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is.rsi.eligible update

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dr. M.S. (Matthijs) Berends 2019-02-04 12:24:07 +01:00
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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.5.0.9016
Date: 2019-02-01
Date: 2019-02-04
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NAMESPACE
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@ -66,6 +66,7 @@ export(atc_property)
export(atc_tradenames)
export(atc_trivial_nl)
export(atc_umcg)
export(availability)
export(brmo)
export(count_I)
export(count_IR)

2
NEWS.md
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@ -77,7 +77,7 @@
* A note to the manual pages of the `portion` functions, that low counts can influence the outcome and that the `portion` functions may camouflage this, since they only return the portion (albeit being dependent on the `minimum` parameter)
* Merged data sets `microorganisms.certe` and `microorganisms.umcg` into `microorganisms.codes`
* Function `mo_taxonomy()` now contains the kingdom too
* Reduce false positives for `is.rsi.eligible()`
* Reduce false positives for `is.rsi.eligible()` using the new `threshold` parameter
* New colours for `scale_rsi_colours()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
* Small text updates to summaries of class `rsi` and `mic`

61
R/availability.R Normal file
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@ -0,0 +1,61 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Check availability of columns
#'
#' Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
#' @param tbl a \code{data.frame} or \code{list}
#' @return \code{data.frame} with column names of \code{tbl} as row names and columns: \code{percent_IR}, \code{count}, \code{percent}, \code{visual_availability}.
#' @export
#' @examples
#' availability(septic_patients)
#'
#' library(dplyr)
#' septic_patients %>% availability()
#'
#' septic_patients %>%
#' select_if(is.rsi) %>%
#' availability()
#'
#' septic_patients %>%
#' filter(mo == as.mo("E. coli")) %>%
#' select_if(is.rsi) %>%
#' availability()
availability <- function(tbl) {
x <- base::sapply(tbl, function(x) { 1 - base::sum(base::is.na(x)) / base::length(x) })
n <- base::sapply(tbl, function(x) base::length(x[!base::is.na(x)]))
IR <- base::sapply(tbl, function(x) base::ifelse(is.rsi(x), base::round(portion_IR(x, minimum = 0) * 100, 1), "NaN"))
IR <- paste0(IR, "%")
IR <- gsub("NaN%", "", IR)
max_chars <- 50
x_chars <- strrep("#", round(x, digits = 2) / (1 / max_chars))
x_chars_empty <- strrep("-", max_chars - nchar(x_chars))
# x_abnames <- character(length(x))
# for (i in 1:length(x)) {
# if (tbl %>% pull(i) %>% is.rsi()) {
# x_abnames[i] <- atc_name(colnames(tbl)[i])
# }
# }
data.frame(percent_IR = IR,
count = n,
percent = paste0(round(x * 100, 1), "%"),
visual_availabilty = paste0("|", x_chars, x_chars_empty, "|"))
}

4
R/data.R
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@ -211,7 +211,7 @@
#' \describe{
#' \item{\code{Identification number}}{ID of the sample}
#' \item{\code{Specimen number}}{ID of the specimen}
#' \item{\code{Organism}}{Microorganisms, can be coerced with \code{\link{as.mo}}}
#' \item{\code{Organism}}{Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using \code{\link{as.mo}}.}
#' \item{\code{Country}}{Country of origin}
#' \item{\code{Laboratory}}{Name of laboratory}
#' \item{\code{Last name}}{Last name of patient}
@ -234,7 +234,7 @@
#' \item{\code{Inducible clindamycin resistance}}{Clindamycin can be induced?}
#' \item{\code{Comment}}{Other comments}
#' \item{\code{Date of data entry}}{Date this data was entered in WHONET}
#' \item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately.}
#' \item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link{as.rsi}}.}
#' }
#' @inheritSection AMR Read more on our website!
"WHONET"

2
R/first_isolate.R
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@ -381,7 +381,7 @@ first_isolate <- function(tbl,
if (abs(row.start) == Inf | abs(row.end) == Inf) {
if (info == TRUE) {
message('No isolates found.')
message(paste("=> Found", bold("no isolates")))
}
# NAs where genus is unavailable
return(tbl %>%

43
R/rsi.R
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@ -24,6 +24,7 @@
#' This transforms a vector to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
#' @rdname as.rsi
#' @param x vector
#' @param threshold maximum fraction of \code{x} that is allowed to fail transformation, see Examples
#' @details The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
#' @return Ordered factor with new class \code{rsi}
#' @keywords rsi
@ -48,10 +49,15 @@
#' septic_patients %>%
#' mutate_at(vars(peni:rifa), as.rsi)
#'
#'
#' # fastest way to transform all columns with already valid AB results to class `rsi`:
#' septic_patients %>%
#' mutate_if(is.rsi.eligible,
#' as.rsi)
#'
#' # default threshold of `is.rsi.eligible` is 5%.
#' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
#' is.rsi.eligible(WHONET$`First name`, threhold = 0.9) # succeeds
as.rsi <- function(x) {
if (is.rsi(x)) {
x
@ -99,28 +105,37 @@ as.rsi <- function(x) {
#' @rdname as.rsi
#' @export
#' @importFrom dplyr %>%
is.rsi <- function(x) {
class(x) %>% identical(c('rsi', 'ordered', 'factor'))
identical(class(x),
c('rsi', 'ordered', 'factor'))
}
#' @rdname as.rsi
#' @export
#' @importFrom dplyr %>%
is.rsi.eligible <- function(x) {
if (is.logical(x)
| is.numeric(x)
| is.mo(x)
| identical(class(x), "Date")
| is.rsi(x)) {
is.rsi.eligible <- function(x, threshold = 0.05) {
if (NCOL(x) > 1) {
stop('`x` must be a one-dimensional vector.')
}
if (any(c("logical",
"numeric",
"integer",
"mo",
"Date",
"POSIXct",
"rsi",
"raw",
"hms")
%in% class(x))) {
# no transformation needed
FALSE
} else {
# check all but a-z
y <- unique(gsub("[^RSIrsi]+", "", unique(x)))
!all(y %in% c("", NA_character_)) &
all(y %in% c("R", "I", "S", "", NA_character_)) &
max(nchar(as.character(x)), na.rm = TRUE) < 8
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
if (length(x) == 0) {
return(FALSE)
}
checked <- suppressWarnings(as.rsi(x))
outcome <- sum(is.na(checked)) / length(x)
outcome <= threshold
}
}

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docs/index.html
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@ -190,11 +190,13 @@
<p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
<hr>
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
<p>After installing this package, R knows almost all ~20.000 microorganisms and ~500 antibiotics by name and code, and knows all about valid RSI and MIC values.</p>
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but <strong>not</strong> patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license <a href="./LICENSE-text.html">here</a>.</p>
<p>This package can be used for:</p>
<ul>
<li>Calculating antimicrobial resistance</li>
<li>Predicting antimicrobial resistance using regression models</li>
<li>Predicting empiric susceptibility of both mono therapy and combination therapy</li>
<li>Predicting future antimicrobial resistance using regression models</li>
<li>Getting properties for any microorganism (like Gram stain, species, genus or family)</li>
<li>Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)</li>
<li>Plotting antimicrobial resistance</li>
@ -236,15 +238,15 @@
<h4 class="hasAnchor">
<a href="#latest-released-version" class="anchor"></a>Latest released version</h4>
<p>This package is available <a href="https://cran.r-project.org/package=AMR">on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R with:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</code></pre></div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
</div>
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>The latest and unpublished development version can be installed with (precaution: may be unstable):</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"devtools"</span>)
devtools::<span class="kw">install_gitlab</span>(<span class="st">"msberends/AMR"</span>)</code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"devtools"</span>)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2">devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</a></code></pre></div>
</div>
</div>
<div id="get-started" class="section level2">
@ -284,17 +286,17 @@ devtools::<span class="kw">install_gitlab</span>(<span class="st">"msberends/AMR
<a href="#overview-of-functions" class="anchor"></a>Overview of functions</h4>
<p>The <code>AMR</code> package basically does four important things:</p>
<ol>
<li>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). With this package, you learn R everything about microbiology that is needed for analysis. These functions all use artificial intelligence to guess results that you would expect:</li>
</ol>
<li>
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use artificial intelligence to guess results that you would expect:</p>
<ul>
<li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using artificial intelligence (AI) on the included ITIS data set, consisting of almost 20,000 microorganisms. It is <em>very</em> fast, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
<li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
<li>Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
</ul>
<ol>
<li>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</li>
</ol>
</li>
<li>
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<ul>
<li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li>
<li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
@ -306,9 +308,9 @@ devtools::<span class="kw">install_gitlab</span>(<span class="st">"msberends/AMR
<li>The <a href="./reference/microorganisms.html">data set <code>microorganisms</code></a> contains the complete taxonomic tree of almost 20,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use artificial intelligence. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The <a href="./reference/antibiotics.html">data set <code>antibiotics</code></a> contains almost 500 antimicrobial drugs with their ATC code, EARS-Net code, common LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains hundreds of trade names. Use functions like <code><a href="reference/atc_property.html">atc_name()</a></code> and <code><a href="reference/atc_property.html">atc_tradenames()</a></code> to look up values. The <code>atc_*</code> functions use <code><a href="reference/as.atc.html">as.atc()</a></code> internally so they support AI to guess your expected result. For example, <code><a href="reference/atc_property.html">atc_name("Fluclox")</a></code>, <code><a href="reference/atc_property.html">atc_name("Floxapen")</a></code> and <code><a href="reference/atc_property.html">atc_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul>
<ol>
<li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li>
</ol>
</li>
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
@ -316,9 +318,9 @@ devtools::<span class="kw">install_gitlab</span>(<span class="st">"msberends/AMR
<li>Conduct descriptive statistics to enhance base R: calculate <code><a href="reference/kurtosis.html">kurtosis()</a></code>, <code><a href="reference/skewness.html">skewness()</a></code> and create frequency tables with <code><a href="reference/freq.html">freq()</a></code>
</li>
</ul>
<ol>
<li>It <strong>teaches the user</strong> how to use all the above actions.</li>
</ol>
</li>
<li>
<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
<ul>
<li>Aside from this website with many tutorials, the package itself contains extensive help pages with many examples for all functions.</li>
<li>It also contains an <a href=".reference/septic_patients.html">example data set called <code>septic_patients</code></a>. This data set contains:
@ -329,6 +331,8 @@ devtools::<span class="kw">install_gitlab</span>(<span class="st">"msberends/AMR
</ul>
</li>
</ul>
</li>
</ol>
</div>
<div id="partners" class="section level4">
<h4 class="hasAnchor">

258
docs/news/index.html
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@ -236,13 +236,28 @@
<ul>
<li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
<li>This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the <code>antibiotics</code> data set now contains a column <code>ears_net</code>.</li>
<li>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions: <code>r ab_property -&gt; atc_property() ab_name -&gt; atc_name() ab_official -&gt; atc_official() ab_trivial_nl -&gt; atc_trivial_nl() ab_certe -&gt; atc_certe() ab_umcg -&gt; atc_umcg() ab_tradenames -&gt; atc_tradenames()</code> These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</li>
</ul>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_property</a></span>()</a>
<a class="sourceLine" id="cb1-2" data-line-number="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_name</a></span>()</a>
<a class="sourceLine" id="cb1-3" data-line-number="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_official</a></span>()</a>
<a class="sourceLine" id="cb1-4" data-line-number="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_trivial_nl</a></span>()</a>
<a class="sourceLine" id="cb1-5" data-line-number="5">ab_certe -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_certe</a></span>()</a>
<a class="sourceLine" id="cb1-6" data-line-number="6">ab_umcg -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a>
<a class="sourceLine" id="cb1-7" data-line-number="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul>
</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
@ -250,11 +265,24 @@
<li>New function <code><a href="../reference/mo_renamed.html">mo_renamed()</a></code> to get a list of all returned values from <code><a href="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li>
<li>New function <code><a href="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>: <code>r x &lt;- resistance_predict(septic_patients, col_ab = "amox") plot(x) ggplot_rsi_predict(x)</code>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
</li>
<li>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.: <code>r septic_patients %&gt;% filter_first_isolate(...) # or filter_first_isolate(septic_patients, ...)</code> is equal to: <code>r septic_patients %&gt;% mutate(only_firsts = first_isolate(septic_patients, ...)) %&gt;% filter(only_firsts == TRUE) %&gt;% select(-only_firsts)</code>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li>
<li>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</li>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
</div>
<div id="changed" class="section level4">
@ -266,12 +294,16 @@
<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_atc()</a></code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</li>
<li>Function <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
<li>Updated EUCAST Clinical breakpoints to <a href="http://www.eucast.org/clinical_breakpoints/">version 9.0 of 1 January 2019</a>
</li>
<li>Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Emphasised in manual that penicillin is meant as benzylpenicillin (ATC <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01">J01CE01</a>)</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:</li>
</ul>
</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li>
<li>Better handling for subspecies</li>
@ -282,40 +314,45 @@
<li>Progress bar will be shown when it takes more than 3 seconds to get results</li>
<li>Support for formatted console text</li>
<li>Console will return the percentage of uncoercable input</li>
<li>Function <code><a href="../reference/first_isolate.html">first_isolate()</a></code>:</li>
</ul>
</li>
<li>Function <code><a href="../reference/first_isolate.html">first_isolate()</a></code>:
<ul>
<li>Fixed a bug where distances between dates would not be calculated right - in the <code>septic_patients</code> data set this yielded a difference of 0.15% more isolates</li>
<li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (parameter <code>col_keyantibiotics()</code>), when this parameter was left blank</li>
<li>Removed parameter <code>output_logical</code>, the function will now always return a logical value</li>
<li>Renamed parameter <code>filter_specimen</code> to <code>specimen_group</code>, although using <code>filter_specimen</code> will still work</li>
</ul>
</li>
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Merged data sets <code>microorganisms.certe</code> and <code>microorganisms.umcg</code> into <code>microorganisms.codes</code>
</li>
<li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> using the new <code>threshold</code> parameter</li>
<li>New colours for <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code>
</li>
<li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary(mo)</a></code>
</li>
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
</li>
<li>Frequency tables (<code><a href="../reference/freq.html">freq()</a></code> function):</li>
<li>Frequency tables (<code><a href="../reference/freq.html">freq()</a></code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
septic_patients %&gt;%
<span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) %&gt;%
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)
<span class="co"># NEW WAY</span>
septic_patients %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))
<span class="co"># Even supports grouping variables:</span>
septic_patients %&gt;%
<span class="st"> </span><span class="kw">group_by</span>(gender) %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb5-9" data-line-number="9"></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
</li>
<li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@ -328,11 +365,13 @@ septic_patients %&gt;%
<li>New parameter <code>droplevels</code> to exclude empty factor levels when input is a factor</li>
<li>Factor levels will be in header when present in input data (maximum of 5)</li>
<li>Fix for using <code>select()</code> on frequency tables</li>
</ul>
</li>
<li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <code>limits</code> parameter</li>
<li>Automatic parameter filling for <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
<li>Updated examples for resistance prediction (<code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> function)</li>
<li><p>Fix for <code><a href="../reference/as.mic.html">as.mic()</a></code> to support more values ending in (several) zeroes</p></li>
<li>Fix for <code><a href="../reference/as.mic.html">as.mic()</a></code> to support more values ending in (several) zeroes</li>
</ul>
</div>
<div id="other" class="section level4">
@ -369,7 +408,8 @@ septic_patients %&gt;%
</li>
<li>
<code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</li>
<li>Big changes to the <code>eucast_rules</code> function:</li>
<li>Big changes to the <code>eucast_rules</code> function:
<ul>
<li>Now also applies rules from the EUCAST ‘Breakpoint tables for bacteria’, version 8.1, 2018, <a href="http://www.eucast.org/clinical_breakpoints/" class="uri">http://www.eucast.org/clinical_breakpoints/</a> (see Source of the function)</li>
<li>New parameter <code>rules</code> to specify which rules should be applied (expert rules, breakpoints, others or all)</li>
<li>New parameter <code>verbose</code> which can be set to <code>TRUE</code> to get very specific messages about which columns and rows were affected</li>
@ -378,11 +418,18 @@ septic_patients %&gt;%
<li>Data set <code>septic_patients</code> now reflects these changes</li>
<li>Added parameter <code>pipe</code> for piperacillin (J01CA12), also to the <code>mdro</code> function</li>
<li>Small fixes to EUCAST clinical breakpoint rules</li>
</ul>
</li>
<li>Added column <code>kingdom</code> to the microorganisms data set, and function <code>mo_kingdom</code> to look up values</li>
<li>Tremendous speed improvement for <code>as.mo</code> (and subsequently all <code>mo_*</code> functions), as empty values wil be ignored <em>a priori</em>
</li>
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached <code>r as.mo("E. species") # B_ESCHR mo_fullname("E. spp.") # "Escherichia species" as.mo("S. spp") # B_STPHY mo_fullname("S. species") # "Staphylococcus species"</code>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -391,18 +438,19 @@ septic_patients %&gt;%
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
</li>
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
<li>Frequency tables - <code><a href="../reference/freq.html">freq()</a></code>:</li>
<li>Frequency tables - <code><a href="../reference/freq.html">freq()</a></code>:
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw">group_by</span>(hospital_id) %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</code></pre></div>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb7-2" data-line-number="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb7-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">septic_patients %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) %&gt;%<span class="st"> </span>
<span class="st"> </span><span class="kw">select</span>(-count, -cum_count) <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-3" data-line-number="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li>
@ -413,6 +461,8 @@ septic_patients %&gt;%
<li>New parameter <code>na</code>, to choose which character to print for empty values</li>
<li>New parameter <code>header</code> to turn the header info off (default when <code>markdown = TRUE</code>)</li>
<li>New parameter <code>title</code> to manually setbthe title of the frequency table</li>
</ul>
</li>
<li>
<code>first_isolate</code> now tries to find columns to use as input when parameters are left blank</li>
<li>Improvements for MDRO algorithm (function <code>mdro</code>)</li>
@ -424,7 +474,8 @@ septic_patients %&gt;%
</li>
<li>
<code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> parameter</li>
<li>AI improvements for <code>as.mo</code>:</li>
<li>AI improvements for <code>as.mo</code>:
<ul>
<li>
<code>"CRS"</code> -&gt; <em>Stenotrophomonas maltophilia</em>
</li>
@ -437,6 +488,8 @@ septic_patients %&gt;%
<li>
<code>"MSSE"</code> -&gt; <em>Staphylococcus epidermidis</em>
</li>
</ul>
</li>
<li>Fix for <code>join</code> functions</li>
<li>Speed improvement for <code>is.rsi.eligible</code>, now 15-20 times faster</li>
<li>In <code>g.test</code>, when <code><a href="https://www.rdocumentation.org/packages/base/topics/sum">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
@ -465,7 +518,8 @@ septic_patients %&gt;%
<a href="#new-2" class="anchor"></a>New</h4>
<ul>
<li>The data set <code>microorganisms</code> now contains <strong>all microbial taxonomic data from ITIS</strong> (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via <a href="https://itis.gov" class="uri">https://itis.gov</a>. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set <code>microorganisms.old</code> contains all previously known taxonomic names from those kingdoms.</li>
<li>New functions based on the existing function <code>mo_property</code>:</li>
<li>New functions based on the existing function <code>mo_property</code>:
<ul>
<li>Taxonomic names: <code>mo_phylum</code>, <code>mo_class</code>, <code>mo_order</code>, <code>mo_family</code>, <code>mo_genus</code>, <code>mo_species</code>, <code>mo_subspecies</code>
</li>
<li>Semantic names: <code>mo_fullname</code>, <code>mo_shortname</code>
@ -475,22 +529,52 @@ septic_patients %&gt;%
<li>Author and year: <code>mo_ref</code>
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese: <code>r mo_gramstain("E. coli") # [1] "Gram negative" mo_gramstain("E. coli", language = "de") # German # [1] "Gramnegativ" mo_gramstain("E. coli", language = "es") # Spanish # [1] "Gram negativo" mo_fullname("S. group A", language = "pt") # Portuguese # [1] "Streptococcus grupo A"</code></p>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name: <code>r mo_gramstain("Esc blattae") # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010) # [1] "Gram negative"</code></p>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb10-3" data-line-number="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates</li>
<li>Extra function <code>count_df</code> (which works like <code>portion_df</code>) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code>
</li>
<li>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI): <code>r as.mo("E. coli") # [1] B_ESCHR_COL as.mo("MRSA") # [1] B_STPHY_AUR as.mo("S group A") # [1] B_STRPTC_GRA</code> And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items: <code>r thousands_of_E_colis &lt;- rep("E. coli", 25000) microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s") # Unit: seconds # min median max neval # 0.01817717 0.01843957 0.03878077 100</code>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb11-3" data-line-number="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb11-4" data-line-number="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb11-5" data-line-number="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb11-6" data-line-number="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb12-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb12-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb12-4" data-line-number="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb12-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
<ul>
<li>Column names inputs of <code>EUCAST_rules</code>, <code>first_isolate</code> and <code>key_antibiotics</code>
</li>
<li>Column names of datasets <code>microorganisms</code> and <code>septic_patients</code>
</li>
<li>All old syntaxes will still work with this version, but will throw warnings</li>
</ul>
</li>
<li>Function <code>labels_rsi_count</code> to print datalabels on a RSI <code>ggplot2</code> model</li>
<li><p>Functions <code>as.atc</code> and <code>is.atc</code> to transform/look up antibiotic ATC codes as defined by the WHO. The existing function <code>guess_atc</code> is now an alias of <code>as.atc</code>.</p></li>
<li>Function <code>ab_property</code> and its aliases: <code>ab_name</code>, <code>ab_tradenames</code>, <code>ab_certe</code>, <code>ab_umcg</code> and <code>ab_trivial_nl</code>
@ -505,7 +589,14 @@ septic_patients %&gt;%
<a href="#changed-2" class="anchor"></a>Changed</h4>
<ul>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.: <code>r ab_official("Bactroban") # [1] "Mupirocin" ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin" ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</code>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb13-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb13-3" data-line-number="3"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb13-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb13-5" data-line-number="5"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb13-6" data-line-number="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -514,9 +605,36 @@ septic_patients %&gt;%
<li>Added <code>prevalence</code> column to the <code>microorganisms</code> data set</li>
<li>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code>
</li>
<li>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns. ```r septic_patients %&gt;% select(amox, cipr) %&gt;% count_IR() # which is the same as: septic_patients %&gt;% count_IR(amox, cipr)</li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb14-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb14-4" data-line-number="4"></a>
<a class="sourceLine" id="cb14-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb14-6" data-line-number="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb14-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
<li>Added datalabels function <code>labels_rsi_count</code> to <code>ggplot_rsi</code>
</li>
<li>Added possibility to set any parameter to <code>geom_rsi</code> (and <code>ggplot_rsi</code>) so you can set your own preferences</li>
<li>Fix for joins, where predefined suffices would not be honoured</li>
<li>Added parameter <code>quote</code> to the <code>freq</code> function</li>
<li>Added generic function <code>diff</code> for frequency tables</li>
<li>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code>
</li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb15-2" data-line-number="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb16-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb16-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
</ul>
<p>septic_patients %&gt;% portion_S(amcl) septic_patients %&gt;% portion_S(amcl, gent) septic_patients %&gt;% portion_S(amcl, gent, pita) <code>* Edited `ggplot_rsi` and `geom_rsi` so they can cope with `count_df`. The new `fun` parameter has value `portion_df` at default, but can be set to `count_df`. * Fix for `ggplot_rsi` when the `ggplot2` package was not loaded * Added datalabels function `labels_rsi_count` to `ggplot_rsi` * Added possibility to set any parameter to `geom_rsi` (and `ggplot_rsi`) so you can set your own preferences * Fix for joins, where predefined suffices would not be honoured * Added parameter `quote` to the `freq` function * Added generic function `diff` for frequency tables * Added longest en shortest character length in the frequency table (`freq`) header of class `character` * Support for types (classes) list and matrix for `freq`</code>r my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2)) freq(my_matrix) <code>For lists, subsetting is possible:</code>r my_list = list(age = septic_patients$age, gender = septic_patients$gender) my_list %&gt;% freq(age) my_list %&gt;% freq(gender) ```</p>
</div>
<div id="other-2" class="section level4">
<h4 class="hasAnchor">
@ -535,15 +653,21 @@ septic_patients %&gt;%
<a href="#new-3" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.</li>
<strong>BREAKING</strong>: <code>rsi_df</code> was removed in favour of new functions <code>portion_R</code>, <code>portion_IR</code>, <code>portion_I</code>, <code>portion_SI</code> and <code>portion_S</code> to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old <code>rsi</code> function. The old function still works, but is deprecated.
<ul>
<li>New function <code>portion_df</code> to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables</li>
</ul>
</li>
<li>
<strong>BREAKING</strong>: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call <em>key antibiotics</em>) to include more first isolates (afterwards called first <em>weighted</em> isolates) are now as follows:</li>
<strong>BREAKING</strong>: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call <em>key antibiotics</em>) to include more first isolates (afterwards called first <em>weighted</em> isolates) are now as follows:
<ul>
<li>Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole</li>
<li>Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin</li>
<li>Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem</li>
<li>Support for <code>ggplot2</code>
</ul>
</li>
<li>Support for <code>ggplot2</code>
<ul>
<li>New functions <code>geom_rsi</code>, <code>facet_rsi</code>, <code>scale_y_percent</code>, <code>scale_rsi_colours</code> and <code>theme_rsi</code>
</li>
<li>New wrapper function <code>ggplot_rsi</code> to apply all above functions on a data set:
@ -554,22 +678,32 @@ septic_patients %&gt;%
</li>
</ul>
</li>
<li>Determining bacterial ID:</li>
</ul>
</li>
<li>Determining bacterial ID:
<ul>
<li>New functions <code>as.bactid</code> and <code>is.bactid</code> to transform/ look up microbial ID’s.</li>
<li>The existing function <code>guess_bactid</code> is now an alias of <code>as.bactid</code>
</li>
<li>New Becker classification for <em>Staphylococcus</em> to categorise them into Coagulase Negative <em>Staphylococci</em> (CoNS) and Coagulase Positve <em>Staphylococci</em> (CoPS)</li>
<li>New Lancefield classification for <em>Streptococcus</em> to categorise them into Lancefield groups</li>
</ul>
</li>
<li>For convience, new descriptive statistical functions <code>kurtosis</code> and <code>skewness</code> that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices</li>
<li>Function <code>g.test</code> to perform the Χ<sup>2</sup> distributed <a href="https://en.wikipedia.org/wiki/G-test"><em>G</em>-test</a>, which use is the same as <code>chisq.test</code>
</li>
<li><del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del></li>
<li>
<del>Function <code>ratio</code> to transform a vector of values to a preset ratio</del>
<ul>
<li><del>For example: <code><a href="../reference/AMR-deprecated.html">ratio(c(10, 500, 10), ratio = "1:2:1")</a></code> would return <code>130, 260, 130</code></del></li>
</ul>
</li>
<li>Support for Addins menu in RStudio to quickly insert <code>%in%</code> or <code>%like%</code> (and give them keyboard shortcuts), or to view the datasets that come with this package</li>
<li>Function <code>p.symbol</code> to transform p values to their related symbols: <code>0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code>
</li>
<li>Functions <code>clipboard_import</code> and <code>clipboard_export</code> as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the <code>clipr</code> package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)</li>
<li>New for frequency tables (function <code>freq</code>):</li>
<li>New for frequency tables (function <code>freq</code>):
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><a href="../reference/freq.html">freq(table(x, y))</a></code>
@ -584,6 +718,8 @@ septic_patients %&gt;%
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
</ul>
</li>
</ul>
</div>
<div id="changed-3" class="section level4">
<h4 class="hasAnchor">
@ -605,21 +741,27 @@ septic_patients %&gt;%
</li>
<li>Small improvements to the <code>microorganisms</code> dataset (especially for <em>Salmonella</em>) and the column <code>bactid</code> now has the new class <code>"bactid"</code>
</li>
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:</li>
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:
<ul>
<li>
<code><a href="../reference/as.rsi.html">as.rsi("&lt;=0.002; S")</a></code> will return <code>S</code>
</li>
<li>
<code><a href="../reference/as.mic.html">as.mic("&lt;=0.002; S")</a></code> will return <code>&lt;=0.002</code>
</li>
</ul>
</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><a href="../reference/as.mic.html">as.mic("&lt;= 0.002")</a></code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for <code><a href="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <a href="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
<li>Improved <code>first_isolate</code> algorithm to exclude isolates where bacteria ID or genus is unavailable</li>
<li>Fix for warning <em>hybrid evaluation forced for row_number</em> (<a href="https://github.com/tidyverse/dplyr/commit/924b62"><code>924b62</code></a>) from the <code>dplyr</code> package v0.7.5 and above</li>
<li>Support for empty values and for 1 or 2 columns as input for <code>guess_bactid</code> (now called <code>as.bactid</code>)</li>
<li>Support for empty values and for 1 or 2 columns as input for <code>guess_bactid</code> (now called <code>as.bactid</code>)
<ul>
<li>So <code>yourdata %&gt;% select(genus, species) %&gt;% as.bactid()</code> now also works</li>
</ul>
</li>
<li>Other small fixes</li>
</ul>
</div>
@ -627,11 +769,14 @@ septic_patients %&gt;%
<h4 class="hasAnchor">
<a href="#other-3" class="anchor"></a>Other</h4>
<ul>
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher</li>
<li>Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
<ul>
<li>Linux and macOS: <a href="https://travis-ci.org/msberends/AMR" class="uri">https://travis-ci.org/msberends/AMR</a>
</li>
<li>Windows: <a href="https://ci.appveyor.com/project/msberends/amr" class="uri">https://ci.appveyor.com/project/msberends/amr</a>
</li>
</ul>
</li>
<li>Added thesis advisors to DESCRIPTION file</li>
</ul>
</div>
@ -650,10 +795,13 @@ septic_patients %&gt;%
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
<li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.</li>
<li>Function <code>MDRO</code> to <strong>determine Multi Drug Resistant Organisms (MDRO)</strong> with support for country-specific guidelines.
<ul>
<li>
<a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance">Exceptional resistances defined by EUCAST</a> are also supported instead of countries alone</li>
<li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>
</ul>
</li>
<li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><a href="../reference/first_isolate.html">?first_isolate</a></code>
</li>
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>

2
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@ -1,4 +1,4 @@
pandoc: 1.17.2
pandoc: 2.3.1
pkgdown: 1.3.0
pkgdown_sha: ~
articles:

4
docs/reference/WHONET.html
View File

@ -241,7 +241,7 @@
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 500 observations and 53 variables:</p><dl class='dl-horizontal'>
<dt><code>Identification number</code></dt><dd><p>ID of the sample</p></dd>
<dt><code>Specimen number</code></dt><dd><p>ID of the specimen</p></dd>
<dt><code>Organism</code></dt><dd><p>Microorganisms, can be coerced with <code><a href='as.mo.html'>as.mo</a></code></p></dd>
<dt><code>Organism</code></dt><dd><p>Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using <code><a href='as.mo.html'>as.mo</a></code>.</p></dd>
<dt><code>Country</code></dt><dd><p>Country of origin</p></dd>
<dt><code>Laboratory</code></dt><dd><p>Name of laboratory</p></dd>
<dt><code>Last name</code></dt><dd><p>Last name of patient</p></dd>
@ -264,7 +264,7 @@
<dt><code>Inducible clindamycin resistance</code></dt><dd><p>Clindamycin can be induced?</p></dd>
<dt><code>Comment</code></dt><dd><p>Other comments</p></dd>
<dt><code>Date of data entry</code></dt><dd><p>Date this data was entered in WHONET</p></dd>
<dt><code>AMP_ND10:CIP_EE</code></dt><dd><p>27 different antibiotics. You can lookup the abbreviatons in the <code><a href='antibiotics.html'>antibiotics</a></code> data set, or use e.g. <code><a href='atc_property.html'>atc_name</a>("AMP")</code> to get the official name immediately.</p></dd>
<dt><code>AMP_ND10:CIP_EE</code></dt><dd><p>27 different antibiotics. You can lookup the abbreviatons in the <code><a href='antibiotics.html'>antibiotics</a></code> data set, or use e.g. <code><a href='atc_property.html'>atc_name</a>("AMP")</code> to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using <code><a href='as.rsi.html'>as.rsi</a></code>.</p></dd>
</dl>
<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>

11
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@ -238,7 +238,7 @@
<span class='fu'>is.rsi</span>(<span class='no'>x</span>)
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>)</pre>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>x</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -247,6 +247,10 @@
<th>x</th>
<td><p>vector</p></td>
</tr>
<tr>
<th>threshold</th>
<td><p>maximum fraction of <code>x</code> that is allowed to fail transformation, see Examples</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -286,10 +290,15 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='no'>as.rsi</span>)
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
<span class='fu'>is.rsi.eligible</span>(<span class='no'>WHONET</span>$<span class='no'>`First name`</span>, <span class='kw'>threhold</span> <span class='kw'>=</span> <span class='fl'>0.9</span>) <span class='co'># succeeds</span>
<span class='co'># }</span></pre>
</div>
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315
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@ -0,0 +1,315 @@
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<h1>Check availability of columns</h1>
<div class="hidden name"><code>availability.Rd</code></div>
</div>
<div class="ref-description">
<p>Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. <code><a href='portion.html'>portion_IR</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>availability</span>(<span class='no'>tbl</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>tbl</th>
<td><p>a <code>data.frame</code> or <code>list</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p><code>data.frame</code> with column names of <code>tbl</code> as row names and columns: <code>percent_IR</code>, <code>count</code>, <code>percent</code>, <code>visual_availability</code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'>availability</span>(<span class='no'>septic_patients</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>availability</span>()
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>availability</span>()
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>)) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select_all.html'>select_if</a></span>(<span class='no'>is.rsi</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>availability</span>()
<span class='co'># }</span></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#examples">Examples</a></li>
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@ -48,6 +48,9 @@
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@ -6,13 +6,16 @@
`AMR` is a free and open-source [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.
After installing this package, R knows almost all ~20.000 microorganisms and ~500 antibiotics by name and code, and knows all about valid RSI and MIC values.
We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but **not** patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license [here](./LICENSE-text.html).
This package can be used for:
* Calculating antimicrobial resistance
* Predicting antimicrobial resistance using regression models
* Predicting empiric susceptibility of both mono therapy and combination therapy
* Predicting future antimicrobial resistance using regression models
* Getting properties for any microorganism (like Gram stain, species, genus or family)
* Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)
* Plotting antimicrobial resistance
@ -104,7 +107,7 @@ Read more about the data from ITIS [in our manual](./reference/ITIS.html).
The `AMR` package basically does four important things:
1. It **cleanses existing data** by providing new *classes* for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). With this package, you learn R everything about microbiology that is needed for analysis. These functions all use artificial intelligence to guess results that you would expect:
1. It **cleanses existing data** by providing new *classes* for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use artificial intelligence to guess results that you would expect:
* Use `as.mo()` to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of *Klebsiella pneumoniae* is "B_KLBSL_PNE" (B stands for Bacteria) and the ID of *S. aureus* is "B_STPHY_AUR". The function takes almost any text as input that looks like the name or code of a microorganism like "E. coli", "esco" or "esccol" and tries to find expected results using artificial intelligence (AI) on the included ITIS data set, consisting of almost 20,000 microorganisms. It is *very* fast, please see our [benchmarks](./articles/benchmarks.html). Moreover, it can group *Staphylococci* into coagulase negative and positive (CoNS and CoPS, see [source](./reference/as.mo.html#source)) and can categorise *Streptococci* into Lancefield groups (like beta-haemolytic *Streptococcus* Group B, [source](./reference/as.mo.html#source)).
* Use `as.rsi()` to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like "<=0.002; S" (combined MIC/RSI) will result in "S".

4
man/WHONET.Rd
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@ -8,7 +8,7 @@
\describe{
\item{\code{Identification number}}{ID of the sample}
\item{\code{Specimen number}}{ID of the specimen}
\item{\code{Organism}}{Microorganisms, can be coerced with \code{\link{as.mo}}}
\item{\code{Organism}}{Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using \code{\link{as.mo}}.}
\item{\code{Country}}{Country of origin}
\item{\code{Laboratory}}{Name of laboratory}
\item{\code{Last name}}{Last name of patient}
@ -31,7 +31,7 @@
\item{\code{Inducible clindamycin resistance}}{Clindamycin can be induced?}
\item{\code{Comment}}{Other comments}
\item{\code{Date of data entry}}{Date this data was entered in WHONET}
\item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately.}
\item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link{as.rsi}}.}
}}
\usage{
WHONET

9
man/as.rsi.Rd
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@ -10,10 +10,12 @@ as.rsi(x)
is.rsi(x)
is.rsi.eligible(x)
is.rsi.eligible(x, threshold = 0.05)
}
\arguments{
\item{x}{vector}
\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
}
\value{
Ordered factor with new class \code{rsi}
@ -47,10 +49,15 @@ library(dplyr)
septic_patients \%>\%
mutate_at(vars(peni:rifa), as.rsi)
# fastest way to transform all columns with already valid AB results to class `rsi`:
septic_patients \%>\%
mutate_if(is.rsi.eligible,
as.rsi)
# default threshold of `is.rsi.eligible` is 5\%.
is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid
is.rsi.eligible(WHONET$`First name`, threhold = 0.9) # succeeds
}
\seealso{
\code{\link{as.mic}}

32
man/availability.Rd Normal file
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@ -0,0 +1,32 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/availability.R
\name{availability}
\alias{availability}
\title{Check availability of columns}
\usage{
availability(tbl)
}
\arguments{
\item{tbl}{a \code{data.frame} or \code{list}}
}
\value{
\code{data.frame} with column names of \code{tbl} as row names and columns: \code{percent_IR}, \code{count}, \code{percent}, \code{visual_availability}.
}
\description{
Easy check for availability of columns in a data set. This makes it easy to get an idea of which antibiotic combination can be used for calculation with e.g. \code{\link{portion_IR}}.
}
\examples{
availability(septic_patients)
library(dplyr)
septic_patients \%>\% availability()
septic_patients \%>\%
select_if(is.rsi) \%>\%
availability()
septic_patients \%>\%
filter(mo == as.mo("E. coli")) \%>\%
select_if(is.rsi) \%>\%
availability()
}

26
tests/testthat/test-availability.R Normal file
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@ -0,0 +1,26 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
context("availability.R")
test_that("availability works", {
expect_equal(class(availability(septic_patients)), "data.frame")
})