* 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 *Blastocystis*
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. **IMPORTANT:** Because of these changes, the microorganism IDs have been changed to a slightly different format. Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format.
@ -105,6 +106,7 @@
* Using negative values for `x` in `age_groups()` will now introduce `NA`s and not return an error anymore
* Fix for determining the system's language
* Fix for `key_antibiotics()` on foreign systems
* Added 80 new LIS codes for microorganisms
#### Other
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 69,454 observations and 16 variables:
#' @format A \code{\link{data.frame}} with 69,465 observations and 16 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID}
@ -72,6 +72,7 @@
#' \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
#' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
#' \item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)}
#' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
#' \item{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
#' }
@ -114,7 +115,7 @@ catalogue_of_life <- list(
#' Translation table for common microorganism codes
#'
#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 4,927 observations and 2 variables:
#' @format A \code{\link{data.frame}} with 5,006 observations and 2 variables:
#' \describe{
#' \item{\code{code}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}
#' @param ab_class an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{AMR::antibiotics$group}
#' @param result an antibiotic result: S, I or R (or a combination of more of them)
#' @param scope the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}
#' @param ... parameters passed on to \code{\link[dplyr]{filter_at}}
#' @param ... parameters passed on to \code{filter_at} from the \code{dplyr} package
#' @details The \code{group} column in \code{\link{antibiotics}} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
<p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <ahref="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code><ahref="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
<p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <ahref="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code>catalogue_of_life_version()</code> can be checked which version of the CoL is included in this package.</p>
<p>Read more about which data from the Catalogue of Life <ahref="./reference/catalogue_of_life.html">in our manual</a>.</p>
<p>It <strong>cleanses existing data</strong> by providing new <em>classes</em> for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:</p>
<ul>
<li>Use <code><ahref="reference/as.mo.html">as.mo()</a></code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <ahref="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <ahref="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <ahref="./reference/as.mo.html#source">source</a>).</li>
<li>Use <code><ahref="reference/as.ab.html">as.ab()</a></code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code><ahref="reference/as.ab.html">as.ab()</a></code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
<li>Use <code><ahref="reference/as.rsi.html">as.rsi()</a></code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code><ahref="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
<li>Use <code>as.mo()</code> to get a microbial ID. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNMN” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AURS”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our <ahref="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <ahref="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <ahref="./reference/as.mo.html#source">source</a>).</li>
<li>Use <code>as.ab()</code> to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is <code>AMX</code> and the ID of gentamicin is <code>GEN</code>. The <code>as.ab()</code> function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, ATC codes, defined daily doses (DDD) and drug categories of antibiotics.</li>
<li>Use <code>as.rsi()</code> to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.</li>
<li>Use <code>as.mic()</code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.</li>
</ul>
</li>
<li>
<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
<ul>
<li>Use <code><ahref="reference/eucast_rules.html">eucast_rules()</a></code> to apply <ahref="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to RSI values, use <code><ahref="reference/as.rsi.html">as.rsi()</a></code> for that).</li>
<li>Use <code><ahref="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <ahref="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<li>Use <code>eucast_rules()</code> to apply <ahref="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a> (not the translation from MIC to RSI values, use <code>as.rsi()</code> for that).</li>
<li>Use <code>first_isolate()</code> to identify the first isolates of every patient <ahref="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
<ul>
<li>You can also identify first <em>weighted</em> isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.</li>
</ul>
</li>
<li>Use <code><ahref="reference/mdro.html">mdro()</a></code> (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.</li>
<li>The <ahref="./reference/microorganisms.html">data set <code>microorganisms</code></a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g.different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><ahref="reference/mo_property.html">mo_genus()</a></code>, <code><ahref="reference/mo_property.html">mo_family()</a></code>, <code><ahref="reference/mo_property.html">mo_gramstain()</a></code> or even <code><ahref="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><ahref="reference/as.mo.html">as.mo()</a></code> internally, they also use the same intelligent rules for determination. For example, <code><ahref="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><ahref="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The <ahref="./reference/antibiotics.html">data set <code>antibiotics</code></a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. The function <code><ahref="reference/ab_property.html">ab_atc()</a></code> will return the ATC code of an antibiotic as defined by the WHO. Use functions like <code><ahref="reference/ab_property.html">ab_name()</a></code>, <code><ahref="reference/ab_property.html">ab_group()</a></code> and <code><ahref="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><ahref="reference/as.ab.html">as.ab()</a></code> internally so they support the same intelligent rules to guess the most probable result. For example, <code><ahref="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><ahref="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><ahref="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
<li>Use <code>mdro()</code> (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.</li>
<li>The <ahref="./reference/microorganisms.html">data set <code>microorganisms</code></a> contains the complete taxonomic tree of ~70,000 microorganisms. Furthermore, some colloquial names and all Gram stains are available, which enables resistance analysis of e.g.different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code>mo_genus()</code>, <code>mo_family()</code>, <code>mo_gramstain()</code> or even <code>mo_phylum()</code>. As they use <code>as.mo()</code> internally, they also use the same intelligent rules for determination. For example, <code>mo_genus("MRSA")</code> and <code>mo_genus("S. aureus")</code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
<li>The <ahref="./reference/antibiotics.html">data set <code>antibiotics</code></a> contains ~450 antimicrobial drugs with their EARS-Net code, ATC code, PubChem compound ID, official name, common LIS codes and DDDs of both oral and parenteral administration. It also contains all (thousands of) trade names found in PubChem. The function <code>ab_atc()</code> will return the ATC code of an antibiotic as defined by the WHO. Use functions like <code>ab_name()</code>, <code>ab_group()</code> and <code>ab_tradenames()</code> to look up values. The <code>ab_*</code> functions use <code>as.ab()</code> internally so they support the same intelligent rules to guess the most probable result. For example, <code>ab_name("Fluclox")</code>, <code>ab_name("Floxapen")</code> and <code>ab_name("J01CF05")</code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
</ul>
</li>
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><ahref="reference/portion.html">portion_R()</a></code>, <code><ahref="reference/portion.html">portion_IR()</a></code>, <code><ahref="reference/portion.html">portion_I()</a></code>, <code><ahref="reference/portion.html">portion_SI()</a></code> and <code><ahref="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_R()</a></code>, <code><ahref="reference/count.html">count_IR()</a></code>, <code><ahref="reference/count.html">count_I()</a></code>, <code><ahref="reference/count.html">count_SI()</a></code> and <code><ahref="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code>summarise()</code>)</li>
<li>Plot AMR results with <code><ahref="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><ahref="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
<li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code>portion_R()</code>, <code>portion_IR()</code>, <code>portion_I()</code>, <code>portion_SI()</code> and <code>portion_S()</code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code>count_R()</code>, <code>count_IR()</code>, <code>count_I()</code>, <code>count_SI()</code> and <code>count_S()</code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code>summarise()</code>)</li>
<li>Plot AMR results with <code>geom_rsi()</code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code>resistance_predict()</code> function</li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e.microbial code <code>"UNKNOWN"</code>. They can be included with the new parameter <code>include_unknown</code>:</p>
For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
@ -247,12 +247,12 @@ For WHONET users, this means that all records/isolates with organism code <code>
<aclass="sourceLine"id="cb2-5"data-line-number="5"><spanclass="co">#> invalid factor level, NA generated</span></a>
<aclass="sourceLine"id="cb2-11"data-line-number="11"><spanclass="co">#> invalid microorganism code, NA generated</span></a></code></pre></div>
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><ahref="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</li>
<li><p>Function <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> has moved to a new package, <ahref="https://github.com/msberends/clean"><code>clean</code></a> (<ahref="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code>mo_name()</code>, although the class would suggest a valid microbial code.</li>
<li><p>Function <code>freq()</code> has moved to a new package, <ahref="https://github.com/msberends/clean"><code>clean</code></a> (<ahref="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
</ul>
</div>
<divid="new"class="section level3">
@ -260,8 +260,8 @@ This is important, because a value like <code>"testvalue"</code> could never be
<ahref="#new"class="anchor"></a>New</h3>
<ul>
<li>
<p>Function <code><ahref="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p>
<p>Function <code>bug_drug_combinations()</code> to quickly get a <code>data.frame</code> with the antimicrobial resistance of any bug-drug combination in a data set:</p>
<aclass="sourceLine"id="cb3-3"data-line-number="3"><spanclass="co"># </span><spanclass="al">NOTE</span><spanclass="co">: Using column `mo` as input for `col_mo`.</span></a>
<aclass="sourceLine"id="cb3-4"data-line-number="4"><spanclass="co">#> ab mo S I R total</span></a>
@ -306,48 +306,51 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<h3class="hasAnchor">
<ahref="#changed"class="anchor"></a>Changed</h3>
<ul>
<li>Many algorithm improvements for <code><ahref="../reference/as.mo.html">as.mo()</a></code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<li>Many algorithm improvements for <code>as.mo()</code> (of which some led to additions to the <code>microorganisms</code> data set). Many thanks to all contributors that helped improving the algorithms.
<ul>
<li>Self-learning algorithm - the function now gains experience from previously determined microorganism IDs and learns from it (yielding 80-95% speed improvement for any guess after the first try)</li>
<li>Big improvement for misspelled input</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology</li>
<li>Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)</li>
<li>Added support for <em>Blastocystis</em>
</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
<li>Changed most microorganism IDs to improve readability. <strong>IMPORTANT:</strong> Because of these changes, the microorganism IDs have been changed to a slightly different format. Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> on your old codes to transform them to the new format.</li>
<li>Changed most microorganism IDs to improve readability. <strong>IMPORTANT:</strong> Because of these changes, the microorganism IDs have been changed to a slightly different format. Old microorganism IDs are still supported, but support will be dropped in a future version. Use <code>as.mo()</code> on your old codes to transform them to the new format.</li>
</ul>
</li>
<li>Renamed data set <code>septic_patients</code> to <code>example_isolates</code>
<li>Fixed a bug for <em>Yersinia pseudotuberculosis</em>
</li>
<li>Added more informative errors and warnings</li>
<li>Printed info now distinguishes between added and changes values</li>
<li>Using Verbose mode (i.e. <code><ahref="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code>) returns more informative and readable output</li>
<li>Using Verbose mode (i.e. <code>eucast_rules(..., verbose = TRUE)</code>) returns more informative and readable output</li>
<li>Using factors as input now adds missing factors levels when the function changes antibiotic results</li>
</ul>
</li>
<li>Improved the internal auto-guessing function for determining antibiotics in your data set (<code>AMR:::get_column_abx()</code>)</li>
<li>Removed class <code>atc</code> - using <code><ahref="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><ahref="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
<li>Removed class <code>atc</code> - using <code>as.atc()</code> is now deprecated in favour of <code>ab_atc()</code> and this will return a character, not the <code>atc</code> class anymore</li>
<li>Fix and speed improvement for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code>
<li>Fix and speed improvement for <code>mo_shortname()</code>
</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><ahref="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><ahref="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code>mo_uncertainties()</code> and <code>mo_failures()</code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code>mdro()</code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name and all cephalosporins now have their generation between brackets</li>
<li>Speed improvement for <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code> which is now 30 times faster for antibiotic abbreviations</li>
<li>Improved <code><ahref="../reference/filter_ab_class.html">filter_ab_class()</a></code> to be more reliable and to support 5th generation cephalosporins</li>
<li>Function <code><ahref="../reference/availability.html">availability()</a></code> now uses <code><ahref="../reference/portion.html">portion_R()</a></code> instead of <code><ahref="../reference/portion.html">portion_IR()</a></code>, to comply with EUCAST insights</li>
<li>Functions <code><ahref="../reference/age.html">age()</a></code> and <code><ahref="../reference/age_groups.html">age_groups()</a></code> now have a <code>na.rm</code> parameter to remove empty values</li>
<li>Renamed function <code><ahref="../reference/AMR-deprecated.html">p.symbol()</a></code> to <code><ahref="../reference/p_symbol.html">p_symbol()</a></code> (the former is now deprecated and will be removed in a future version)</li>
<li>Using negative values for <code>x</code> in <code><ahref="../reference/age_groups.html">age_groups()</a></code> will now introduce <code>NA</code>s and not return an error anymore</li>
<li>Speed improvement for <code>guess_ab_col()</code> which is now 30 times faster for antibiotic abbreviations</li>
<li>Improved <code>filter_ab_class()</code> to be more reliable and to support 5th generation cephalosporins</li>
<li>Function <code>availability()</code> now uses <code>portion_R()</code> instead of <code>portion_IR()</code>, to comply with EUCAST insights</li>
<li>Functions <code>age()</code> and <code>age_groups()</code> now have a <code>na.rm</code> parameter to remove empty values</li>
<li>Renamed function <code>p.symbol()</code> to <code>p_symbol()</code> (the former is now deprecated and will be removed in a future version)</li>
<li>Using negative values for <code>x</code> in <code>age_groups()</code> will now introduce <code>NA</code>s and not return an error anymore</li>
<li>Fix for determining the system’s language</li>
<li>Fix for <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> on foreign systems</li>
<li>Fix for <code>key_antibiotics()</code> on foreign systems</li>
<li>Added 80 new LIS codes for microorganisms</li>
</ul>
<divid="other"class="section level4">
<h4class="hasAnchor">
@ -367,10 +370,10 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<ahref="#new-1"class="anchor"></a>New</h4>
<ul>
<li>
<p>Function <code><ahref="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><ahref="../reference/count.html">count_df()</a></code> and <code><ahref="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<p>Function <code>rsi_df()</code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code>count_df()</code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
<li>Function <code><ahref="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><ahref="../reference/ab_property.html">ab_info()</a></code>. The <code><ahref="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
<li><p>Function <code><ahref="../reference/mo_property.html">mo_synonyms()</a></code> to get all previously accepted taxonomic names of a microorganism</p></li>
<li>Function <code>mo_info()</code> as an analogy to <code>ab_info()</code>. The <code>mo_info()</code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</li>
<li><p>Function <code>mo_synonyms()</code> to get all previously accepted taxonomic names of a microorganism</p></li>
<li>Column names of output <code><ahref="../reference/count.html">count_df()</a></code> and <code><ahref="../reference/portion.html">portion_df()</a></code> are now lowercase</li>
<li>Column names of output <code>count_df()</code> and <code>portion_df()</code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
<li>Fixed bug in determining taxonomic kingdoms</li>
<li>Algorithm improvements for <code><ahref="../reference/as.ab.html">as.ab()</a></code> and <code><ahref="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
<li>Function <code><ahref="../reference/as.ab.html">as.ab()</a></code> now allows spaces for coercing antibiotics names</li>
<li>Algorithm improvements for <code>as.ab()</code> and <code>as.mo()</code> to understand even more severely misspelled input</li>
<li>Function <code>as.ab()</code> now allows spaces for coercing antibiotics names</li>
<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
</li>
<li>Added names of object in the header in frequency tables, even when using pipes</li>
<li>Prevented <code>"bacteria"</code> from getting coerced by <code><ahref="../reference/as.ab.html">as.ab()</a></code> because Bacterial is a brand name of trimethoprim (TMP)</li>
<li>Fixed a bug where setting an antibiotic would not work for <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><ahref="../reference/mdro.html">mdro()</a></code>
<li>Prevented <code>"bacteria"</code> from getting coerced by <code>as.ab()</code> because Bacterial is a brand name of trimethoprim (TMP)</li>
<li>Fixed a bug where setting an antibiotic would not work for <code>eucast_rules()</code> and <code>mdro()</code>
</li>
<li>Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin</li>
<li>Removed <code>latest_annual_release</code> from the <code><ahref="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
<li>Removed <code>latest_annual_release</code> from the <code>catalogue_of_life_version()</code> function</li>
<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
</li>
<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><ahref="../reference/as.mo.html">as.mo()</a></code>
<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code>as.mo()</code>
</li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
<li>Small improvements to <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
<li>Allow Catalogue of Life IDs to be coerced by <code><ahref="../reference/as.mo.html">as.mo()</a></code>
<li>Allow Catalogue of Life IDs to be coerced by <code>as.mo()</code>
</li>
</ul>
</div>
@ -447,18 +450,18 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<h4class="hasAnchor">
<ahref="#new-2"class="anchor"></a>New</h4>
<ul>
<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><ahref="../reference/as.rsi.html">as.rsi()</a></code> on an MIC value (created with <code><ahref="../reference/as.mic.html">as.mic()</a></code>), a disk diffusion value (created with the new <code><ahref="../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><ahref="../reference/mo_property.html">mo_name()</a></code> as alias of <code><ahref="../reference/mo_property.html">mo_fullname()</a></code>
<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>as.rsi()</code> on an MIC value (created with <code>as.mic()</code>), a disk diffusion value (created with the new <code>as.disk()</code>) or on a complete date set containing columns with MIC or disk diffusion values.</li>
<li>Function <code>mo_name()</code> as alias of <code>mo_fullname()</code>
</li>
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code><ahref="../reference/mdro.html">mdr_tb()</a></code>) and added a new vignette about MDR. Read this tutorial <ahref="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
<li>Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (<code>mdr_tb()</code>) and added a new vignette about MDR. Read this tutorial <ahref="https://msberends.gitlab.io/AMR/articles/MDR.html">here on our website</a>.</li>
<li>Fixed a critical bug in <code><ahref="../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>Fixed a bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Fixed a critical bug in <code>first_isolate()</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>Fixed a bug in <code>eucast_rules()</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:
@ -477,20 +480,20 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
Please <ahref="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Translation%20suggestion">create an issue in one of our repositories</a> if you want additions in this file.</li>
</ul>
</li>
<li>Improvements to plotting AMR results with <code><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
<li>Improvements to plotting AMR results with <code>ggplot_rsi()</code>:
<ul>
<li>New parameter <code>colours</code> to set the bar colours</li>
<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 columns in a data set using <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>
<li>Improved intelligence of looking up antibiotic columns in a data set using <code>guess_ab_col()</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><ahref="../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><ahref="../reference/portion.html">portion_df()</a></code> and <code><ahref="../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><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change since it uses <code><ahref="../reference/count.html">count_df()</a></code> internally.</li>
<li>The <code><ahref="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</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>as.mo()</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>portion_df()</code> and <code>count_df()</code> this means that their new parameter <code>combine_SI</code> is TRUE at default. Our plotting function <code>ggplot_rsi()</code> also reflects this change since it uses <code>count_df()</code> internally.</li>
<li>The <code>age()</code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
Please <ahref="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUCAST%20edit">create an issue in one of our repositories</a> if you want changes in this file.</li>
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><ahref="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> for when all values are <code>NA</code>
<li>Changed default settings for <code>age_groups()</code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>
<li>Fix for <code>first_isolate()</code> for when dates are missing</li>
<li>Improved speed of <code>guess_ab_col()</code>
</li>
<li>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now gently interprets any number of whitespace characters (like tabs) as one space</li>
<li>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now returns <code>UNKNOWN</code> for <code>"con"</code> (WHONET ID of ‘contamination’) and returns <code>NA</code> for <code>"xxx"</code>(WHONET ID of ‘no growth’)</li>
<li>Small algorithm fix for <code><ahref="../reference/as.mo.html">as.mo()</a></code>
<li>Function <code>as.mo()</code> now gently interprets any number of whitespace characters (like tabs) as one space</li>
<li>Function <code>as.mo()</code> now returns <code>UNKNOWN</code> for <code>"con"</code> (WHONET ID of ‘contamination’) and returns <code>NA</code> for <code>"xxx"</code>(WHONET ID of ‘no growth’)</li>
<li>Small algorithm fix for <code>as.mo()</code>
</li>
<li>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</li>
<li><p>Fix for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
<li><p>Fix for <code>mo_shortname()</code> where species would not be determined correctly</p></li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><ahref="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code>as.mo()</code> to identify an MO code.</li>
<li>Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The <code>microorganisms</code> data set now contains:
<ul>
<li>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa</li>
<li>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</li>
<li>
<p>The responsible author(s) and year of scientific publication</p>
This data is updated annually - check the included version with the new function <code><ahref="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</li>
This data is updated annually - check the included version with the new function <code>catalogue_of_life_version()</code>.</li>
<li>Due to this change, some <code>mo</code> codes changed (e.g. <em>Streptococcus</em> changed from <code>B_STRPTC</code> to <code>B_STRPT</code>). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.</li>
<li>New function <code><ahref="../reference/mo_property.html">mo_rank()</a></code> for the taxonomic rank (genus, species, infraspecies, etc.)</li>
<li>New function <code><ahref="../reference/mo_property.html">mo_url()</a></code> to get the direct URL of a species from the Catalogue of Life</li>
<li>New function <code>mo_rank()</code> for the taxonomic rank (genus, species, infraspecies, etc.)</li>
<li>New function <code>mo_url()</code> to get the direct URL of a species from the Catalogue of Life</li>
</ul>
</li>
<li>Support for data from <ahref="https://whonet.org/">WHONET</a> and <ahref="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> and <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
<li>Exported files from WHONET can be read and used in this package. For functions like <code>first_isolate()</code> and <code>eucast_rules()</code>, all parameters will be filled in automatically.</li>
<li>This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the <code>antibiotics</code> data set now contains a column <code>ears_net</code>.</li>
<li>The function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to the <code>microorganisms.codes</code> data set.</li>
<li>The function <code>as.mo()</code> now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to the <code>microorganisms.codes</code> data set.</li>
</ul>
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<aclass="sourceLine"id="cb11-2"data-line-number="2"><spanclass="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<aclass="sourceLine"id="cb11-4"data-line-number="4"><spanclass="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
</li>
<li>
@ -615,33 +618,33 @@ This data is updated annually - check the included version with the new function
These functions use <code><ahref="../reference/AMR-deprecated.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><ahref="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><ahref="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code><ahref="../reference/mo_source.html">set_mo_source()</a></code> and <code><ahref="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><ahref="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
These functions use <code>as.atc()</code> internally. The old <code>atc_property</code> has been renamed <code>atc_online_property()</code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code>as.mo()</code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code>set_mo_source()</code> and <code>get_mo_source()</code> to use your own predefined MO codes as input for <code>as.mo()</code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <ahref="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
<li>New function <code><ahref="../reference/as.mo.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><ahref="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 10 uncoerced values and will refer to <code><ahref="../reference/as.mo.html">mo_failures()</a></code>.</li>
<li>New function <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code> to review values that could be coerced to a valid MO code using <code><ahref="../reference/as.mo.html">as.mo()</a></code>, but with uncertainty.</li>
<li>New function <code><ahref="../reference/as.mo.html">mo_renamed()</a></code> to get a list of all returned values from <code><ahref="../reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li>
<li>New function <code><ahref="../reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
<li>New function <code><ahref="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>New function <code>guess_ab_col()</code> to find an antibiotic column in a table</li>
<li>New function <code>mo_failures()</code> to review values that could not be coerced to a valid MO code, using <code>as.mo()</code>. This latter function will now only show a maximum of 10 uncoerced values and will refer to <code>mo_failures()</code>.</li>
<li>New function <code>mo_uncertainties()</code> to review values that could be coerced to a valid MO code using <code>as.mo()</code>, but with uncertainty.</li>
<li>New function <code>mo_renamed()</code> to get a list of all returned values from <code>as.mo()</code> that have had taxonomic renaming</li>
<li>New function <code>age()</code> to calculate the (patients) age in years</li>
<li>New function <code>age_groups()</code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>
<p>New function <code><ahref="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<p>New function <code>ggplot_rsi_predict()</code> as well as the base R <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code>resistance_predict()</code>:</p>
<p>Functions <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><ahref="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<p>Functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<li>New function <code><ahref="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
<li>New function <code>availability()</code> to check the number of available (non-empty) results in a <code>data.frame</code>
</li>
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <ahref="https://msberends.gitlab.io/AMR"class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
</ul>
@ -650,48 +653,48 @@ These functions use <code><a href="../reference/AMR-deprecated.html">as.atc()</a
<li>Updated EUCAST Clinical breakpoints to <ahref="http://www.eucast.org/clinical_breakpoints/">version 9.0 of 1 January 2019</a>, the data set <code>septic_patients</code> now reflects these changes</li>
<li>Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Emphasised in manual that penicillin is meant as benzylpenicillin (ATC <ahref="https://www.whocc.no/atc_ddd_index/?code=J01CE01">J01CE01</a>)</li>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code><ahref="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> to get a data set with all changed per bug and drug combination.</li>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code>eucast_rules(..., verbose = TRUE)</code> to get a data set with all changed per bug and drug combination.</li>
</ul>
</li>
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <ahref="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code><ahref="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><ahref="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code>guess_mo()</code> is now deprecated in favour of <code><ahref="../reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code>guess_atc()</code> is now deprecated in favour of <code><ahref="../reference/AMR-deprecated.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Improvements for <code><ahref="../reference/as.mo.html">as.mo()</a></code>:
<li>Functions <code>atc_ddd()</code> and <code>atc_groups()</code> have been renamed <code>atc_online_ddd()</code> and <code>atc_online_groups()</code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code>guess_mo()</code> is now deprecated in favour of <code>as.mo()</code> and will be removed in future versions</li>
<li>Function <code>guess_atc()</code> is now deprecated in favour of <code>as.atc()</code> and will be removed in future versions</li>
<li>Improvements for <code>as.mo()</code>:
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><ahref="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code>?as.mo</code> for more info about these levels.</p>
Using <code>as.mo(..., allow_uncertain = 3)</code> could lead to very unreliable results.</li>
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
</li>
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<aclass="sourceLine"id="cb18-3"data-line-number="3"><spanclass="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
<li>Fixed a bug where distances between dates would not be calculated right - in the <code>septic_patients</code> data set this yielded a difference of 0.15% more isolates</li>
<li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li>
@ -721,38 +724,38 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Merged data sets <code>microorganisms.certe</code> and <code>microorganisms.umcg</code> into <code>microorganisms.codes</code>
</li>
<li>Function <code><ahref="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
<li>Reduce false positives for <code><ahref="../reference/as.rsi.html">is.rsi.eligible()</a></code> using the new <code>threshold</code> parameter</li>
<li>New colours for <code><ahref="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code>
<li>Function <code>mo_taxonomy()</code> now contains the kingdom too</li>
<li>Reduce false positives for <code>is.rsi.eligible()</code> using the new <code>threshold</code> parameter</li>
<li>New colours for <code>scale_rsi_colours()</code>
</li>
<li>Summaries of class <code>mo</code> will now return the top 3 and the unique count, e.g.using <code><ahref="https://www.rdocumentation.org/packages/base/topics/summary">summary(mo)</a></code>
</li>
<li>Small text updates to summaries of class <code>rsi</code> and <code>mic</code>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<divclass="sourceCode"id="cb19"><preclass="sourceCode r"><codeclass="sourceCode r"><aclass="sourceLine"id="cb19-1"data-line-number="1"><spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<aclass="sourceLine"id="cb19-2"data-line-number="2"><spanclass="co"># OLD WAY</span></a>
<li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@ -767,11 +770,11 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Fix for using <code><ahref="https://dplyr.tidyverse.org/reference/select.html">select()</a></code> on frequency tables</li>
</ul>
</li>
<li>Function <code><ahref="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <code>limits</code> parameter</li>
<li>Automatic parameter filling for <code><ahref="../reference/mdro.html">mdro()</a></code>, <code><ahref="../reference/key_antibiotics.html">key_antibiotics()</a></code> and <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code>
<li>Function <code>scale_y_percent()</code> now contains the <code>limits</code> parameter</li>
<li>Automatic parameter filling for <code>mdro()</code>, <code>key_antibiotics()</code> and <code>eucast_rules()</code>
</li>
<li>Updated examples for resistance prediction (<code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code> function)</li>
<li>Fix for <code><ahref="../reference/as.mic.html">as.mic()</a></code> to support more values ending in (several) zeroes</li>
<li>Updated examples for resistance prediction (<code>resistance_predict()</code> function)</li>
<li>Fix for <code>as.mic()</code> to support more values ending in (several) zeroes</li>
<li>if using different lengths of pattern and x in <code>%like%</code>, it will now return the call</li>
</ul>
</div>
@ -827,30 +830,30 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs.IR (susceptible vs.non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
<li>Added parameter <code>also_single_tested</code> for <code>portion_*</code> and <code>count_*</code> functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see <code><ahref="../reference/portion.html">?portion</a></code>
<li>Added parameter <code>also_single_tested</code> for <code>portion_*</code> and <code>count_*</code> functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see <code>?portion</code>
</li>
<li>Using <code>portion_*</code> functions now throws a warning when total available isolate is below parameter <code>minimum</code>
</li>
<li>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</li>
<aclass="sourceLine"id="cb22-3"data-line-number="3"><spanclass="st"></span><spanclass="kw"><ahref="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<spanclass="op">-</span>count, <spanclass="op">-</span>cum_count) <spanclass="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li>
<li>Check for <code><ahref="https://www.rdocumentation.org/packages/hms/topics/Deprecated">hms::is.hms</a></code>
@ -931,16 +934,16 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
@ -953,15 +956,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<aclass="sourceLine"id="cb25-5"data-line-number="5"><spanclass="kw"><ahref="../reference/as.mo.html">as.mo</a></span>(<spanclass="st">"S group A"</span>)</a>
<aclass="sourceLine"id="cb25-5"data-line-number="5"><spanclass="kw">as.mo</span>(<spanclass="st">"S group A"</span>)</a>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
@ -1008,13 +1011,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@ -1029,11 +1032,11 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
@ -1075,7 +1078,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul>
<li>
<code>septic_patients %>% select(tobr, gent) %>% ggplot_rsi</code> will show portions of S, I and R immediately in a pretty plot</li>
<li>Support for grouped variables, see <code><ahref="../reference/ggplot_rsi.html">?ggplot_rsi</a></code>
<li>Support for grouped variables, see <code>?ggplot_rsi</code>
</li>
</ul>
</li>
@ -1107,13 +1110,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul>
<li>A vignette to explain its usage</li>
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
<li>Support for <code>table</code> to use as input: <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq(table(x, y))</a></code>
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
</li>
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/hist">hist(freq(df$age))</a></code>
</li>
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
</li>
<li>Support for quasiquotation: <code><ahref="https://www.rdocumentation.org/packages/clean/topics/freq">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
</li>
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
@ -1145,14 +1148,14 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Combined MIC/RSI values will now be coerced by the <code>rsi</code> and <code>mic</code> functions:
<ul>
<li>
<code><ahref="../reference/as.rsi.html">as.rsi("<=0.002; S")</a></code> will return <code>S</code>
<code>as.rsi("<=0.002; S")</code> will return <code>S</code>
</li>
<li>
<code><ahref="../reference/as.mic.html">as.mic("<=0.002; S")</a></code> will return <code><=0.002</code>
<code>as.mic("<=0.002; S")</code> will return <code><=0.002</code>
</li>
</ul>
</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code><ahref="../reference/as.mic.html">as.mic("<= 0.002")</a></code> now works</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e. <code>as.mic("<= 0.002")</code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for <code>atc_property(..., property)</code>. It will return a vector of the ATC hierarchy as defined by the <ahref="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
@ -1203,7 +1206,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Functions <code>BRMO</code> and <code>MRGN</code> are wrappers for Dutch and German guidelines, respectively</li>
</ul>
</li>
<li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code><ahref="../reference/first_isolate.html">?first_isolate</a></code>
<li>New algorithm to determine weighted isolates, can now be <code>"points"</code> or <code>"keyantibiotics"</code>, see <code>?first_isolate</code>
</li>
<li>New print format for <code>tibble</code>s and <code>data.table</code>s</li>
</ul>
@ -1267,7 +1270,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<p>The <code>group</code> column in <code><ahref='antibiotics.html'>antibiotics</a></code> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set.</p>
<p>The <code>group</code> column in <code>antibiotics</code> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set.</p>
<p>A <code><ahref='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 4,927 observations and 2 variables:</p><dlclass='dl-horizontal'>
<p>A <code><ahref='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 5,006 observations and 2 variables:</p><dlclass='dl-horizontal'>
<dt><code>code</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
<dt><code>mo</code></dt><dd><p>ID of the microorganism in the <code><ahref='microorganisms.html'>microorganisms</a></code> data set</p></dd>
<p>A <code><ahref='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 69,454 observations and 16 variables:</p><dlclass='dl-horizontal'>
<p>A <code><ahref='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 69,465 observations and 16 variables:</p><dlclass='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@ -261,6 +261,7 @@
<li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
<li><p>1 entry of <em>Blastocystis</em> (<em>Blastocystis hominis</em>), although it officially does not exist (Noel et al. 2005, PMID 15634993)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications</p></li>
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{...}{parameters passed on to \code{\link[dplyr]{filter_at}}}
\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
}
\description{
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
\format{A \code{\link{data.frame}} with 69,454 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,465 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -33,6 +33,7 @@ Manually added were:
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
