antibiotics$group`) of 'Linezolid' (`LNZ`), 'Cycloserine' (`CYC`), 'Tedizolid' (`TZD`) and 'Thiacetazone' (`THA`) is now "Oxazolidinones" instead of "Other antibacterials"
* Added support for using `unique()` on classes `<rsi>`, `<mic>`, `<disk>`, `<ab>` and `<mo>`
* Added parameter `excess` to the `kurtosis()` function (defaults to `FALSE`), to return the *excess kurtosis*, defined as the kurtosis minus three.
### Other
* Removed functions `portion_R()`, `portion_S()` and `portion_I()` that were deprecated since version 0.9.0 (November 2019) and were replaced with `proportion_R()`, `proportion_S()` and `proportion_I()`

2
R/ab.R
View File

@ -22,7 +22,7 @@
#' Transform input to an antibiotic ID
#'
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @inheritSection lifecycle Maturing lifecycle
#' @inheritSection lifecycle Stable lifecycle
#' @param x character vector to determine to antibiotic ID
#' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
#' @param info logical to indicate whether a progress bar should be printed

2
R/guess_ab_col.R
View File

@ -22,7 +22,7 @@
#' Guess antibiotic column
#'
#' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
#' @inheritSection lifecycle Maturing lifecycle
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [data.frame]
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed

22
R/kurtosis.R
View File

@ -21,41 +21,43 @@
#' Kurtosis of the sample
#'
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
#' @inheritSection lifecycle Questioning lifecycle
#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a vector of values, a [`matrix`] or a [data.frame]
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
#' @param na.rm a logical to indicate whether `NA` values should be stripped before the computation proceeds
#' @param excess a logical to indicate whether the *excess kurtosis* should be returned, defined as the kurtosis minus 3.
#' @seealso [skewness()]
#' @rdname kurtosis
#' @inheritSection AMR Read more on our website!
#' @export
kurtosis <- function(x, na.rm = FALSE) {
kurtosis <- function(x, na.rm = FALSE, excess = FALSE) {
UseMethod("kurtosis")
}
#' @method kurtosis default
#' @rdname kurtosis
#' @export
kurtosis.default <- function(x, na.rm = FALSE) {
kurtosis.default <- function(x, na.rm = FALSE, excess = FALSE) {
x <- as.vector(x)
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}
n <- length(x)
n * sum((x - mean(x, na.rm = na.rm))^4, na.rm = na.rm) /
k <- n * sum((x - mean(x, na.rm = na.rm))^4, na.rm = na.rm) /
(sum((x - mean(x, na.rm = na.rm))^2, na.rm = na.rm)^2)
k - ifelse(excess, 3, 0)
}
#' @method kurtosis matrix
#' @rdname kurtosis
#' @export
kurtosis.matrix <- function(x, na.rm = FALSE) {
apply(x, 2, kurtosis.default, na.rm = na.rm)
kurtosis.matrix <- function(x, na.rm = FALSE, excess = FALSE) {
apply(x, 2, kurtosis.default, na.rm = na.rm, excess = excess)
}
#' @method kurtosis data.frame
#' @rdname kurtosis
#' @export
kurtosis.data.frame <- function(x, na.rm = FALSE) {
sapply(x, kurtosis.default, na.rm = na.rm)
kurtosis.data.frame <- function(x, na.rm = FALSE, excess = FALSE) {
sapply(x, kurtosis.default, na.rm = na.rm, excess = excess)
}

2
R/mdro.R
View File

@ -22,7 +22,7 @@
#' Determine multidrug-resistant organisms (MDRO)
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
#' @inheritSection lifecycle Maturing lifecycle
#' @inheritSection lifecycle Stable lifecycle
#' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
#' @inheritParams eucast_rules
#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.

6
R/skewness.R
View File

@ -23,10 +23,10 @@
#'
#' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
#'
#' When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.
#' @inheritSection lifecycle Questioning lifecycle
#' When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a vector of values, a [`matrix`] or a [data.frame]
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds
#' @seealso [kurtosis()]
#' @rdname skewness
#' @inheritSection AMR Read more on our website!

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

2
docs/articles/EUCAST.html
View File

@ -39,7 +39,7 @@
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

2
docs/index.html
View File

@ -43,7 +43,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

9
docs/news/index.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309038" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9038">
<a href="#amr-1309038" class="anchor"></a>AMR 1.3.0.9038<small> Unreleased </small>
<div id="amr-1309039" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9039">
<a href="#amr-1309039" class="anchor"></a>AMR 1.3.0.9039<small> Unreleased </small>
</h1>
<div id="last-updated-4-october-2020" class="section level2">
<h2 class="hasAnchor">
@ -331,6 +331,7 @@
</ul>
</li>
<li><p>Added support for using <code><a href="https://rdrr.io/r/base/unique.html">unique()</a></code> on classes <code>&lt;rsi&gt;</code>, <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;ab&gt;</code> and <code>&lt;mo&gt;</code></p></li>
<li><p>Added parameter <code>excess</code> to the <code><a href="../reference/kurtosis.html">kurtosis()</a></code> function (defaults to <code>FALSE</code>), to return the <em>excess kurtosis</em>, defined as the kurtosis minus three.</p></li>
</ul>
</div>
<div id="other" class="section level3">

2
docs/pkgdown.yml
View File

@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-10-04T17:22Z
last_built: 2020-10-04T19:01Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

9
docs/reference/as.ab.html
View File

@ -82,7 +82,7 @@
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -288,12 +288,13 @@
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>

2
docs/reference/eucast_rules.html
View File

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

9
docs/reference/guess_ab_col.html
View File

@ -82,7 +82,7 @@
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -267,12 +267,13 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href='antibiotics.html'>antibiotics</a> data set for any column containing a name or code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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>

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

27
docs/reference/kurtosis.html
View File

@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Kurtosis of the sample — kurtosis" />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable." />
<meta property="og:description" content="Kurtosis is a measure of the &quot;tailedness&quot; of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -82,7 +82,7 @@
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -239,19 +239,19 @@
</div>
<div class="ref-description">
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.</p>
<p>Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.</p>
</div>
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<pre class="usage"><span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for default</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for matrix</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)
<span class='co'># S3 method for data.frame</span>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)</pre>
<span class='fu'>kurtosis</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>, excess = <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -262,16 +262,21 @@
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></td>
<td><p>a logical to indicate whether <code>NA</code> values should be stripped before the computation proceeds</p></td>
</tr>
<tr>
<th>excess</th>
<td><p>a logical to indicate whether the <em>excess kurtosis</em> should be returned, defined as the kurtosis minus 3.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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>

9
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -337,12 +337,13 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<p>Please suggest your own (country-specific) guidelines by letting us know: <a href='https://github.com/msberends/AMR/issues/new'>https://github.com/msberends/AMR/issues/new</a>.</p>
<p><strong>Note:</strong> Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named <em>order</em> Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu <em>et al.</em> in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this <code>mdro()</code> function makes sure that results from before 2016 and after 2016 are identical.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

2
docs/reference/mo_source.html
View File

@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

15
docs/reference/skewness.html
View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Skewness of the sample — skewness" />
<meta property="og:description" content="Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure." />
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>
@ -241,7 +241,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<div class="ref-description">
<p>Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.</p>
<p>When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.</p>
<p>When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.</p>
</div>
<pre class="usage"><span class='fu'>skewness</span>(<span class='kw'>x</span>, na.rm = <span class='fl'>FALSE</span>)
@ -264,16 +264,17 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</tr>
<tr>
<th>na.rm</th>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds.</p></td>
<td><p>a logical value indicating whether <code>NA</code> values should be stripped before the computation proceeds</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="questioning-lifecycle"><a class="anchor" href="#questioning-lifecycle"></a>Questioning lifecycle</h2>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
<p><img src='figures/lifecycle_questioning.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioning</strong>. This function might be no longer be optimal approach, or is it questionable whether this function should be in this <code>AMR</code> package at all.</p>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</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>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</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="Latest development version">1.3.0.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9039</span>
</span>
</div>

8
man/as.ab.Rd
View File

@ -47,10 +47,12 @@ WHONET 2019 software: \url{http://www.whonet.org/software.html}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
}
\section{Maturing lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{WHOCC}{

8
man/guess_ab_col.Rd
View File

@ -22,10 +22,12 @@ This tries to find a column name in a data set based on information from the \li
\details{
You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \link{antibiotics} data set for any column containing a name or code of that antibiotic. \strong{Longer columns names take precendence over shorter column names.}
}
\section{Maturing lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Read more on our website!}{

22
man/kurtosis.Rd
View File

@ -7,26 +7,30 @@
\alias{kurtosis.data.frame}
\title{Kurtosis of the sample}
\usage{
kurtosis(x, na.rm = FALSE)
kurtosis(x, na.rm = FALSE, excess = FALSE)
\method{kurtosis}{default}(x, na.rm = FALSE)
\method{kurtosis}{default}(x, na.rm = FALSE, excess = FALSE)
\method{kurtosis}{matrix}(x, na.rm = FALSE)
\method{kurtosis}{matrix}(x, na.rm = FALSE, excess = FALSE)
\method{kurtosis}{data.frame}(x, na.rm = FALSE)
\method{kurtosis}{data.frame}(x, na.rm = FALSE, excess = FALSE)
}
\arguments{
\item{x}{a vector of values, a \code{\link{matrix}} or a \link{data.frame}}
\item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds.}
\item{na.rm}{a logical to indicate whether \code{NA} values should be stripped before the computation proceeds}
\item{excess}{a logical to indicate whether the \emph{excess kurtosis} should be returned, defined as the kurtosis minus 3.}
}
\description{
Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.
}
\section{Questioning lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Read more on our website!}{

8
man/mdro.Rd
View File

@ -94,10 +94,12 @@ Please suggest your own (country-specific) guidelines by letting us know: \url{h
\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named \emph{order} Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
}
\section{Maturing lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Antibiotics}{

12
man/skewness.Rd
View File

@ -18,17 +18,19 @@ skewness(x, na.rm = FALSE)
\arguments{
\item{x}{a vector of values, a \code{\link{matrix}} or a \link{data.frame}}
\item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds.}
\item{na.rm}{a logical value indicating whether \code{NA} values should be stripped before the computation proceeds}
}
\description{
Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.
When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.
}
\section{Questioning lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Read more on our website!}{

8
tests/testthat/test-kurtosis.R
View File

@ -26,10 +26,18 @@ test_that("kurtosis works", {
expect_equal(kurtosis(example_isolates$age),
3.549319,
tolerance = 0.00001)
expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
3.549319,
tolerance = 0.00001)
expect_equal(unname(kurtosis(data.frame(example_isolates$age), excess = TRUE)),
0.549319,
tolerance = 0.00001)
expect_equal(kurtosis(matrix(example_isolates$age)),
3.549319,
tolerance = 0.00001)
expect_equal(kurtosis(matrix(example_isolates$age), excess = TRUE),
0.549319,
tolerance = 0.00001)
})