* Support for using `dplyr`'s `across()` in `as.rsi()` to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
error=function(e)stop_("an error occurred in import_fn() while using this function",call=FALSE))
error=function(e){
if (isTRUE(error_on_fail)){
stop_("function ",name,"() not found in package '",pkg,"'. Please contact the maintainers of the AMR package at https://github.com/msberends/AMR/issues.",call=FALSE)
#' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
#' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Values that cannot be interpreted will be returned as `NA` with a warning.
#' @inheritSection lifecycle Stable lifecycle
#' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()], will be determined automatically if the `dplyr` package is installed
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be search for a 'specimen' and rows containing 'urin' in that column will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate
@ -34,15 +34,44 @@
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
#' @param ... parameters passed on to methods
#' @details
#' When using [as.rsi()] on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class [`mic`] (using [as.mic()]) or class [`disk`] (using [as.disk()]), the data will be interpreted based on the guideline set with the `guideline` parameter.
#' ## How it works
#'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#' The [as.rsi()] function works in four ways:
#'
#' When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and will in this case return "S" or "I".
#' 1. For **cleaning raw / untransformed data**. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as `"<0.25; S"` will be coerced to `"S"`. Combined interpretations for multiple test methods (as seen in laboratory records) such as `"S; S"` will be coerced to `"S"`, but a value like `"S; I"` will return `NA` with a warning that the input is unclear.
#'
#' 2. For **interpreting minimum inhibitory concentration (MIC) values** according to EUCAST or CLSI. You must clean your MIC values first using [as.mic()], that also gives your columns the new data class [`mic`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` parameter.
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
#' ```
#' your_data %>% mutate_if(is.mic, as.rsi) # until dplyr 1.0.0
#' your_data %>% mutate(across(where(is.mic), as.rsi)) # since dplyr 1.0.0
#' ```
#' * Operators like "<=" will be stripped before interpretation. When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
#'
#' 3. For **interpreting disk diffusion diameters** according to EUCAST or CLSI. You must clean your disk zones first using [as.disk()], that also gives your columns the new data class [`disk`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` parameter.
#' * Using `dplyr`, R/SI interpretation can be done very easily with either:
#' ```
#' your_data %>% mutate_if(is.disk, as.rsi) # until dplyr 1.0.0
#' your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
#' ```
#'
#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`.
#'
#' ## Supported guidelines
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`.
#'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#'
#' ## After interpretation
#'
#' After using [as.rsi()], you can use the [eucast_rules()] defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'
#' ## Machine readable interpretation guidelines
#'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#' ## Other
#'
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter.
#' @section Interpretation of R and S/I:
@ -59,7 +88,7 @@
#' @return Ordered factor with new class [`rsi`]
#' @aliases rsi
#' @export
#' @seealso [as.mic()]
#' @seealso [as.mic()], [as.disk()], [as.mo()]
#' @inheritSection AMR Read more on our website!
#' @examples
#' summary(example_isolates) # see all R/SI results at a glance
@ -79,12 +108,12 @@
#'
#' # the dplyr way
#' library(dplyr)
#' df %>% mutate_at(vars(AMP:TOB), as.rsi)
#' df %>% mutate(across(AMP:TOB), as.rsi)
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
#'
#' df %>%
#' mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
#'
#' # to include information about urinary tract infections (UTI)
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.3.0.9000</span>
</span>
</div>
@ -192,7 +192,7 @@
</h1></div>
<blockquote>
<p><em>July 2020</em><br><spanclass="fa fa-clipboard-list"style="color: #128f76; font-size: 20pt; margin-right: 5px;"></span><strong>PLEASE TAKE PART IN OUR SURVEY!</strong><br>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <ahref="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!</p>
Since you are one of our users, we would like to know how you use the package and what it brought you or your organisation. <strong>If you have a minute, please <ahref="./survey.html">anonymously fill in this short questionnaire</a></strong>. Your valuable input will help to improve the package and its functionalities. You can answer the open questions in either English, Spanish, French, Dutch, or German. Thank you very much in advance!<br><aclass="btn btn-info btn-amr">Take me to the 5-min survey!</a></p>
<ahref="#last-updated-10-august-2020"class="anchor"></a><small>Last updated: 10 August 2020</small>
</h2>
<divid="changed"class="section level3">
<h3class="hasAnchor">
<ahref="#changed"class="anchor"></a>Changed</h3>
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><ahref="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> in <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC values or disk zone diameters, that now also automatically determines the column with microorganism names or codes.</p>
<divclass="sourceCode"id="cb1"><preclass="r"><spanclass="co"># until dplyr 1.0.0</span>
<li><p>Function <code><ahref="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g.health care records, which also corrects for misspelling since it uses <code><ahref="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><ahref="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><ahref="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><ahref="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<li><p>Added parameter <code>conserve_capped_values</code> to <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour of <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> has not changed, so you need to specifically do <code><ahref="../reference/as.rsi.html">as.rsi(..., conserve_capped_values = TRUE)</a></code>.</p></li>
<p>Big speed improvement for using any function on microorganism codes from earlier package versions (prior to <code>AMR</code> v1.2.0), such as <code><ahref="../reference/as.mo.html">as.mo()</a></code>, <code><ahref="../reference/mo_property.html">mo_name()</a></code>, <code><ahref="../reference/first_isolate.html">first_isolate()</a></code>, <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code>, <code><ahref="../reference/mdro.html">mdro()</a></code>, etc.</p>
<li>Improvements for the algorithm used by <code><ahref="../reference/as.mo.html">as.mo()</a></code> (and consequently all <code>mo_*</code> functions, that use <code><ahref="../reference/as.mo.html">as.mo()</a></code> internally):
<ul>
@ -420,14 +446,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
@ -454,7 +480,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><ahref="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
@ -463,7 +489,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><ahref="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
@ -540,7 +566,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Functions <code><ahref="../reference/proportion.html">susceptibility()</a></code> and <code><ahref="../reference/proportion.html">resistance()</a></code> as aliases of <code><ahref="../reference/proportion.html">proportion_SI()</a></code> and <code><ahref="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
@ -567,7 +593,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li>
<p>Added a score (a certainty percentage) to <code><ahref="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <ahref="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
<spanclass="co">#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.</span>
@ -624,12 +650,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<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>
<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.</p>
</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>
<divclass="sourceCode"id="cb10"><preclass="r"><spanclass="co"># how it works in base R:</span>
<divclass="sourceCode"id="cb11"><preclass="r"><spanclass="co"># how it works in base R:</span>
@ -652,7 +678,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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 results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<spanclass="co">#> NOTE: Use 'format()' on this result to get a publicable/printable format.</span></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g.Excel with the base R <code><ahref="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<p>Additional way to calculate co-resistance, i.e.when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new parameter <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
# Drug A Drug B include as include as include as include as
@ -697,7 +723,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code><code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<divclass="sourceCode"id="cb14"><preclass="r"><spanclass="co"># (run this on your own console, as this page does not support colour printing)</span>
<divclass="sourceCode"id="cb15"><preclass="r"><spanclass="co"># (run this on your own console, as this page does not support colour printing)</span>
<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.
<ul>
@ -778,7 +804,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><ahref="../reference/proportion.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/AMR-deprecated.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
@ -814,9 +840,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>Column names of output <code><ahref="../reference/count.html">count_df()</a></code> and <code><ahref="../reference/AMR-deprecated.html">portion_df()</a></code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li>
@ -863,9 +889,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>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>
@ -906,7 +932,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
<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>
@ -1037,17 +1063,17 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>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.</p></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://rdrr.io/r/base/plot.html">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>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>
@ -1056,9 +1082,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>
@ -1088,7 +1114,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<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>
@ -1101,7 +1127,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>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.</p></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>
<li><p>Functions <code>MDRO</code>, <code>BRMO</code>, <code>MRGN</code> and <code>EUCAST_exceptional_phenotypes</code> were renamed to <code>mdro</code>, <code>brmo</code>, <code>mrgn</code> and <code>eucast_exceptional_phenotypes</code></p></li>
<li><p><code>EUCAST_rules</code> was renamed to <code>eucast_rules</code>, the old function still exists as a deprecated function</p></li>
@ -1231,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(-<spanclass="no">count</span>, -<spanclass="no">cum_count</span>) <spanclass="co"># only get item, percent, cum_percent</span></pre></div>
</li>
@ -1330,7 +1356,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
@ -1352,14 +1378,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %>% mutate_if(is.rsi.eligible, as.rsi)</code></p></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>
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
@ -1406,7 +1432,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added parameters <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></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>
