* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -57,12 +57,13 @@
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Algorithm improvements for `as.mo()` (by which some additions were made to the `microorganisms` data set:
* Big improvement for misspelled input
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
* Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology
* Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Updated the `microorganisms` data set to contain the latest taxonomic data from the IJSEM journal (now up to date until August 2019)
* Added almost 5,000 new fungi to the `microorganisms` data set
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* The `name` of `RIF` is now Rifampicin instead of Rifampin
@ -144,7 +145,7 @@
#### 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
* Fixed 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
#' This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#'
#' \link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
#' \link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
#' @section Included taxa:
#' Included are:
#' \itemize{
@ -38,7 +38,7 @@
#' \item{The responsible author(s) and year of scientific publication}
#' }
#'
#' The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
#' The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
#'
#' The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [3]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
#'
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
#' @param allow_uncertain a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details
#' @param allow_uncertain a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details
#' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ... other parameters passed on to functions
#' @rdname as.mo
@ -50,8 +50,7 @@
#' | | ----> species, a 3-4 letter acronym
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
#' ----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
#' C (Chromista), F (Fungi), P (Protozoa) or
#' PL (Plantae)
#' C (Chromista), F (Fungi), P (Protozoa)
#' }
#'
#' Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
@ -60,13 +59,14 @@
#'
#' The algorithm uses data from the Catalogue of Life (see below) and from one other source (see \code{?microorganisms}).
#'
# /// THIS PART WAS DELETED FROM THE MAN PAGE
# \strong{Self-learning algoritm} \cr
# The \code{as.mo()} function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use \code{clean_mo_history()} to reset the algorithms. Only experience from your current \code{AMR} package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge.
#
# Usually, any guess after the first try runs 80-95\% faster than the first try.
#
# For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.
#
# ////
#' \strong{Intelligent rules} \cr
#' This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:
#' \itemize{
@ -169,7 +169,8 @@
#'
#' # All mo_* functions use as.mo() internally too (see ?mo_property):
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.7.1.9038</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS
<footer>
<divclass="copyright">
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</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 08 August 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 <ahref="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 13 August 2019.</p>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers 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><ahref="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<aclass="sourceLine"id="cb15-25"data-line-number="25"><spanclass="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,293 values changed)</span></a>
<aclass="sourceLine"id="cb15-26"data-line-number="26"><spanclass="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no values changed)</span></a>
<aclass="sourceLine"id="cb15-27"data-line-number="27"><spanclass="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no values changed)</span></a>
<aclass="sourceLine"id="cb15-29"data-line-number="29"><spanclass="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no values changed)</span></a>
<aclass="sourceLine"id="cb15-30"data-line-number="30"><spanclass="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no values changed)</span></a>
<aclass="sourceLine"id="cb15-31"data-line-number="31"><spanclass="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no values changed)</span></a>
<aclass="sourceLine"id="cb15-32"data-line-number="32"><spanclass="co"># Table 12: Interpretive rules for aminoglycosides (no values changed)</span></a>
<aclass="sourceLine"id="cb15-33"data-line-number="33"><spanclass="co"># Table 13: Interpretive rules for quinolones (no values changed)</span></a>
<aclass="sourceLine"id="cb15-25"data-line-number="25"><spanclass="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,313 values changed)</span></a>
<aclass="sourceLine"id="cb15-26"data-line-number="26"><spanclass="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb15-27"data-line-number="27"><spanclass="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<aclass="sourceLine"id="cb15-29"data-line-number="29"><spanclass="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<aclass="sourceLine"id="cb15-30"data-line-number="30"><spanclass="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<aclass="sourceLine"id="cb15-31"data-line-number="31"><spanclass="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<aclass="sourceLine"id="cb15-32"data-line-number="32"><spanclass="co"># Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<aclass="sourceLine"id="cb15-33"data-line-number="33"><spanclass="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<aclass="sourceLine"id="cb15-35"data-line-number="35"><spanclass="co"># Other rules</span></a>
<aclass="sourceLine"id="cb15-36"data-line-number="36"><spanclass="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,251 values changed)</span></a>
<aclass="sourceLine"id="cb15-37"data-line-number="37"><spanclass="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (117 values changed)</span></a>
<aclass="sourceLine"id="cb15-38"data-line-number="38"><spanclass="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no values changed)</span></a>
<aclass="sourceLine"id="cb15-39"data-line-number="39"><spanclass="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no values changed)</span></a>
<aclass="sourceLine"id="cb15-40"data-line-number="40"><spanclass="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no values changed)</span></a>
<aclass="sourceLine"id="cb15-41"data-line-number="41"><spanclass="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no values changed)</span></a>
<aclass="sourceLine"id="cb15-36"data-line-number="36"><spanclass="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,240 values changed)</span></a>
<aclass="sourceLine"id="cb15-37"data-line-number="37"><spanclass="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (123 values changed)</span></a>
<aclass="sourceLine"id="cb15-38"data-line-number="38"><spanclass="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<aclass="sourceLine"id="cb15-39"data-line-number="39"><spanclass="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<aclass="sourceLine"id="cb15-40"data-line-number="40"><spanclass="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<aclass="sourceLine"id="cb15-41"data-line-number="41"><spanclass="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<aclass="sourceLine"id="cb15-44"data-line-number="44"><spanclass="co"># EUCAST rules affected 6,550 out of 20,000 rows, making a total of 7,913 edits</span></a>
<aclass="sourceLine"id="cb15-44"data-line-number="44"><spanclass="co"># EUCAST rules affected 6,513 out of 20,000 rows, making a total of 7,843 edits</span></a>
<aclass="sourceLine"id="cb15-45"data-line-number="45"><spanclass="co"># => added 0 test results</span></a>
<aclass="sourceLine"id="cb15-56"data-line-number="56"><spanclass="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -497,7 +497,7 @@
<aclass="sourceLine"id="cb17-3"data-line-number="3"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb17-4"data-line-number="4"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `date` as input for `col_date`.</span></a>
<aclass="sourceLine"id="cb17-5"data-line-number="5"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<aclass="sourceLine"id="cb17-6"data-line-number="6"><spanclass="co"># => Found 5,610 first isolates (28.0% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb17-6"data-line-number="6"><spanclass="co"># => Found 5,643 first isolates (28.2% of total)</span></a></code></pre></div>
<p>So only 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 W2, 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 Q10, sorted on date:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -524,74 +524,74 @@
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-02-15</td>
<tdalign="center">W2</td>
<tdalign="center">2010-01-12</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-05-10</td>
<tdalign="center">W2</td>
<tdalign="center">2010-01-16</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-08-30</td>
<tdalign="center">W2</td>
<tdalign="center">2010-03-09</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-09-27</td>
<tdalign="center">W2</td>
<tdalign="center">2010-03-31</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-10-28</td>
<tdalign="center">W2</td>
<tdalign="center">2010-04-06</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</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="even">
<tdalign="center">6</td>
<tdalign="center">2010-12-01</td>
<tdalign="center">W2</td>
<tdalign="center">2010-05-24</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-01-20</td>
<tdalign="center">W2</td>
<tdalign="center">2010-05-25</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -601,8 +601,8 @@
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-02-09</td>
<tdalign="center">W2</td>
<tdalign="center">2010-07-08</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -612,21 +612,21 @@
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-03-08</td>
<tdalign="center">W2</td>
<tdalign="center">2010-10-22</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">TRUE</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-04-14</td>
<tdalign="center">W2</td>
<tdalign="center">2010-11-30</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -634,7 +634,7 @@
</tr>
</tbody>
</table>
<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>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>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>
<aclass="sourceLine"id="cb20-7"data-line-number="7"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<aclass="sourceLine"id="cb20-8"data-line-number="8"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<aclass="sourceLine"id="cb20-9"data-line-number="9"><spanclass="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<aclass="sourceLine"id="cb20-10"data-line-number="10"><spanclass="co"># => Found 15,032 first weighted isolates (75.2% of total)</span></a></code></pre></div>
<aclass="sourceLine"id="cb20-10"data-line-number="10"><spanclass="co"># => Found 15,004 first weighted isolates (75.0% of total)</span></a></code></pre></div>
<tableclass="table">
<thead><trclass="header">
<thalign="center">isolate</th>
@ -662,59 +662,59 @@
<tbody>
<trclass="odd">
<tdalign="center">1</td>
<tdalign="center">2010-02-15</td>
<tdalign="center">W2</td>
<tdalign="center">2010-01-12</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">TRUE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">2</td>
<tdalign="center">2010-05-10</td>
<tdalign="center">W2</td>
<tdalign="center">2010-01-16</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="odd">
<tdalign="center">3</td>
<tdalign="center">2010-08-30</td>
<tdalign="center">W2</td>
<tdalign="center">2010-03-09</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">4</td>
<tdalign="center">2010-09-27</td>
<tdalign="center">W2</td>
<tdalign="center">2010-03-31</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">I</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">5</td>
<tdalign="center">2010-10-28</td>
<tdalign="center">W2</td>
<tdalign="center">2010-04-06</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</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>
@ -722,32 +722,32 @@
</tr>
<trclass="even">
<tdalign="center">6</td>
<tdalign="center">2010-12-01</td>
<tdalign="center">W2</td>
<tdalign="center">2010-05-24</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="odd">
<tdalign="center">7</td>
<tdalign="center">2011-01-20</td>
<tdalign="center">W2</td>
<tdalign="center">2010-05-25</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
<tdalign="center">FALSE</td>
</tr>
<trclass="even">
<tdalign="center">8</td>
<tdalign="center">2011-02-09</td>
<tdalign="center">W2</td>
<tdalign="center">2010-07-08</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
@ -758,35 +758,35 @@
</tr>
<trclass="odd">
<tdalign="center">9</td>
<tdalign="center">2011-03-08</td>
<tdalign="center">W2</td>
<tdalign="center">2010-10-22</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">R</td>
<tdalign="center">S</td>
<tdalign="center">S</td>
<tdalign="center">R</td>
<tdalign="center">TRUE</td>
<tdalign="center">S</td>
<tdalign="center">FALSE</td>
<tdalign="center">TRUE</td>
</tr>
<trclass="even">
<tdalign="center">10</td>
<tdalign="center">2011-04-14</td>
<tdalign="center">W2</td>
<tdalign="center">2010-11-30</td>
<tdalign="center">Q10</td>
<tdalign="center">B_ESCHR_COL</td>
<tdalign="center">S</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>
<tdalign="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - 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 1, now 6 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - 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>
