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(v0.7.1.9088) bug_drug improvement

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  1. 4
      DESCRIPTION
  2. 4
      NEWS.md
  3. 70
      R/bug_drug_combinations.R
  4. 1
      R/globals.R
  5. BIN
      R/sysdata.rda
  6. 2
      data-raw/translations.tsv
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4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -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

@ -1,5 +1,5 @@ @@ -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

@ -21,15 +21,17 @@ @@ -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, @@ -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, @@ -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, @@ -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

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

BIN
R/sysdata.rda

Binary file not shown.

2
data-raw/translations.tsv

@ -54,6 +54,8 @@ nl ([([ ]*?)group \\1groep FALSE FALSE @@ -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.

276
docs/404.html

@ -0,0 +1,276 @@ @@ -0,0 +1,276 @@
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@ -62,6 +67,7 @@ @@ -62,6 +67,7 @@
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@ -187,7 +193,6 @@ @@ -187,7 +193,6 @@
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38
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@ -45,13 +49,14 @@ @@ -45,13 +49,14 @@
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@ -62,6 +67,7 @@ @@ -62,6 +67,7 @@
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@ -78,7 +84,7 @@ @@ -78,7 +84,7 @@
</button>
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<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>
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@ -187,7 +193,6 @@ @@ -187,7 +193,6 @@
</a>
</li>
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@ -205,7 +210,7 @@ @@ -205,7 +210,7 @@
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</header>
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@ -226,27 +232,27 @@ @@ -226,27 +232,27 @@
<ul class="list-unstyled">
<li>
<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 @@ @@ -280,14 +286,16 @@
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@ -92,3 +92,4 @@ @@ -92,3 +92,4 @@
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@ -13,8 +13,9 @@ @@ -13,8 +13,9 @@
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<div class="contents col-md-9">
<div id="amr-for-r" class="section level1">
@ -260,7 +262,7 @@ @@ -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 @@ @@ -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 @@ @@ -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 @@ @@ -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>
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<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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@ -15,21 +15,25 @@ @@ -15,21 +15,25 @@
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@ -45,13 +49,14 @@ @@ -45,13 +49,14 @@
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<meta property="og:title" content="Changelog" />
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@ -62,6 +67,7 @@ @@ -62,6 +67,7 @@
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@ -78,7 +84,7 @@ @@ -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 @@ @@ -187,7 +193,6 @@
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<ul class="nav navbar-nav navbar-right">
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<a href="https://gitlab.com/msberends/AMR">
@ -205,7 +210,7 @@ @@ -205,7 +210,7 @@
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<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
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@ -216,6 +221,7 @@ @@ -216,6 +221,7 @@
</div><!--/.navbar -->
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@ -225,11 +231,11 @@ @@ -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> @@ -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> @@ -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 @@ -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 @@ -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 @@ -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