* Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`.
#' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
#' - Principal component analysis for AMR
#'
#' @section Reference data publicly available:
#' All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this `AMR` package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find [all download links on our website](https://msberends.github.io/AMR/articles/datasets.html), which is automatically updated with every code change.
#' @section Read more on our website!:
#' On our website <https://msberends.github.io/AMR> you can find [a comprehensive tutorial](https://msberends.github.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.github.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.github.io/AMR/articles/WHONET.html). As we would like to better understand the backgrounds and needs of our users, please [participate in our survey](https://msberends.github.io/AMR/survey.html)!
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
#' @inheritSection AMR Reference data publicly available
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#'
#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
#' @inheritSection AMR Reference data publicly available
#' @format A [`data.frame`] with `r format(nrow(microorganisms.codes), big.mark = ",")` observations and `r ncol(microorganisms.codes)` variables:
#' - `code`\cr Commonly used code of a microorganism
#' - `mo`\cr ID of the microorganism in the [microorganisms] data set
#' @inheritSection AMR Reference data publicly available
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection AMR Read more on our website!
#' @seealso [as.mo()] [microorganisms]
@ -171,6 +175,7 @@ catalogue_of_life <- list(
#' - `patient_id`\cr ID of the patient
#' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms]
#' - `PEN:RIF`\cr `r sum(sapply(example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
"example_isolates"
@ -183,6 +188,7 @@ catalogue_of_life <- list(
#' - `hospital`\cr ID of the hospital, from A to C
#' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
#' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.rsi()]
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
"example_isolates_unclean"
@ -216,6 +222,7 @@ catalogue_of_life <- list(
#' - `Comment`\cr Other comments
#' - `Date of data entry`\cr Date this data was entered in WHONET
#' - `AMP_ND10:CIP_EE`\cr `r sum(sapply(WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
"WHONET"
@ -234,8 +241,7 @@ catalogue_of_life <- list(
#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
#'
#'
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @seealso [intrinsic_resistant]
"rsi_translation"
@ -249,6 +255,7 @@ catalogue_of_life <- list(
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#'
#' This data set is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' @inheritSection AMR Reference data publicly available
<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 <ahref="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 14 August 2020.</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 <ahref="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 21 August 2020.</p>
<spanclass="co"># NOTE: Using column `date` as input for `col_date`.</span>
<spanclass="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span>
</pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient N8, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient C8, sorted on date:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -541,10 +548,10 @@ Longest: 1</p>
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-05-17</td>
<tdalign="center">N8</td>
<tdalign="center">2010-01-13</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -552,8 +559,8 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-07-03</td>
<tdalign="center">N8</td>
<tdalign="center">2010-02-19</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -563,52 +570,52 @@ Longest: 1</p>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-07-31</td>
<tdalign="center">N8</td>
<tdalign="center">2010-03-12</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-09-13</td>
<tdalign="center">N8</td>
<tdalign="center">2010-03-25</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-09-15</td>
<tdalign="center">N8</td>
<tdalign="center">2010-04-28</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2010-10-16</td>
<tdalign="center">N8</td>
<tdalign="center">2010-07-22</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2010-10-17</td>
<tdalign="center">N8</td>
<tdalign="center">2010-12-05</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -618,30 +625,30 @@ Longest: 1</p>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2010-10-24</td>
<tdalign="center">N8</td>
<tdalign="center">2011-01-18</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2010-12-27</td>
<tdalign="center">N8</td>
<tdalign="center">2011-05-24</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">I</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-02-25</td>
<tdalign="center">N8</td>
<tdalign="center">2011-06-24</td>
<tdalign="center">C8</td>
<tdalign="center">B_ESCHR_COLI</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -651,7 +658,7 @@ Longest: 1</p>
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<p>Instead of 1, now 9 isolates are flagged. In total, 78.0% of all isolates are marked ‘first weighted’ - 49.7% 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 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
