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v0.7.0

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dr. M.S. (Matthijs) Berends 2019-06-03 17:45:22 +02:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.6.1.9053
Date: 2019-06-02
Version: 0.7.0
Date: 2019-06-03
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

9
NEWS.md
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@ -1,12 +1,13 @@
# AMR 0.6.1.9053
# AMR 0.7.0
#### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
* Function `mo_name()` as alias of `mo_fullname()`
* Added guidelines of the WHO to determine mutli-drug resistance (MDR) for TB (`mdr_tb()`) and added a new vignette about MDR
* Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (`mdr_tb()`) and added a new vignette about MDR. Read this tutorial [here on our website](https://msberends.gitlab.io/AMR/articles/MDR.html).
#### Changed
* Fixed a critical bug in `first_isolate()` where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.
* Fixedd a bug in `eucast_rules()` where antibiotics from WHONET software would not be recognised
* Completely reworked the `antibiotics` data set:
* All entries now have 3 different identifiers:
* Column `ab` contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package
@ -22,9 +23,9 @@
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New parameter `colours` to set the bar colours
* New parameters `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
* Improved intelligence of looking up antibiotic tables in data set using `guess_ab_col()`
* Improved intelligence of looking up antibiotic columns in a data set using `guess_ab_col()`
* Added ~5,000 more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function
* This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as 'increased exposure' and not 'intermediate' anymore. For functions like `portion_df()` and `count_df()` this means that their new parameter `combine_SI` is TRUE at default.
* This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as 'increased exposure' and not 'intermediate' anymore. For functions like `portion_df()` and `count_df()` this means that their new parameter `combine_SI` is TRUE at default. Our plotting function `ggplot_rsi()` also reflects this change since it uses `count_df()` internally.
* The `age()` function gained a new parameter `exact` to determine ages with decimals
* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()`, `rsi()`
* Frequency tables (`freq()`):

2
R/age.R
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@ -24,7 +24,7 @@
#' Calculates age in years based on a reference date, which is the sytem date at default.
#' @param x date(s), will be coerced with \code{\link{as.POSIXlt}}
#' @param reference reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in a year of \code{reference} (either 365 or 366).
#' @return An integer (no decimals) if \code{exact = FALSE}, a double (with decimals) otherwise
#' @seealso \code{\link{age_groups}} to split age into age groups
#' @importFrom dplyr if_else

2
R/amr.R
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@ -46,7 +46,7 @@
#' Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
#'
#' [1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
#' @section Read more on our website!:
#' On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.

4
R/data.R
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@ -78,7 +78,7 @@
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
#'
#' From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html}
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
#' @inheritSection AMR Read more on our website!
@ -104,7 +104,7 @@ catalogue_of_life <- list(
#' \item{\code{fullname}}{Old full taxonomic name of the microorganism}
#' \item{\code{ref}}{Author(s) and year of concerning scientific publication}
#' }
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old"

3
R/mdro.R
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@ -69,6 +69,9 @@ mdro <- function(x,
if (length(guideline) > 1) {
stop("`guideline` must be a length one character string.", call. = FALSE)
}
if (length(country) > 1) {
stop("`country` must be a length one character string.", call. = FALSE)
}
if (!is.null(country)) {
guideline <- country
}

7
R/misc.R
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@ -154,6 +154,7 @@ search_type_in_df <- function(x, type) {
found
}
#' @importFrom crayon blue bold
get_column_abx <- function(x,
soft_dependencies = NULL,
hard_dependencies = NULL,
@ -219,10 +220,8 @@ get_column_abx <- function(x,
if (!all(soft_dependencies %in% names(x))) {
# missing a soft dependency may lower the reliability
missing <- soft_dependencies[!soft_dependencies %in% names(x)]
missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE), ")")
warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "),
immediate. = TRUE,
call. = FALSE)
missing <- paste0(bold(missing), " (", ab_name(missing, tolower = TRUE), ")")
message(blue('NOTE: Reliability might be improved if these antimicrobial results would be available too:', paste(missing, collapse = ", ")))
}
}
x

2
R/mo.R
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@ -130,7 +130,7 @@
#'
#' [3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
#'
#' [4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' [4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' @export
#' @return Character (vector) with class \code{"mo"}
#' @seealso \code{\link{microorganisms}} for the \code{data.frame} that is being used to determine ID's. \cr

1
R/zzz.R
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@ -254,6 +254,7 @@ make_trans_tbl <- function() {
F_CCCCS = "F_CRYPT",
# renamings of old genus + species
F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "F_ISSTC_ORI",
F_CANDD_GUI = "F_MYRZY_GUI",
F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
B_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")

8
_pkgdown.yml
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@ -55,18 +55,16 @@ navbar:
href: 'articles/EUCAST.html'
- text: 'Get properties of a microorganism'
icon: 'fa-bug'
# href: 'articles/mo_property.html'
href: 'reference/mo_property.html'
href: 'reference/mo_property.html' # reference instead of article
- text: 'Get properties of an antibiotic'
icon: 'fa-capsules'
# href: 'articles/ab_property.html'
href: 'reference/ab_property.html'
href: 'reference/ab_property.html' # reference instead of article
- text: 'Create frequency tables'
icon: 'fa-sort-amount-down'
href: 'articles/freq.html'
- text: 'Use the G-test'
icon: 'fa-clipboard-check'
href: 'articles/G_test.html'
href: 'reference/g.test.html' # reference instead of article
- text: 'Other: benchmarks'
icon: 'fa-shipping-fast'
href: 'articles/benchmarks.html'

4
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -164,7 +164,7 @@
</a>
</li>
<li>
<a href="articles/G_test.html">
<a href="reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

507
docs/articles/AMR.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -208,7 +208,7 @@
<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 02 June 2019.</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 03 June 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -224,21 +224,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-06-02</td>
<td align="center">2019-06-03</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">2019-06-02</td>
<td align="center">2019-06-03</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">2019-06-02</td>
<td align="center">2019-06-03</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -334,64 +334,20 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-12-18</td>
<td align="center">S8</td>
<td align="center">Hospital D</td>
<td align="center">2010-12-01</td>
<td align="center">Y6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-05-29</td>
<td align="center">Z4</td>
<td align="center">Hospital C</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">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-11-20</td>
<td align="center">G6</td>
<td align="center">Hospital C</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-11-07</td>
<td align="center">Q10</td>
<td align="center">Hospital D</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">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-11-26</td>
<td align="center">P8</td>
<td align="center">Hospital B</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">F</td>
</tr>
<tr class="even">
<td align="center">2014-07-30</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">2011-05-31</td>
<td align="center">C8</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
@ -399,6 +355,50 @@
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-04-18</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2011-04-24</td>
<td align="center">W4</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2011-11-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2016-09-07</td>
<td align="center">Y6</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -418,8 +418,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,420 52.1% 10,420 52.1%
# 2 F 9,580 47.9% 20,000 100.0%</code></pre>
# 1 M 10,407 52.0% 10,407 52.0%
# 2 F 9,593 48.0% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -449,14 +449,14 @@
<a class="sourceLine" id="cb14-18" title="18"><span class="co"># Pasteurella multocida (no new changes)</span></a>
<a class="sourceLine" id="cb14-19" title="19"><span class="co"># Staphylococcus (no new changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co"># Streptococcus groups A, B, C, G (no new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1421 new changes)</span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co"># Streptococcus pneumoniae (1431 new changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co"># Viridans group streptococci (no new changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1367 new changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1230 new changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2632 new changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2646 new changes)</span></a>
<a class="sourceLine" id="cb14-29" title="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)</span></a>
<a class="sourceLine" id="cb14-30" title="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)</span></a>
<a class="sourceLine" id="cb14-31" title="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)</span></a>
@ -464,24 +464,24 @@
<a class="sourceLine" id="cb14-33" title="33"><span class="co"># Table 13: Interpretive rules for quinolones (no new changes)</span></a>
<a class="sourceLine" id="cb14-34" title="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" title="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2233 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (113 new changes)</span></a>
<a class="sourceLine" id="cb14-36" title="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2197 new changes)</span></a>
<a class="sourceLine" id="cb14-37" title="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (99 new changes)</span></a>
<a class="sourceLine" id="cb14-38" title="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,458 out of 20,000 rows, making a total of 7,766 edits</span></a>
<a class="sourceLine" id="cb14-44" title="44"><span class="co"># EUCAST rules affected 6,284 out of 20,000 rows, making a total of 7,603 edits</span></a>
<a class="sourceLine" id="cb14-45" title="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-46" title="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,766 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 106 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,695 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,068 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 323 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,556 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 18 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-47" title="47"><span class="co"># =&gt; changed 7,603 test results</span></a>
<a class="sourceLine" id="cb14-48" title="48"><span class="co"># - 111 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-49" title="49"><span class="co"># - 4,561 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-50" title="50"><span class="co"># - 1,028 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-51" title="51"><span class="co"># - 292 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-52" title="52"><span class="co"># - 1,595 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-53" title="53"><span class="co"># - 16 test results changed from R to I</span></a>
<a class="sourceLine" id="cb14-54" title="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-55" title="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-56" title="56"><span class="co"># Use verbose = TRUE to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -509,7 +509,7 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,665 first isolates (28.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># =&gt; Found 5,652 first isolates (28.3% of total)</span></a></code></pre></div>
<p>So only 28.3% 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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -536,8 +536,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-18</td>
<td align="center">T2</td>
<td align="center">2010-03-08</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -547,21 +547,21 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-26</td>
<td align="center">T2</td>
<td align="center">2010-04-14</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-26</td>
<td align="center">T2</td>
<td align="center">2010-04-18</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -569,21 +569,21 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-13</td>
<td align="center">T2</td>
<td align="center">2010-04-22</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-18</td>
<td align="center">T2</td>
<td align="center">2010-05-30</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</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>
@ -591,32 +591,32 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-12-10</td>
<td align="center">T2</td>
<td align="center">2010-10-09</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-02</td>
<td align="center">T2</td>
<td align="center">2011-01-26</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-02</td>
<td align="center">T2</td>
<td align="center">2011-02-19</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</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>
@ -624,24 +624,24 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-15</td>
<td align="center">T2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-05-15</td>
<td align="center">T2</td>
<td align="center">2011-03-25</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-17</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -657,7 +657,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" title="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" title="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,064 first weighted isolates (75.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co"># =&gt; Found 15,076 first weighted isolates (75.4% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -674,8 +674,8 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-18</td>
<td align="center">T2</td>
<td align="center">2010-03-08</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -686,22 +686,22 @@
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-26</td>
<td align="center">T2</td>
<td align="center">2010-04-14</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</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">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-02-26</td>
<td align="center">T2</td>
<td align="center">2010-04-18</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -710,22 +710,22 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-03-13</td>
<td align="center">T2</td>
<td align="center">2010-04-22</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-08-18</td>
<td align="center">T2</td>
<td align="center">2010-05-30</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</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>
@ -734,71 +734,71 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-12-10</td>
<td align="center">T2</td>
<td align="center">2010-10-09</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-05-02</td>
<td align="center">T2</td>
<td align="center">2011-01-26</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-05-02</td>
<td align="center">T2</td>
<td align="center">2011-02-19</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-25</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-05-15</td>
<td align="center">T2</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-05-15</td>
<td align="center">T2</td>
<td align="center">2011-04-17</td>
<td align="center">C7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.3% of all isolates are marked ‘first weighted’ - 47% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 9 isolates are flagged. In total, 75.4% of all isolates are marked ‘first weighted’ - 47.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,064 isolates for analysis.</p>
<p>So we end up with 15,076 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -806,7 +806,6 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -823,28 +822,11 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>3</td>
<td align="center">2015-11-20</td>
<td align="center">G6</td>
<td align="center">2010-12-01</td>
<td align="center">Y6</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</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>4</td>
<td align="center">2015-11-07</td>
<td align="center">Q10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</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>
@ -854,46 +836,58 @@
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2013-11-26</td>
<td align="center">P8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</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">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2014-07-30</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</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">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2016-04-08</td>
<td align="center">C7</td>
<td align="center">2011-05-31</td>
<td align="center">C8</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</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">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-04-18</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</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 negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-04-24</td>
<td align="center">W4</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-11-05</td>
<td align="center">A9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</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>
@ -903,19 +897,18 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>8</td>
<td align="center">2010-02-28</td>
<td align="center">A8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">2016-09-07</td>
<td align="center">Y6</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</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">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -935,9 +928,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,064 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,076 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,064 (of which NA: 0 = 0.00%)<br>
Length: 15,076 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -954,33 +947,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,474</td>
<td align="right">49.6%</td>
<td align="right">7,474</td>
<td align="right">49.6%</td>
<td align="right">7,402</td>
<td align="right">49.1%</td>
<td align="right">7,402</td>
<td align="right">49.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,691</td>
<td align="right">24.5%</td>
<td align="right">11,165</td>
<td align="right">74.1%</td>
<td align="right">3,887</td>
<td align="right">25.8%</td>
<td align="right">11,289</td>
<td align="right">74.9%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,238</td>
<td align="right">2,244</td>
<td align="right">14.9%</td>
<td align="right">13,403</td>
<td align="right">89.0%</td>
<td align="right">13,533</td>
<td align="right">89.8%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,661</td>
<td align="right">11.0%</td>
<td align="right">15,064</td>
<td align="right">1,543</td>
<td align="right">10.2%</td>
<td align="right">15,076</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -991,7 +984,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4719862</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co"># [1] 0.4678297</span></a></code></pre></div>
<p>Or can be used in conjuction 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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -1004,19 +997,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4641785</td>
<td align="center">0.4700949</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4697084</td>
<td align="center">0.4625218</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4838129</td>
<td align="center">0.4715272</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4796271</td>
<td align="center">0.4706266</td>
</tr>
</tbody>
</table>
@ -1034,23 +1027,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4641785</td>
<td align="center">4662</td>
<td align="center">0.4700949</td>
<td align="center">4531</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4697084</td>
<td align="center">5282</td>
<td align="center">0.4625218</td>
<td align="center">5163</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4838129</td>
<td align="center">2224</td>
<td align="center">0.4715272</td>
<td align="center">2318</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4796271</td>
<td align="center">2896</td>
<td align="center">0.4706266</td>
<td align="center">3064</td>
</tr>
</tbody>
</table>
@ -1070,27 +1063,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9211935</td>
<td align="center">0.8898849</td>
<td align="center">0.9933101</td>
<td align="center">0.9297487</td>
<td align="center">0.8940827</td>
<td align="center">0.9944610</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8169777</td>
<td align="center">0.8832029</td>
<td align="center">0.9843468</td>
<td align="center">0.8243681</td>
<td align="center">0.9047310</td>
<td align="center">0.9831497</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9184503</td>
<td align="center">0.9170956</td>
<td align="center">0.9937686</td>
<td align="center">0.9248778</td>
<td align="center">0.9253923</td>
<td align="center">0.9935683</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6090259</td>
<td align="center">0.6114082</td>
<td align="center">0.0000000</td>
<td align="center">0.6090259</td>
<td align="center">0.6114082</td>
</tr>
</tbody>
</table>

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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

62
docs/articles/MDR.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -242,18 +242,18 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S R R S S S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 S I S S R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S I S S S S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S I S R S R</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 I S S S S R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 S S R S R I</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S S S R I S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R R R I R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S S S I</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S R S R S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R S S S S R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S S R R</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 I</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
@ -285,40 +285,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,249</td>
<td align="right">65.0%</td>
<td align="right">3,249</td>
<td align="right">65.0%</td>
<td align="right">3,238</td>
<td align="right">64.8%</td>
<td align="right">3,238</td>
<td align="right">64.8%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">670</td>
<td align="right">13.4%</td>
<td align="right">3,919</td>
<td align="right">78.4%</td>
<td align="right">662</td>
<td align="right">13.2%</td>
<td align="right">3,900</td>
<td align="right">78.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">604</td>
<td align="right">12.1%</td>
<td align="right">4,523</td>
<td align="right">90.5%</td>
<td align="right">613</td>
<td align="right">12.3%</td>
<td align="right">4,513</td>
<td align="right">90.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">289</td>
<td align="right">5.8%</td>
<td align="right">4,812</td>
<td align="right">96.2%</td>
<td align="right">279</td>
<td align="right">5.6%</td>
<td align="right">4,792</td>
<td align="right">95.8%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">188</td>
<td align="right">3.8%</td>
<td align="right">208</td>
<td align="right">4.2%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>

6
docs/articles/SPSS.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

10
docs/articles/WHONET.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -215,7 +215,7 @@
<p>An example syntax could look like this:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(readxl)</a>
<a class="sourceLine" id="cb1-2" title="2">data &lt;-<span class="st"> </span><span class="kw"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="dt">path =</span> <span class="st">"path/to/your/file.xlsx"</span>)</a></code></pre></div>
<p>This package comes with an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
<p>This package comes with an <a href="https://msberends.gitlab.io/AMR/reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level1">
<h1 class="hasAnchor">
@ -226,7 +226,7 @@
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR) <span class="co"># this package</span></a></code></pre></div>
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="./reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="https://msberends.gitlab.io/AMR/reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="co"># transform variables</span></a>

6
docs/articles/ab_property.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>ab_property.Rmd</code></div>

74
docs/articles/benchmarks.html
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@ -40,7 +40,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -126,7 +126,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -199,7 +199,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -224,14 +224,14 @@
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18 18 27.0 18 18.0 62.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 48 48 48.0 48 48.0 48.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 18 18 27.0 18 18.0 63.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18 18 28.0 18 18.0 81.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28 28 33.0 29 29.0 73.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28 29 47.0 30 72.0 110.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8 8 8.1 8 8.1 8.2 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co"># as.mo("sau") 18 18 22.0 18.0 18.0 62 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co"># as.mo("stau") 48 48 53.0 48.0 48.0 93 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co"># as.mo("staaur") 17 18 22.0 18.0 18.0 62 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co"># as.mo("STAAUR") 18 18 22.0 18.0 18.0 62 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co"># as.mo("S. aureus") 28 28 29.0 28.0 29.0 29 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co"># as.mo("S. aureus") 28 28 57.0 51.0 73.0 130 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co"># as.mo("Staphylococcus aureus") 8 8 9.3 8.1 8.3 20 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -243,11 +243,11 @@
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 470 470 500 520 520 520 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 500 500 520 530 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 74 86 74 76 140 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 74 80 76 77 120 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 73 73 89 74 120 140 10</span></a></code></pre></div>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># as.mo("theisl") 470 470 500 510 520 530 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># as.mo("THEISL") 470 470 480 470 510 520 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># as.mo("T. islandicus") 74 75 84 75 77 120 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># as.mo("T. islandicus") 74 74 93 74 120 120 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># as.mo("Thermus islandicus") 72 73 84 74 77 120 10</span></a></code></pre></div>
<p>That takes 8.1 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
@ -294,8 +294,8 @@
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1080 1120 1160 1130 1180 1340 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.13 seconds (1128 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-27" title="27"><span class="co"># mo_fullname(x) 1120 1150 1210 1190 1220 1430 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 1.19 seconds (1194 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -308,10 +308,10 @@
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.10 13.5 13.70 13.60 13.70 14.70 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.70 25.9 31.10 27.00 27.70 70.30 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.61 1.8 1.87 1.85 1.95 2.05 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<a class="sourceLine" id="cb6-8" title="8"><span class="co"># A 13.20 13.4 13.80 13.70 14.20 14.40 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co"># B 25.50 25.9 31.00 26.20 27.60 72.30 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co"># C 1.78 1.8 1.89 1.84 2.03 2.06 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0018 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
@ -324,14 +324,14 @@
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.495 0.521 0.626 0.631 0.723 0.822 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.581 0.652 0.710 0.716 0.760 0.841 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.520 1.610 1.810 1.780 1.940 2.220 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.617 0.655 0.742 0.724 0.798 0.973 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.506 0.573 0.648 0.615 0.707 0.902 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.515 0.555 0.621 0.589 0.638 0.868 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.512 0.572 0.633 0.608 0.713 0.805 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.191 0.284 0.303 0.303 0.334 0.397 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co"># A 0.526 0.606 0.652 0.639 0.721 0.771 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co"># B 0.575 0.582 0.665 0.658 0.689 0.898 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co"># C 1.820 1.870 1.940 1.950 2.020 2.070 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co"># D 0.547 0.596 0.702 0.665 0.850 0.891 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co"># E 0.521 0.560 0.624 0.625 0.655 0.843 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co"># F 0.487 0.518 0.596 0.559 0.720 0.754 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co"># G 0.483 0.573 0.621 0.605 0.667 0.762 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co"># H 0.196 0.270 0.304 0.314 0.348 0.418 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -358,13 +358,13 @@
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.44 18.47 18.68 18.57 18.79 19.33 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 21.04 21.07 21.27 21.15 21.26 21.85 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 34.34 34.55 34.70 34.67 34.87 35.06 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 20.91 21.01 30.28 21.28 21.55 67.00 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 20.80 20.98 25.89 21.46 21.86 66.53 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 20.93 21.08 21.12 21.11 21.13 21.42 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 20.94 21.03 25.81 21.40 21.64 66.15 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co"># en 18.45 18.62 18.93 18.81 19.03 20.02 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co"># de 21.13 21.19 21.67 21.26 21.37 25.28 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co"># nl 34.19 34.39 34.74 34.55 34.93 35.99 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co"># es 20.92 21.03 25.70 21.26 21.47 65.90 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co"># it 20.79 20.94 25.96 21.23 21.88 65.69 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co"># fr 20.97 21.04 21.30 21.27 21.44 21.86 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co"># pt 20.81 20.91 25.66 21.01 21.24 66.88 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
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</button>
<span class="navbar-brand">
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@ -199,7 +199,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
<h4 class="date">03 June 2019</h4>
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<ul>
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<li><a href="G_test.html">How to use the *G*-test</a></li>
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@ -199,7 +199,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
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<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">02 June 2019</h4>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
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@ -239,9 +239,9 @@
</div>
<div id="amr-0619053" class="section level1">
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<h1 class="page-header">
<a href="#amr-0619053" class="anchor"></a>AMR 0.6.1.9053<small> Unreleased </small>
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> Unreleased </small>
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<h4 class="hasAnchor">
@ -250,7 +250,7 @@
<li>Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><a href="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><a href="../reference/as.disk.html">as.disk()</a></code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code><a href="../reference/mo_property.html">mo_name()</a></code> as alias of <code><a href="../reference/mo_property.html">mo_fullname()</a></code>
</li>
<li>Added guidelines of the WHO to determine mutli-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR</li>
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><a href="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <a href="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
</ul>
</div>
<div id="changed" class="section level4">
@ -258,6 +258,7 @@
<a href="#changed" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixedd a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Completely reworked the <code>antibiotics</code> data set:
<ul>
<li>All entries now have 3 different identifiers:
@ -282,10 +283,10 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
<li>New parameters <code>title</code>, <code>subtitle</code>, <code>caption</code>, <code>x.title</code> and <code>y.title</code> to set titles and axis descriptions</li>
</ul>
</li>
<li>Improved intelligence of looking up antibiotic tables in data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
<li>Improved intelligence of looking up antibiotic columns in a data set using <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><a href="../reference/as.mo.html">as.mo()</a></code> function</li>
<li>This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like <code><a href="../reference/portion.html">portion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code> this means that their new parameter <code>combine_SI</code> is TRUE at default.</li>
<li>This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like <code><a href="../reference/portion.html">portion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code> this means that their new parameter <code>combine_SI</code> is TRUE at default. Our plotting function <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change since it uses <code><a href="../reference/count.html">count_df()</a></code> internally.</li>
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code>rsi()</code>
</li>
@ -1066,7 +1067,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0619053">0.6.1.9053</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>
<li><a href="#amr-050">0.5.0</a></li>

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articles:
AMR: AMR.html
EUCAST: EUCAST.html
G_test: G_test.html
MDR: MDR.html
SPSS: SPSS.html
WHONET: WHONET.html

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</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">0.6.1.9053</span>
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</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
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Use the G-test

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -273,7 +273,7 @@
<p>Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] <br /></p>
<p>[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href='https://www.rug.nl'>https://www.rug.nl</a> <a href='https://www.umcg.nl'>https://www.umcg.nl</a> <br />
[2] Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href='certe.nl'>certe.nl</a></p>
[2] Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href='https://www.certe.nl'>https://www.certe.nl</a></p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -263,7 +263,7 @@
</tr>
<tr>
<th>exact</th>
<td><p>a logical to indicate whether age calculation should be exact, i.e. with decimals</p></td>
<td><p>a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of <a href='https://en.wikipedia.org/wiki/Year-to-date'>year-to-date</a> (YTD) of <code>x</code> by the number of days in a year of <code>reference</code> (either 365 or 366).</p></td>
</tr>
</table>

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
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Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
@ -360,7 +360,7 @@ The intelligent rules take into account microbial prevalence of pathogens in hum
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
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Use the G-test

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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
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</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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</span>
</div>
@ -167,7 +167,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</a>
</li>
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<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
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Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
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</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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@ -80,7 +80,7 @@
</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">0.6.1.9053</span>
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</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test

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</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">0.6.1.9053</span>
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</span>
</div>
@ -166,7 +166,7 @@
</a>
</li>
<li>
<a href="../articles/G_test.html">
<a href="../reference/g.test.html">
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Use the G-test

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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.6.1.9053</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0</span>
</span>
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@ -167,7 +167,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
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<a href="../articles/G_test.html">
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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docs/reference/guess_ab_col.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -78,7 +78,7 @@
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@ -164,7 +164,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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docs/reference/mdro.html
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@ -80,7 +80,7 @@
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docs/reference/microorganisms.codes.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -266,7 +266,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date'>http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

6
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -261,7 +261,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>

6
docs/reference/mo_property.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -348,7 +348,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>[1] Becker K <em>et al.</em> <strong>Coagulase-Negative Staphylococci</strong>. 2014. Clin Microbiol Rev. 27(4): 870–926. <a href='https://dx.doi.org/10.1128/CMR.00109-13'>https://dx.doi.org/10.1128/CMR.00109-13</a></p>
<p>[2] Becker K <em>et al.</em> <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> 2019. Clin Microbiol Infect. <a href='https://doi.org/10.1016/j.cmi.2019.02.028'>https://doi.org/10.1016/j.cmi.2019.02.028</a></p>
<p>[3] Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95. <a href='https://dx.doi.org/10.1084/jem.57.4.571'>https://dx.doi.org/10.1084/jem.57.4.571</a></p>
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<p>[4] Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

4
docs/reference/mo_source.html
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -167,7 +167,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -80,7 +80,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
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@ -166,7 +166,7 @@
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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@ -167,7 +167,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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docs/reference/septic_patients.html
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@ -80,7 +80,7 @@
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@ -166,7 +166,7 @@
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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@ -167,7 +167,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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docs/reference/translate.html
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@ -80,7 +80,7 @@
</button>
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@ -166,7 +166,7 @@
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Use the G-test

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docs/sitemap.xml
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@ -141,9 +141,6 @@
<url>
<loc>https://msberends.gitlab.io/AMR/articles/EUCAST.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/articles/G_test.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/articles/MDR.html</loc>
</url>

2
man/AMR.Rd
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@ -32,7 +32,7 @@ This package can be used for:
Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] \cr
[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
}
\section{Read more on our website!}{

2
man/age.Rd
View File

@ -11,7 +11,7 @@ age(x, reference = Sys.Date(), exact = FALSE)
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}}
\item{exact}{a logical to indicate whether age calculation should be exact, i.e. with decimals}
\item{exact}{a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in a year of \code{reference} (either 365 or 366).}
}
\value{
An integer (no decimals) if \code{exact = FALSE}, a double (with decimals) otherwise

2
man/as.mo.Rd
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@ -131,7 +131,7 @@ Group 2 probably contains less microbial pathogens; all other members of phyla t
[3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\section{Catalogue of Life}{

2
man/microorganisms.Rd
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@ -17,7 +17,7 @@
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
}

2
man/microorganisms.old.Rd
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@ -12,7 +12,7 @@
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
}}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\usage{
microorganisms.old

2
man/mo_property.Rd
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@ -115,7 +115,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
[3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
}
\section{Read more on our website!}{

49
tests/testthat/test-mdro.R
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@ -24,17 +24,17 @@ context("mdro.R")
test_that("mdro works", {
library(dplyr)
expect_error(suppressWarnings(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, country = "fr", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
expect_error(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE))
expect_error(mdro(septic_patients, country = "fr", info = TRUE))
expect_error(mdro(septic_patients, country = c("de", "nl"), info = TRUE))
expect_error(mdro(septic_patients, col_mo = "invalid", info = TRUE))
outcome <- suppressWarnings(mdro(septic_patients))
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
outcome <- mdro(septic_patients)
outcome <- eucast_exceptional_phenotypes(septic_patients, info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
outcome <- mdro(septic_patients, "nl", info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
@ -42,19 +42,14 @@ test_that("mdro works", {
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(
suppressWarnings(
brmo(septic_patients, info = FALSE)),
suppressWarnings(
mdro(septic_patients, country = "nl", info = FALSE)
)
)
expect_equal(brmo(septic_patients, info = FALSE),
mdro(septic_patients, country = "nl", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
# test Dutch P. aeruginosa MDRO
expect_equal(suppressWarnings(
expect_equal(
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cfta = "S",
cipr = "S",
@ -65,9 +60,9 @@ test_that("mdro works", {
pita = "S"),
country = "nl",
col_mo = "mo",
info = FALSE))
), "Negative")
expect_equal(suppressWarnings(
info = FALSE)),
"Negative")
expect_equal(
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cefta = "R",
cipr = "R",
@ -78,16 +73,14 @@ test_that("mdro works", {
pita = "R"),
country = "nl",
col_mo = "mo",
info = FALSE))
), "Positive")
info = FALSE)),
"Positive")
# MDR TB
expect_equal(
suppressWarnings(
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2]
),
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(septic_patients$RIF))
sample_rsi <- function() {
@ -97,7 +90,7 @@ test_that("mdro works", {
replace = TRUE)
}
expect_gt(
suppressWarnings(
#suppressWarnings(
data.frame(rifampicin = sample_rsi(),
inh = sample_rsi(),
gatifloxacin = sample_rsi(),
@ -106,7 +99,9 @@ test_that("mdro works", {
MFX = sample_rsi(),
KAN = sample_rsi()) %>%
mdr_tb() %>%
n_distinct()),
n_distinct()
#)
,
2)
})

2
tests/testthat/test-misc.R
View File

@ -47,7 +47,7 @@ test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
expect_warning(get_column_abx(septic_patients, soft_dependencies = "FUS"))
expect_message(get_column_abx(septic_patients, soft_dependencies = "FUS"))
expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_error(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
})

23
vignettes/G_test.Rmd
View File

@ -1,23 +0,0 @@
---
title: "How to use the *G*-test"
author: "Matthijs S. Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true
vignette: >
%\VignetteIndexEntry{How to use the G-test}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
editor_options:
chunk_output_type: console
---
```{r setup, include = FALSE, results = 'markup'}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#"
)
```
*(will be available soon - in the meanwhile, please read about [this *G*-test in the manual](./../reference/g.test.html))*

4
vignettes/WHONET.Rmd
View File

@ -34,7 +34,7 @@ library(readxl)
data <- read_excel(path = "path/to/your/file.xlsx")
```
This package comes with an [example data set `WHONET`](./reference/WHONET.html). We will use it for this analysis.
This package comes with an [example data set `WHONET`](https://msberends.gitlab.io/AMR/reference/WHONET.html). We will use it for this analysis.
# Preparation
@ -48,7 +48,7 @@ library(AMR) # this package
We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](./reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](https://msberends.gitlab.io/AMR/reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
```{r}