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(v0.7.1.9088) bug_drug improvement

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dr. M.S. (Matthijs) Berends 2019-09-25 15:43:22 +02:00
parent 04cd0d25db
commit 99d0fe76dd
19 changed files with 603 additions and 186 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9087
Date: 2019-09-23
Version: 0.7.1.9088
Date: 2019-09-25
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.7.1.9087
<small>Last updated: 23-Sep-2019</small>
# AMR 0.7.1.9088
<small>Last updated: 25-Sep-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:

70
R/bug_drug_combinations.R
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@ -21,15 +21,17 @@
#' Determine bug-drug combinations
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples.
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}
#' @param ... argumments passed on to \code{FUN}
#' @param translate_ab a character of length 1 containing column names of the \code{\link{antibiotics}} data set
#' @param ... arguments passed on to \code{FUN}
#' @inheritParams rsi_df
#' @inheritParams base::formatC
#' @importFrom dplyr rename
#' @importFrom dplyr %>% rename group_by select mutate filter pull
#' @importFrom tidyr spread
#' @importFrom clean freq
#' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
@ -74,9 +76,9 @@ bug_drug_combinations <- function(x,
x <- x %>%
mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>%
filter(mo %in% (clean::freq(mo) %>%
filter(count >= minimum) %>%
pull(item))) %>%
filter(mo %in% (freq(mo) %>%
filter(count >= minimum) %>%
pull(item))) %>%
group_by(mo) %>%
AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>%
select(-value) %>%
@ -88,41 +90,73 @@ bug_drug_combinations <- function(x,
structure(.Data = x, class = c("bug_drug_combinations", class(x)))
}
#' @importFrom dplyr everything rename
#' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag
#' @importFrom tidyr spread
#' @exportMethod format.bug_drug_combinations
#' @export
#' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x,
combine_IR = FALSE,
format.bug_drug_combinations <- function(x,
translate_ab = "name (ab, atc)",
language = get_locale(),
minimum = 30,
combine_SI = TRUE,
combine_IR = FALSE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
...) {
if (combine_IR == FALSE) {
if (remove_intrinsic_resistant == TRUE) {
x <- x %>% filter(R != total)
}
if (combine_IR == FALSE | combine_SI == TRUE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
}
give_ab_name <- function(ab, format, language) {
format <- tolower(format)
ab_txt <- rep(format, length(ab))
for (i in 1:length(ab_txt)) {
ab_txt[i] <- gsub("ab", ab[i], ab_txt[i])
ab_txt[i] <- gsub("cid", ab_cid(ab[i]), ab_txt[i])
ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i])
ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i])
ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i])
ab_txt[i]
}
ab_txt
}
y <- x %>%
filter(total >= minimum) %>%
mutate(ab = as.ab(ab),
ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>%
group_by(ab, ab_txt, mo) %>%
summarise(isolates = sum(isolates, na.rm = TRUE),
total = sum(total, na.rm = TRUE)) %>%
ungroup() %>%
mutate(txt = paste0(percent(isolates / total, force_zero = TRUE, decimal.mark = decimal.mark, big.mark = big.mark),
" (", trimws(format(isolates, big.mark = big.mark)), "/",
trimws(format(total, big.mark = big.mark)), ")")) %>%
select(ab, mo, txt) %>%
select(ab, ab_txt, mo, txt) %>%
spread(mo, txt) %>%
mutate_all(~ifelse(is.na(.), "", .)) %>%
mutate(ab_group = ab_group(ab),
ab = paste0(ab_name(ab), " (", as.ab(ab), ", ", ab_atc(ab), ")")) %>%
select(ab_group, ab, everything()) %>%
arrange(ab_group, ab) %>%
mutate(ab_group = ab_group(ab, language = language),
ab_txt) %>%
select(ab_group, ab_txt, everything(), -ab) %>%
arrange(ab_group, ab_txt) %>%
mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, ""))
if (add_ab_group == FALSE) {
y <- y %>% select(-ab_group) %>% rename("Antibiotic" = ab)
y <- y %>% select(-ab_group) %>% rename("Drug" = ab_txt)
colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE)
} else {
y <- y %>% rename("Group" = ab_group,
"Antibiotic" = ab)
"Drug" = ab_txt)
colnames(y)[1:2] <- translate_AMR(colnames(y)[1:2], language = get_locale(), only_unknown = FALSE)
}
y
@ -133,5 +167,5 @@ format.bug_drug_combinations <- function(x,
#' @importFrom crayon blue
print.bug_drug_combinations <- function(x, ...) {
print(as.data.frame(x, stringsAsFactors = FALSE))
message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing."))
message(blue("NOTE: Use 'format()' on this result to get a publicable/printable format."))
}

1
R/globals.R
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@ -22,6 +22,7 @@
globalVariables(c(".",
"..property",
"ab",
"ab_txt",
"abbreviations",
"antibiotic",
"CNS_CPS",

BIN
R/sysdata.rda
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2
data-raw/translations.tsv
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@ -54,6 +54,8 @@ nl ([([ ]*?)group \\1groep FALSE FALSE
nl ([([ ]*?)Group \\1Groep FALSE FALSE
nl antibiotic antibioticum FALSE FALSE
nl Antibiotic Antibioticum FALSE FALSE
nl Drug Middel FALSE FALSE
nl drug middel FALSE FALSE
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE

Can't render this file because it has a wrong number of fields in line 57.

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docs/404.html Normal file
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@ -187,7 +193,6 @@
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@ -187,7 +193,6 @@
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@ -226,27 +232,27 @@
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<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a></strong>. Author, maintainer. <a href='https://orcid.org/0000-0001-7620-1800' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author, contributor. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0002-9213-6743' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a>
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@ -280,14 +286,16 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -310,6 +318,8 @@
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@ -42,7 +43,7 @@
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@ -167,7 +168,7 @@
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@ -181,6 +182,7 @@
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@ -260,7 +262,7 @@
<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" 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>
<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://rdrr.io/r/utils/install.packages.html">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>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
@ -268,8 +270,8 @@
<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 (<strong>precaution: may be unstable</strong>):</p>
<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 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://rdrr.io/r/utils/install.packages.html">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://rdrr.io/pkg/devtools/man/remote-reexports.html">install_gitlab</a></span>(<span class="st">"msberends/AMR"</span>)</a></code></pre></div>
</div>
</div>
<div id="get-started" class="section level3">
@ -407,17 +409,17 @@
<h2>Developers</h2>
<ul class="list-unstyled">
<li>
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
</div>
@ -425,13 +427,15 @@
</div>
</div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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118
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@ -15,21 +15,25 @@
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<link href="../pkgdown.css" rel="stylesheet">
@ -45,13 +49,14 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Changelog" />
<meta property="og:title" content="Changelog" />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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@ -62,6 +67,7 @@
<![endif]-->
</head>
<body>
@ -78,7 +84,7 @@
</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">0.7.1.9087</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9088</span>
</span>
</div>
@ -187,7 +193,6 @@
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
@ -205,7 +210,7 @@
</li>
</ul>
<form class="navbar-form navbar-right" role="search">
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
@ -216,6 +221,7 @@
</div><!--/.navbar -->
</header>
<div class="row">
@ -225,11 +231,11 @@
</div>
<div id="amr-0-7-1-9087" class="section level1">
<div id="amr-0-7-1-9088" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9087" class="anchor"></a>AMR 0.7.1.9087<small> Unreleased </small>
<a href="#amr-0-7-1-9088" class="anchor"></a>AMR 0.7.1.9088<small> Unreleased </small>
</h1>
<p><small>Last updated: 23-Sep-2019</small></p>
<p><small>Last updated: 25-Sep-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -241,7 +247,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</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"><span class="co"># how it works in base R:</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2">x &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/factor">factor</a></span>(<span class="st">"A"</span>)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2">x &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/factor.html">factor</a></span>(<span class="st">"A"</span>)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3">x[<span class="dv">1</span>] &lt;-<span class="st"> "B"</span></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">#&gt; Warning message:</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co">#&gt; invalid factor level, NA generated</span></a>
@ -252,7 +258,7 @@ For WHONET users, this means that all records/isolates with organism code <code>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co">#&gt; Warning message:</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co">#&gt; invalid microorganism code, NA generated</span></a></code></pre></div>
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
<li><p>Function <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
<li><p>Function <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
</ul>
</div>
<div id="new" class="section level3">
@ -280,8 +286,8 @@ This is important, because a value like <code>"testvalue"</code> could never be
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co">#&gt; 2 AMC Gram-positive 873 2 272 1147</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co">#&gt; 3 AMK Gram-negative 251 0 2 253</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co">#&gt; 4 AMK Gram-positive 0 0 100 100</span></a></code></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://www.rdocumentation.org/packages/base/topics/format">format()</a></code> function:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/format">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/format.html">format</a></span>(x, <span class="dt">combine_IR =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
@ -305,7 +311,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</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="co"># (run this on your own console, as this page does not support colour printing)</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(dplyr)</a>
<a class="sourceLine" id="cb6-3" data-line-number="3">example_isolates <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(mo<span class="op">:</span>AMC) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/reexports.html">as_tibble</a></span>()</a></code></pre></div>
@ -439,7 +445,7 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
<li>Small improvements to <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> and <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> for MIC and RSI classes</li>
<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li>
</ul>
@ -503,7 +509,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
</li>
<li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>):
<ul>
<li>speed improvement for microbial IDs</li>
<li>fixed factor level names for R Markdown</li>
@ -511,13 +517,13 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a>
<a class="sourceLine" id="cb9-4" data-line-number="4"><span class="co"># grouped boxplots:</span></a>
<a class="sourceLine" id="cb9-5" data-line-number="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
<a class="sourceLine" id="cb9-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span>()</a></code></pre></div>
</li>
</ul>
</li>
@ -527,7 +533,7 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUC
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> for when all values are <code>NA</code>
<li>Fix for <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
@ -638,9 +644,9 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
<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>
<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>
<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://rdrr.io/r/graphics/plot.html">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="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" 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="cb13-2" 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="cb13-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(x)</a>
<a class="sourceLine" id="cb13-3" 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>
@ -738,7 +744,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<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>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g. using <code><a href="https://rdrr.io/r/base/summary.html">summary(mo)</a></code>
</li>
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
</li>
@ -749,7 +755,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</ul>
</li>
<li>Frequency tables (<code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function):
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function):
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
@ -757,20 +763,20 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb19-3" data-line-number="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb19-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></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="cb19-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb19-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb19-6" data-line-number="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb19-7" data-line-number="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb19-9" data-line-number="9"></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb19-11" data-line-number="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb19-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
<a class="sourceLine" id="cb19-13" data-line-number="13"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/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>
<li>Added header info for class <code>mo</code> to show unique count of families, genera and species</li>
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://www.rdocumentation.org/packages/base/topics/options">getOption("OutDec")</a></code>
<li>Now honours the <code>decimal.mark</code> setting, which just like <code>format</code> defaults to <code><a href="https://rdrr.io/r/base/options.html">getOption("OutDec")</a></code>
</li>
<li>The new <code>big.mark</code> parameter will at default be <code>","</code> when <code>decimal.mark = "."</code> and <code>"."</code> otherwise</li>
<li>Fix for header text where all observations are <code>NA</code>
@ -785,7 +791,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>Updated examples for resistance prediction (<code><a href="../reference/resistance_predict.html">resistance_predict()</a></code> function)</li>
<li>Fix for <code><a href="../reference/as.mic.html">as.mic()</a></code> to support more values ending in (several) zeroes</li>
<li>if using different lengths of pattern and x in <code>%like%</code>, it will now return the call</li>
<li>if using different lengths of pattern and x in <code><a href="../reference/like.html">%like%</a></code>, it will now return the call</li>
</ul>
</div>
<div id="other-3" class="section level4">
@ -852,21 +858,21 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<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="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code>:
<li>Frequency tables - <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code>:
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
<a class="sourceLine" id="cb21-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></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/Deprecated">hms::is.hms</a></code>
<li>Check for <code><a href="https://rdrr.io/pkg/hms/man/Deprecated.html">hms::is.hms</a></code>
</li>
<li>Now prints in markdown at default in non-interactive sessions</li>
<li>No longer adds the factor level column and sorts factors on count again</li>
@ -906,7 +912,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</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>
<li>In <code>g.test</code>, when <code><a href="https://rdrr.io/r/base/sum.html">sum(x)</a></code> is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested</li>
<li>
<code>ab_name</code> will try to fall back on <code>as.atc</code> when no results are found</li>
<li>Removed the addin to view data sets</li>
@ -973,8 +979,8 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<a class="sourceLine" id="cb25-5" 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="cb25-6" 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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" 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="cb26-2" 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>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/rep.html">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">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="cb26-3" data-line-number="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb26-4" data-line-number="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb26-5" data-line-number="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
@ -1007,9 +1013,9 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<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="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw">ab_official</span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb27-2" data-line-number="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb27-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.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="cb27-3" data-line-number="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">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="cb27-4" data-line-number="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb27-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.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="cb27-5" data-line-number="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">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="cb27-6" 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>
@ -1041,12 +1047,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" 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="cb29-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(my_matrix)</a></code></pre></div>
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/with.html">with</a></span>(septic_patients, <span class="kw"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb29-2" data-line-number="2"><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" 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="cb30-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(age)</a>
<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(gender)</a></code></pre></div>
<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" data-line-number="1">my_list =<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/list.html">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="cb30-2" data-line-number="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb30-3" data-line-number="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li>
</ul>
</div>
@ -1112,7 +1118,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li><del>For example: <code>ratio(c(10, 500, 10), ratio = "1:2:1")</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>Support for Addins menu in RStudio to quickly insert <code><a href="https://rdrr.io/r/base/match.html">%in%</a></code> or <code><a href="../reference/like.html">%like%</a></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>
@ -1120,17 +1126,17 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<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="https://www.rdocumentation.org/packages/clean/topics/freq">freq(table(x, y))</a></code>
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(table(x, y))</a></code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %&gt;% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<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>
<li>Possibility to globally set the default for the amount of items to print, with <code><a href="https://rdrr.io/r/base/options.html">options(max.print.freq = n)</a></code> where <em>n</em> is your preset value</li>
</ul>
</li>
</ul>
@ -1148,7 +1154,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Column names for the <code>key_antibiotics</code> function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs</li>
<li>Speed improvement for the <code>abname</code> function</li>
<li>
<code>%like%</code> now supports multiple patterns</li>
<code><a href="../reference/like.html">%like%</a></code> now supports multiple patterns</li>
<li>Frequency tables are now actual <code>data.frame</code>s with altered console printing to make it look like a frequency table. Because of this, the parameter <code>toConsole</code> is not longer needed.</li>
<li>Fix for <code>freq</code> where the class of an item would be lost</li>
<li>Small translational improvements to the <code>septic_patients</code> dataset and the column <code>bactid</code> now has the new class <code>"bactid"</code>
@ -1236,7 +1242,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>Added support for character vector in <code>join</code> functions</li>
<li>Added warnings when a join results in more rows after than before the join</li>
<li>Altered <code>%like%</code> to make it case insensitive</li>
<li>Altered <code><a href="../reference/like.html">%like%</a></code> to make it case insensitive</li>
<li>For parameters of functions <code>first_isolate</code> and <code>EUCAST_rules</code> column names are now case-insensitive</li>
<li>Functions <code>as.rsi</code> and <code>as.mic</code> now add the package name and version as attributes</li>
</ul>
@ -1280,7 +1286,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9087">0.7.1.9087</a></li>
<li><a href="#amr-0-7-1-9088">0.7.1.9088</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>
@ -1297,14 +1303,16 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
</div>
</footer>
</div>
@ -1327,6 +1335,8 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</script>
</body>
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46
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@ -21,8 +21,6 @@ body > .container {
display: flex;
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flex-direction: column;
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body > .container .row {
@ -102,21 +100,13 @@ a.anchor {
margin-top: -40px;
}
/* Static header placement on mobile devices */
@media (max-width: 767px) {
.navbar-fixed-top {
position: absolute;
}
.navbar {
padding: 0;
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}
/* Sidebar --------------------------*/
#sidebar {
margin-top: 30px;
position: -webkit-sticky;
position: sticky;
top: 70px;
}
#sidebar h2 {
font-size: 1.5em;
@ -133,6 +123,9 @@ a.anchor {
.orcid {
height: 16px;
/* margins are required by official ORCID trademark and display guidelines */
margin-left:4px;
margin-right:4px;
vertical-align: middle;
}
@ -222,6 +215,19 @@ a.sourceLine:hover {
visibility: visible;
}
/* headroom.js ------------------------ */
.headroom {
will-change: transform;
transition: transform 200ms linear;
}
.headroom--pinned {
transform: translateY(0%);
}
.headroom--unpinned {
transform: translateY(-100%);
}
/* mark.js ----------------------------*/
mark {
@ -234,3 +240,17 @@ mark {
.html-widget {
margin-bottom: 10px;
}
/* fontawesome ------------------------ */
.fab {
font-family: "Font Awesome 5 Brands" !important;
}
/* don't display links in code chunks when printing */
/* source: https://stackoverflow.com/a/10781533 */
@media print {
code a:link:after, code a:visited:after {
content: "";
}
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14
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@ -2,14 +2,12 @@
(function($) {
$(function() {
$("#sidebar")
.stick_in_parent({offset_top: 40})
.on('sticky_kit:bottom', function(e) {
$(this).parent().css('position', 'static');
})
.on('sticky_kit:unbottom', function(e) {
$(this).parent().css('position', 'relative');
});
$('.navbar-fixed-top').headroom();
$('body').css('padding-top', $('.navbar').height() + 10);
$(window).resize(function(){
$('body').css('padding-top', $('.navbar').height() + 10);
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$('body').scrollspy({
target: '#sidebar',

2
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@ -1,5 +1,5 @@
pandoc: 2.3.1
pkgdown: 1.3.0
pkgdown: 1.4.1
pkgdown_sha: ~
articles:
AMR: AMR.html

82
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View File

@ -15,21 +15,25 @@
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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<link href="../pkgdown.css" rel="stylesheet">
@ -45,15 +49,15 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Determine bug-drug combinations — bug_drug_combinations" />
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format on the result to prettify it to a printable format, see Examples." />
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format on the result to prettify it to a publicable/printable format, see Examples." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
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@ -64,6 +68,7 @@
<![endif]-->
</head>
<body>
@ -80,7 +85,7 @@
</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">0.7.1.9083</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9088</span>
</span>
</div>
@ -189,7 +194,6 @@
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.com/msberends/AMR">
@ -207,7 +211,7 @@
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</ul>
<form class="navbar-form navbar-right" role="search">
<form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
<div class="form-group">
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
</div>
@ -218,6 +222,7 @@
</div><!--/.navbar -->
</header>
<div class="row">
@ -229,19 +234,20 @@
</div>
<div class="ref-description">
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code>format</code> on the result to prettify it to a printable format, see Examples.</p>
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code>format</code> on the result to prettify it to a publicable/printable format, see Examples.</p>
</div>
<pre class="usage"><span class='fu'>bug_drug_combinations</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_shortname</span>, <span class='no'>...</span>)
<span class='co'># S3 method for bug_drug_combinations</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span> <span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>), <span class='no'>...</span>)</pre>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name (ab, atc)"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>add_ab_group</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>remove_intrinsic_resistant</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>==</span>
<span class='st'>","</span>, <span class='st'>"."</span>, <span class='st'>","</span>), <span class='no'>...</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>
@ -263,7 +269,19 @@
</tr>
<tr>
<th>...</th>
<td><p>argumments passed on to <code>FUN</code></p></td>
<td><p>arguments passed on to <code>FUN</code></p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a character of length 1 containing column names of the <code><a href='antibiotics.html'>antibiotics</a></code> data set</p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption</a>("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>combine_SI</th>
<td><p>a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>
@ -273,6 +291,10 @@
<th>add_ab_group</th>
<td><p>logical to indicate where the group of the antimicrobials must be included as a first column</p></td>
</tr>
<tr>
<th>remove_intrinsic_resistant</th>
<td><p>logical to indicate that rows with 100% resistance for all tested antimicrobials must be removed from the table</p></td>
</tr>
<tr>
<th>decimal.mark</th>
<td><p>the character to be used to indicate the numeric
@ -285,34 +307,32 @@
decimal point.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>format</code> calculates the resistance per bug-drug combination. Use <code>combine_IR = FALSE</code> (default) to test R vs. S+I and <code>combine_IR = TRUE</code> to test R+I vs. S.</p>
<p>The language of the output can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options(AMR_locale)</a></code>, please see <a href='translate.html'>translate</a>.</p>
<p>The language of the output can be overwritten with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_locale)</a></code>, please see <a href='translate.html'>translate</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>)
<span class='no'>x</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>x</span>)
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>x</span>)
<span class='co'># Use FUN to change to transformation of microorganism codes</span>
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>mo_gramstain</span>)
<span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>bug_drug_combinations</span>(<span class='no'>example_isolates</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>x</span> <span class='kw'>==</span> <span class='st'>"B_ESCHR_COLI"</span>,
<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>x</span> <span class='kw'>==</span> <span class='st'>"B_ESCHR_COLI"</span>,
<span class='st'>"E. coli"</span>,
<span class='st'>"Others"</span>))
<span class='co'># }</span></pre>
@ -321,27 +341,25 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -62,6 +67,7 @@
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@ -78,7 +84,7 @@
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21
man/bug_drug_combinations.Rd
View File

@ -11,9 +11,12 @@
bug_drug_combinations(x, col_mo = NULL, minimum = 30,
FUN = mo_shortname, ...)
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE, decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","), ...)
\method{format}{bug_drug_combinations}(x,
translate_ab = "name (ab, atc)", language = get_locale(),
minimum = 30, combine_SI = TRUE, combine_IR = FALSE,
add_ab_group = TRUE, remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark ==
",", ".", ","), ...)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
@ -24,12 +27,20 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}}}
\item{...}{argumments passed on to \code{FUN}}
\item{...}{arguments passed on to \code{FUN}}
\item{translate_ab}{a character of length 1 containing column names of the \code{\link{antibiotics}} data set}
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter \code{combine_IR}, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is \code{TRUE}.}
\item{combine_IR}{logical to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
\item{remove_intrinsic_resistant}{logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table}
\item{decimal.mark}{the character to be used to indicate the numeric
decimal point.}
@ -38,7 +49,7 @@ bug_drug_combinations(x, col_mo = NULL, minimum = 30,
decimal point.}
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples.
}
\details{
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.