(v1.7.1.9014) rep() for S3 classes
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.7.1.9013
|
||||
Date: 2021-07-04
|
||||
Version: 1.7.1.9014
|
||||
Date: 2021-07-06
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
|
@ -93,6 +93,7 @@ S3method(exp,mic)
|
||||
S3method(expm1,mic)
|
||||
S3method(floor,mic)
|
||||
S3method(format,bug_drug_combinations)
|
||||
S3method(format,taxonomic_name)
|
||||
S3method(gamma,mic)
|
||||
S3method(hist,mic)
|
||||
S3method(kurtosis,data.frame)
|
||||
@ -127,7 +128,12 @@ S3method(print,taxonomic_name)
|
||||
S3method(prod,mic)
|
||||
S3method(quantile,mic)
|
||||
S3method(range,mic)
|
||||
S3method(rep,ab)
|
||||
S3method(rep,disk)
|
||||
S3method(rep,mic)
|
||||
S3method(rep,mo)
|
||||
S3method(rep,rsi)
|
||||
S3method(rep,taxonomic_name)
|
||||
S3method(round,mic)
|
||||
S3method(sign,mic)
|
||||
S3method(signif,mic)
|
||||
|
4
NEWS.md
@ -1,5 +1,5 @@
|
||||
# `AMR` 1.7.1.9013
|
||||
## <small>Last updated: 4 July 2021</small>
|
||||
# `AMR` 1.7.1.9014
|
||||
## <small>Last updated: 6 July 2021</small>
|
||||
|
||||
### Changed
|
||||
* Antibiotic class selectors (see `ab_class()`)
|
||||
|
9
R/ab.R
@ -580,6 +580,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep ab
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.ab <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
generalise_antibiotic_name <- function(x) {
|
||||
x <- toupper(x)
|
||||
# remove suffices
|
||||
|
@ -113,7 +113,7 @@ bug_drug_combinations <- function(x,
|
||||
data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
|
||||
})
|
||||
merged <- do.call(rbind, pivot)
|
||||
out_group <- data.frame(mo = unique_mo[i],
|
||||
out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
|
||||
ab = rownames(merged),
|
||||
S = merged$S,
|
||||
I = merged$I,
|
||||
|
9
R/disk.R
@ -195,6 +195,15 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep disk
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.disk <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
get_skimmers.disk <- function(column) {
|
||||
skimr::sfl(
|
||||
|
11
R/mic.R
@ -320,6 +320,15 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.mic <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
#' @method sort mic
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -337,7 +346,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
|
||||
#' @export
|
||||
#' @noRd
|
||||
hist.mic <- function(x, ...) {
|
||||
warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
|
||||
warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
|
||||
hist(log2(x))
|
||||
}
|
||||
|
||||
|
@ -48,7 +48,7 @@
|
||||
#'
|
||||
#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
|
||||
#'
|
||||
#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()].
|
||||
#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()] and markdown tables such as with [knitr::kable()].
|
||||
#'
|
||||
#' All output [will be translated][translate] where possible.
|
||||
#'
|
||||
@ -786,9 +786,9 @@ print.taxonomic_name <- function(x, ...) {
|
||||
as.data.frame.taxonomic_name <- function(x, ...) {
|
||||
nm <- deparse1(substitute(x))
|
||||
if (!"nm" %in% names(list(...))) {
|
||||
as.data.frame(unclass(x), ..., nm = nm)
|
||||
as.data.frame.vector(x, ..., nm = nm)
|
||||
} else {
|
||||
as.data.frame(unclass(x), ...)
|
||||
as.data.frame.vector(x, ...)
|
||||
}
|
||||
}
|
||||
|
||||
@ -801,12 +801,27 @@ type_sum.taxonomic_name <- function(x, ...) {
|
||||
pillar_shaft.taxonomic_name <- function(x, ...) {
|
||||
out <- format(x)
|
||||
hits <- tolower(x) %in% MO_lookup$fullname_lower | tolower(gsub("[^a-zA-Z ]", "", x)) %in% c(MO_lookup$g_species)
|
||||
# grey out the kingdom (part until first "_")
|
||||
out[hits] <- font_italic(x[hits], collapse = NULL)
|
||||
out[is.na(x)] <- font_na(out[is.na(x)], collapse = NULL)
|
||||
create_pillar_column(out, align = "left")
|
||||
}
|
||||
|
||||
#' @method format taxonomic_name
|
||||
#' @export
|
||||
#' @noRd
|
||||
format.taxonomic_name <- function(x, ...) {
|
||||
# format only in case of markdown knitting
|
||||
x <- unclass(x)
|
||||
if (any(as.character(sys.calls()) %like% "(^|:| )kable\\(") ||
|
||||
tryCatch(!is.null(knitr::opts_knit$get("out.format")), error = function(e) FALSE) ||
|
||||
tryCatch(isTRUE(getOption('knitr.in.progress')), error = function(e) FALSE)) {
|
||||
# perhaps this could be extended or better specified in the future?
|
||||
hits <- tolower(x) %in% MO_lookup$fullname_lower | tolower(gsub("[^a-zA-Z ]", "", x)) %in% c(MO_lookup$g_species)
|
||||
x[hits] <- paste0("*", x[hits], "*")
|
||||
}
|
||||
x
|
||||
}
|
||||
|
||||
#' @method [ taxonomic_name
|
||||
#' @export
|
||||
#' @noRd
|
||||
@ -856,3 +871,12 @@ unique.taxonomic_name <- function(x, incomparables = FALSE, ...) {
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep taxonomic_name
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.taxonomic_name <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
9
R/rsi.R
@ -1054,6 +1054,15 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
|
||||
y
|
||||
}
|
||||
|
||||
#' @method rep rsi
|
||||
#' @export
|
||||
#' @noRd
|
||||
rep.rsi <- function(x, ...) {
|
||||
y <- NextMethod()
|
||||
attributes(y) <- attributes(x)
|
||||
y
|
||||
}
|
||||
|
||||
check_reference_data <- function(reference_data) {
|
||||
if (!identical(reference_data, AMR::rsi_translation)) {
|
||||
class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))
|
||||
|
BIN
R/sysdata.rda
@ -18,17 +18,17 @@ unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort
|
||||
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
|
||||
CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
|
||||
CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
|
||||
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
|
||||
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
|
||||
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias
|
||||
^Fungi$ TRUE TRUE FALSE FALSE Pilze Schimmels Hongos Funghi Champignons Fungos
|
||||
^Yeasts$ TRUE TRUE FALSE FALSE Hefen Gisten Levaduras Lieviti Levures Leveduras
|
||||
^Protozoa$ TRUE TRUE FALSE FALSE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários
|
||||
biogroup TRUE TRUE FALSE FALSE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo
|
||||
biotype TRUE TRUE FALSE FALSE Biotyp biotipo biotipo biótipo
|
||||
vegetative TRUE TRUE FALSE FALSE vegetativ vegetatief vegetativo vegetativo végétatif vegetativo
|
||||
([([ ]*?)group TRUE TRUE FALSE FALSE \\1Gruppe \\1groep \\1grupo \\1gruppo \\1groupe \\1grupo
|
||||
([([ ]*?)Group TRUE TRUE FALSE FALSE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
|
||||
Gram-negative TRUE TRUE FALSE TRUE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
|
||||
Gram-positive TRUE TRUE FALSE TRUE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
|
||||
^Bacteria$ TRUE TRUE FALSE TRUE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias
|
||||
^Fungi$ TRUE TRUE FALSE TRUE Pilze Schimmels Hongos Funghi Champignons Fungos
|
||||
^Yeasts$ TRUE TRUE FALSE TRUE Hefen Gisten Levaduras Lieviti Levures Leveduras
|
||||
^Protozoa$ TRUE TRUE FALSE TRUE Protozoen Protozoën Protozoarios Protozoi Protozoaires Protozoários
|
||||
biogroup TRUE TRUE FALSE TRUE Biogruppe biogroep biogrupo biogruppo biogroupe biogrupo
|
||||
biotype TRUE TRUE FALSE TRUE Biotyp biotipo biotipo biótipo
|
||||
vegetative TRUE TRUE FALSE TRUE vegetativ vegetatief vegetativo vegetativo végétatif vegetativo
|
||||
([([ ]*?)group TRUE TRUE FALSE TRUE \\1Gruppe \\1groep \\1grupo \\1gruppo \\1groupe \\1grupo
|
||||
([([ ]*?)Group TRUE TRUE FALSE TRUE \\1Gruppe \\1Groep \\1Grupo \\1Gruppo \\1Groupe \\1Grupo
|
||||
no .*growth TRUE FALSE FALSE FALSE keine? .*wachstum geen .*groei no .*crecimientonon sem .*crescimento pas .*croissance sem .*crescimento
|
||||
no|not TRUE FALSE FALSE FALSE keine? geen|niet no|sin sem non sem
|
||||
Susceptible TRUE FALSE FALSE FALSE Empfindlich Gevoelig Susceptible
|
||||
|
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -193,7 +193,7 @@
|
||||
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">04 July 2021</h4>
|
||||
<h4 class="date">06 July 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@ -202,7 +202,7 @@
|
||||
|
||||
|
||||
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 04 July 2021.</p>
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 06 July 2021.</p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||
@ -233,21 +233,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2021-07-04</td>
|
||||
<td align="center">2021-07-06</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2021-07-04</td>
|
||||
<td align="center">2021-07-06</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2021-07-04</td>
|
||||
<td align="center">2021-07-06</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -344,32 +344,32 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-09-28</td>
|
||||
<td align="center">A1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2016-02-04</td>
|
||||
<td align="center">V9</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-09-28</td>
|
||||
<td align="center">J9</td>
|
||||
<td align="center">2011-09-24</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Streptococcus pneumoniae</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-10-02</td>
|
||||
<td align="center">S7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">2014-06-20</td>
|
||||
<td align="center">Z9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -377,9 +377,9 @@
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-11-15</td>
|
||||
<td align="center">U6</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">2018-01-01</td>
|
||||
<td align="center">P4</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -388,26 +388,26 @@
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-12-08</td>
|
||||
<td align="center">B10</td>
|
||||
<td align="center">2014-12-14</td>
|
||||
<td align="center">W2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2010-05-10</td>
|
||||
<td align="center">M2</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">2016-07-27</td>
|
||||
<td align="center">R6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -441,16 +441,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,434</td>
|
||||
<td align="right">52.17%</td>
|
||||
<td align="right">10,434</td>
|
||||
<td align="right">52.17%</td>
|
||||
<td align="right">10,365</td>
|
||||
<td align="right">51.83%</td>
|
||||
<td align="right">10,365</td>
|
||||
<td align="right">51.83%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,566</td>
|
||||
<td align="right">47.83%</td>
|
||||
<td align="right">9,635</td>
|
||||
<td align="right">48.18%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -505,9 +505,9 @@ Longest: 1</p>
|
||||
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
|
||||
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
|
||||
<span class="co"># 2</span>
|
||||
<span class="co"># => Found 10,702 first weighted isolates (phenotype-based, 53.5% of total</span>
|
||||
<span class="co"># => Found 10,656 first weighted isolates (phenotype-based, 53.3% of total</span>
|
||||
<span class="co"># where a microbial ID was available)</span></code></pre></div>
|
||||
<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<p>So only 53.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
|
||||
@ -515,7 +515,7 @@ Longest: 1</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p>So we end up with 10,702 isolates for analysis. Now our data looks like:</p>
|
||||
<p>So we end up with 10,656 isolates for analysis. Now our data looks like:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
|
||||
<table class="table">
|
||||
@ -531,7 +531,7 @@ Longest: 1</p>
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="12%">
|
||||
<col width="13%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -553,73 +553,25 @@ Longest: 1</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2016-09-28</td>
|
||||
<td align="center">A1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="center">2012-09-28</td>
|
||||
<td align="center">J9</td>
|
||||
<td align="center">2011-09-24</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="center">2016-12-08</td>
|
||||
<td align="center">B10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2015-04-29</td>
|
||||
<td align="center">W8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2010-06-19</td>
|
||||
<td align="center">Q5</td>
|
||||
<td align="left">3</td>
|
||||
<td align="center">2014-06-20</td>
|
||||
<td align="center">Z9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">S</td>
|
||||
@ -628,26 +580,74 @@ Longest: 1</p>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center"><em>Staphylococcus</em></td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">6</td>
|
||||
<td align="center">2016-07-27</td>
|
||||
<td align="center">R6</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center"><em>Staphylococcus</em></td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">9</td>
|
||||
<td align="center">2010-08-20</td>
|
||||
<td align="center">A8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="left">7</td>
|
||||
<td align="center">2011-07-24</td>
|
||||
<td align="center">W2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center"><em>Escherichia</em></td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">9</td>
|
||||
<td align="center">2012-01-12</td>
|
||||
<td align="center">K9</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center"><em>Escherichia</em></td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">11</td>
|
||||
<td align="center">2013-03-11</td>
|
||||
<td align="center">B6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center"><em>Klebsiella</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Time for the analysis!</p>
|
||||
@ -669,8 +669,8 @@ Longest: 1</p>
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 10,702<br>
|
||||
Available: 10,702 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Length: 10,656<br>
|
||||
Available: 10,656 (100.0%, NA: 0 = 0.0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -687,33 +687,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">4,661</td>
|
||||
<td align="right">43.55%</td>
|
||||
<td align="right">4,661</td>
|
||||
<td align="right">43.55%</td>
|
||||
<td align="right">4,664</td>
|
||||
<td align="right">43.77%</td>
|
||||
<td align="right">4,664</td>
|
||||
<td align="right">43.77%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">2,697</td>
|
||||
<td align="right">25.20%</td>
|
||||
<td align="right">7,358</td>
|
||||
<td align="right">68.75%</td>
|
||||
<td align="right">2,730</td>
|
||||
<td align="right">25.62%</td>
|
||||
<td align="right">7,394</td>
|
||||
<td align="right">69.39%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,145</td>
|
||||
<td align="right">20.04%</td>
|
||||
<td align="right">9,503</td>
|
||||
<td align="right">88.80%</td>
|
||||
<td align="right">2,093</td>
|
||||
<td align="right">19.64%</td>
|
||||
<td align="right">9,487</td>
|
||||
<td align="right">89.03%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,199</td>
|
||||
<td align="right">11.20%</td>
|
||||
<td align="right">10,702</td>
|
||||
<td align="right">1,169</td>
|
||||
<td align="right">10.97%</td>
|
||||
<td align="right">10,656</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -732,14 +732,14 @@ Longest: 24</p>
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="9%">
|
||||
<col width="11%">
|
||||
<col width="10%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="3%">
|
||||
<col width="6%">
|
||||
<col width="11%">
|
||||
<col width="11%">
|
||||
<col width="13%">
|
||||
<col width="9%">
|
||||
<col width="5%">
|
||||
</colgroup>
|
||||
@ -760,23 +760,38 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-09-28</td>
|
||||
<td align="center">A1</td>
|
||||
<td align="center">2011-09-24</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-09-28</td>
|
||||
<td align="center">J9</td>
|
||||
<td align="center">2011-07-24</td>
|
||||
<td align="center">W2</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center"><em>Escherichia</em></td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-03-17</td>
|
||||
<td align="center">D5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
@ -785,67 +800,52 @@ Longest: 24</p>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-04-29</td>
|
||||
<td align="center">W8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-02-20</td>
|
||||
<td align="center">P2</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">2011-06-13</td>
|
||||
<td align="center">X10</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-09-14</td>
|
||||
<td align="center">T8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-01-26</td>
|
||||
<td align="center">K8</td>
|
||||
<td align="center">2010-04-12</td>
|
||||
<td align="center">Z4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-02-25</td>
|
||||
<td align="center">B5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
@ -868,52 +868,52 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center"><em>E. coli</em></td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">2209</td>
|
||||
<td align="center">123</td>
|
||||
<td align="center">2329</td>
|
||||
<td align="center">4661</td>
|
||||
<td align="center">2180</td>
|
||||
<td align="center">145</td>
|
||||
<td align="center">2339</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center"><em>E. coli</em></td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">3406</td>
|
||||
<td align="center">165</td>
|
||||
<td align="center">1090</td>
|
||||
<td align="center">4661</td>
|
||||
<td align="center">3360</td>
|
||||
<td align="center">176</td>
|
||||
<td align="center">1128</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center"><em>E. coli</em></td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3416</td>
|
||||
<td align="center">3405</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1245</td>
|
||||
<td align="center">4661</td>
|
||||
<td align="center">1259</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center"><em>E. coli</em></td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4086</td>
|
||||
<td align="center">4078</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">575</td>
|
||||
<td align="center">4661</td>
|
||||
<td align="center">586</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center"><em>K. pneumoniae</em></td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1199</td>
|
||||
<td align="center">1199</td>
|
||||
<td align="center">1169</td>
|
||||
<td align="center">1169</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center"><em>K. pneumoniae</em></td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">933</td>
|
||||
<td align="center">39</td>
|
||||
<td align="center">227</td>
|
||||
<td align="center">1199</td>
|
||||
<td align="center">924</td>
|
||||
<td align="center">49</td>
|
||||
<td align="center">196</td>
|
||||
<td align="center">1169</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -934,36 +934,36 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center"><em>E. coli</em></td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">4086</td>
|
||||
<td align="center">4078</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">575</td>
|
||||
<td align="center">4661</td>
|
||||
<td align="center">586</td>
|
||||
<td align="center">4664</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center"><em>K. pneumoniae</em></td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">1068</td>
|
||||
<td align="center">1042</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">131</td>
|
||||
<td align="center">1199</td>
|
||||
<td align="center">127</td>
|
||||
<td align="center">1169</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center"><em>S. aureus</em></td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">2407</td>
|
||||
<td align="center">2440</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">290</td>
|
||||
<td align="center">2697</td>
|
||||
<td align="center">2730</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center"><em>S. pneumoniae</em></td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">2145</td>
|
||||
<td align="center">2145</td>
|
||||
<td align="center">2093</td>
|
||||
<td align="center">2093</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -977,7 +977,7 @@ Longest: 24</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
||||
<span class="co"># [1] 0.5418613</span></code></pre></div>
|
||||
<span class="co"># [1] 0.5442005</span></code></pre></div>
|
||||
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span>
|
||||
@ -991,19 +991,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5276730</td>
|
||||
<td align="center">0.5512301</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5422819</td>
|
||||
<td align="center">0.5383792</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5609308</td>
|
||||
<td align="center">0.5587121</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5475970</td>
|
||||
<td align="center">0.5329877</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1022,23 +1022,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5276730</td>
|
||||
<td align="center">3180</td>
|
||||
<td align="center">0.5512301</td>
|
||||
<td align="center">3211</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5422819</td>
|
||||
<td align="center">3725</td>
|
||||
<td align="center">0.5383792</td>
|
||||
<td align="center">3739</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5609308</td>
|
||||
<td align="center">1633</td>
|
||||
<td align="center">0.5587121</td>
|
||||
<td align="center">1584</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5475970</td>
|
||||
<td align="center">2164</td>
|
||||
<td align="center">0.5329877</td>
|
||||
<td align="center">2122</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1058,28 +1058,28 @@ Longest: 24</p>
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7661446</td>
|
||||
<td align="center">0.8766359</td>
|
||||
<td align="center">0.9759708</td>
|
||||
<td align="center"><em>Escherichia</em></td>
|
||||
<td align="center">0.7581475</td>
|
||||
<td align="center">0.8743568</td>
|
||||
<td align="center">0.9762007</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8106756</td>
|
||||
<td align="center">0.8907423</td>
|
||||
<td align="center">0.9833194</td>
|
||||
<td align="center"><em>Klebsiella</em></td>
|
||||
<td align="center">0.8323353</td>
|
||||
<td align="center">0.8913601</td>
|
||||
<td align="center">0.9760479</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7942158</td>
|
||||
<td align="center">0.8924731</td>
|
||||
<td align="center">0.9818317</td>
|
||||
<td align="center"><em>Staphylococcus</em></td>
|
||||
<td align="center">0.7945055</td>
|
||||
<td align="center">0.8937729</td>
|
||||
<td align="center">0.9831502</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5501166</td>
|
||||
<td align="center"><em>Streptococcus</em></td>
|
||||
<td align="center">0.5351171</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5501166</td>
|
||||
<td align="center">0.5351171</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1104,23 +1104,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital A</td>
|
||||
<td align="right">52.8%</td>
|
||||
<td align="right">26.0%</td>
|
||||
<td align="right">55.1%</td>
|
||||
<td align="right">27.0%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital B</td>
|
||||
<td align="right">54.2%</td>
|
||||
<td align="right">26.5%</td>
|
||||
<td align="right">53.8%</td>
|
||||
<td align="right">26.2%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">Hospital C</td>
|
||||
<td align="right">56.1%</td>
|
||||
<td align="right">26.7%</td>
|
||||
<td align="right">55.9%</td>
|
||||
<td align="right">27.7%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">Hospital D</td>
|
||||
<td align="right">54.8%</td>
|
||||
<td align="right">27.1%</td>
|
||||
<td align="right">53.3%</td>
|
||||
<td align="right">27.0%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1204,19 +1204,16 @@ Longest: 24</p>
|
||||
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="va">mic_values</span>
|
||||
<span class="co"># Class <mic></span>
|
||||
<span class="co"># [1] 32 2 4 >=128 8 1 <=0.0625 >=128 </span>
|
||||
<span class="co"># [9] <=0.0625 <=0.0625 64 2 0.125 8 <=0.0625 0.125 </span>
|
||||
<span class="co"># [17] 64 >=128 >=128 16 32 2 8 32 </span>
|
||||
<span class="co"># [25] 0.5 0.5 16 8 >=128 2 16 >=128 </span>
|
||||
<span class="co"># [33] 0.5 2 64 64 16 <=0.0625 1 4 </span>
|
||||
<span class="co"># [41] 0.125 16 <=0.0625 0.125 0.25 0.125 8 4 </span>
|
||||
<span class="co"># [49] <=0.0625 32 1 <=0.0625 1 0.5 0.5 64 </span>
|
||||
<span class="co"># [57] 2 <=0.0625 8 <=0.0625 32 4 32 64 </span>
|
||||
<span class="co"># [65] 0.125 0.5 4 0.125 0.5 4 8 8 </span>
|
||||
<span class="co"># [73] 0.5 64 >=128 32 0.25 32 4 4 </span>
|
||||
<span class="co"># [81] 0.25 64 0.125 <=0.0625 2 1 2 <=0.0625</span>
|
||||
<span class="co"># [89] 1 >=128 0.125 2 64 16 1 64 </span>
|
||||
<span class="co"># [97] 32 64 0.125 <=0.0625</span></code></pre></div>
|
||||
<span class="co"># [1] 1 16 8 0.5 64 0.125 4 2 0.25 16 </span>
|
||||
<span class="co"># [11] 8 64 0.25 64 0.25 0.25 0.125 1 0.5 4 </span>
|
||||
<span class="co"># [21] 64 0.0625 >=128 0.5 0.5 >=128 0.25 0.125 16 32 </span>
|
||||
<span class="co"># [31] 16 0.0625 4 8 4 >=128 4 0.25 0.0625 0.5 </span>
|
||||
<span class="co"># [41] 2 0.125 0.25 1 16 2 0.125 1 2 2 </span>
|
||||
<span class="co"># [51] 0.25 0.5 8 4 8 1 4 64 2 32 </span>
|
||||
<span class="co"># [61] 0.5 2 1 8 8 32 64 4 2 32 </span>
|
||||
<span class="co"># [71] >=128 1 64 4 64 8 8 64 0.125 0.0625</span>
|
||||
<span class="co"># [81] 8 >=128 0.0625 0.0625 0.25 8 8 0.0625 32 0.25 </span>
|
||||
<span class="co"># [91] 32 0.0625 0.125 1 >=128 16 0.0625 8 0.0625 2</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
|
||||
@ -1245,10 +1242,10 @@ Longest: 24</p>
|
||||
<span class="co"># to review it.</span>
|
||||
<span class="va">disk_values</span>
|
||||
<span class="co"># Class <disk></span>
|
||||
<span class="co"># [1] 23 19 31 23 17 26 25 27 18 29 30 27 25 23 28 27 28 26 20 22 28 21 22 25 23</span>
|
||||
<span class="co"># [26] 18 20 22 19 30 22 20 23 21 20 24 28 25 31 29 24 21 31 21 23 24 30 17 27 23</span>
|
||||
<span class="co"># [51] 18 24 27 27 22 17 20 26 22 28 28 26 27 26 21 17 28 27 19 21 22 26 17 21 18</span>
|
||||
<span class="co"># [76] 28 22 25 30 29 19 17 29 29 24 29 30 28 17 23 25 28 17 27 28 25 23 22 19 24</span></code></pre></div>
|
||||
<span class="co"># [1] 25 19 26 17 25 27 22 17 29 29 27 28 21 18 26 29 21 27 24 17 18 19 23 19 21</span>
|
||||
<span class="co"># [26] 18 23 21 27 29 18 25 24 17 31 18 22 25 30 19 29 26 27 22 22 28 21 23 22 20</span>
|
||||
<span class="co"># [51] 30 19 23 21 30 17 19 22 18 25 29 28 25 31 20 23 20 22 27 24 21 21 24 19 31</span>
|
||||
<span class="co"># [76] 19 18 27 20 27 21 25 26 29 27 29 21 27 27 25 20 22 25 26 29 19 19 23 19 20</span></code></pre></div>
|
||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># base R:</span>
|
||||
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
|
||||
|
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@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 class="date">04 July 2021</h4>
|
||||
<h4 class="date">06 July 2021</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@ -1035,8 +1035,8 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<col width="8%">
|
||||
<col width="5%">
|
||||
<col width="4%">
|
||||
<col width="12%">
|
||||
<col width="20%">
|
||||
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|
||||
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|
||||
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|
||||
<col width="7%">
|
||||
<col width="9%">
|
||||
@ -1060,7 +1060,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">DISK</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"><em>Enterobacterales</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center">20-10ug</td>
|
||||
@ -1072,7 +1072,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">DISK</td>
|
||||
<td align="center">UTI</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"><em>Enterobacterales</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center">20-10ug</td>
|
||||
@ -1084,7 +1084,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"><em>Enterobacterales</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"></td>
|
||||
@ -1096,7 +1096,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center">UTI</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"><em>Enterobacterales</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Enterobacterales</td>
|
||||
<td align="center"></td>
|
||||
@ -1108,7 +1108,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Actinomyces</td>
|
||||
<td align="center"><em>Actinomyces</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Anaerobes, Grampositive</td>
|
||||
<td align="center"></td>
|
||||
@ -1120,7 +1120,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
<td align="center">EUCAST 2021</td>
|
||||
<td align="center">MIC</td>
|
||||
<td align="center"></td>
|
||||
<td align="center">Bacteroides</td>
|
||||
<td align="center"><em>Bacteroides</em></td>
|
||||
<td align="center">Amoxicillin/clavulanic acid</td>
|
||||
<td align="center">Anaerobes, Gramnegative</td>
|
||||
<td align="center"></td>
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -42,7 +42,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,12 +236,12 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1719013" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1.9013">
|
||||
<a href="#amr-1719013" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9013</h1>
|
||||
<div id="last-updated-4-july-2021" class="section level2">
|
||||
<div id="amr-1719014" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.7.1.9014">
|
||||
<a href="#amr-1719014" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9014</h1>
|
||||
<div id="last-updated-6-july-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>
|
||||
<a href="#last-updated-6-july-2021" class="anchor"></a><small>Last updated: 6 July 2021</small>
|
||||
</h2>
|
||||
<div id="changed" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-07-04T20:09Z
|
||||
last_built: 2021-07-06T14:34Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -352,7 +352,7 @@
|
||||
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
|
||||
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
|
||||
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
|
||||
<p>The functions <code>mo_family()</code>, <code>mo_genus()</code>, <code>mo_name()</code>, <code>mo_fullname()</code> and <code>mo_shortname()</code> are returned with an additional class <code>taxonomic_name</code>, which allows italic printing in <a href='https://tibble.tidyverse.org/reference/tibble.html'>tibbles</a>.</p>
|
||||
<p>The functions <code>mo_family()</code>, <code>mo_genus()</code>, <code>mo_name()</code>, <code>mo_fullname()</code> and <code>mo_shortname()</code> are returned with an additional class <code>taxonomic_name</code>, which allows italic printing in <a href='https://tibble.tidyverse.org/reference/tibble.html'>tibbles</a> and markdown tables such as with <code><a href='https://rdrr.io/pkg/knitr/man/kable.html'>knitr::kable()</a></code>.</p>
|
||||
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
|
||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
|
||||
|
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9013</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -131,7 +131,7 @@ Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be ba
|
||||
|
||||
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
|
||||
|
||||
The functions \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}} are returned with an additional class \code{taxonomic_name}, which allows italic printing in \link[tibble:tibble]{tibbles}.
|
||||
The functions \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}} are returned with an additional class \code{taxonomic_name}, which allows italic printing in \link[tibble:tibble]{tibbles} and markdown tables such as with \code{\link[knitr:kable]{knitr::kable()}}.
|
||||
|
||||
All output \link[=translate]{will be translated} where possible.
|
||||
|
||||
|