* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
@ -420,7 +420,7 @@ Since you are one of our users, we would like to know how you use the package an
<li>
<li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul>
<ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><ahref="reference/proportion.html">susceptibility()</a></code> and <code><ahref="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><ahref="reference/proportion.html">proportion_R()</a></code>, <code><ahref="reference/proportion.html">proportion_IR()</a></code>, <code><ahref="reference/proportion.html">proportion_I()</a></code>, <code><ahref="reference/proportion.html">proportion_SI()</a></code> and <code><ahref="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><ahref="reference/count.html">count_resistant()</a></code>, <code><ahref="reference/count.html">count_susceptible()</a></code> and <code><ahref="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g.in conjunction with <code><ahref="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></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>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>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>
<p>Functions <code><ahref="../reference/get_episode.html">get_episode()</a></code> and <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><ahref="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e.using <code><ahref="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
<p>Functions <code><ahref="../reference/get_episode.html">get_episode()</a></code> and <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><ahref="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><ahref="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e.using <code><ahref="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by()</a></code>):</p>
<li><p>Functions <code><ahref="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
<li><p>Functions <code><ahref="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
<li><p>Function <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <ahref="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
<li><p>Function <code><ahref="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <ahref="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
@ -280,7 +280,7 @@
</ul>
</ul>
</li>
</li>
<li>
<li>
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><ahref="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions:</p>
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><ahref="https://rdrr.io/pkg/dplyr/man/filter.html">filter()</a></code>, <code><ahref="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate()</a></code> and <code><ahref="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions:</p>
<p>Improvements for <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>:</p>
<p>Improvements for <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>:</p>
<ul>
<ul>
<li>
<li>
<p>Support for using <code>dplyr</code>’s <code><ahref="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
<p>Support for using <code>dplyr</code>’s <code><ahref="https://rdrr.io/pkg/dplyr/man/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g.<code><ahref="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></li>
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g.<code><ahref="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></li>
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
@ -469,14 +469,14 @@
<ul>
<ul>
<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>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>
<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>
<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://rdrr.io/pkg/dplyr/man/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 <code><ahref="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><ahref="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
<li><p>Added <code><ahref="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><ahref="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
@ -658,14 +658,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<ul>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<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>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><ahref="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><spanclass="op">(</span><spanclass="va">antibiotic1</span><spanclass="op">:</span><spanclass="va">antibiotic25</span><spanclass="op">)</span>, <spanclass="va">as.rsi</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span><spanclass="op">)</span>
<spanclass="fu"><ahref="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/pkg/dplyr/man/vars.html">vars</a></span><spanclass="op">(</span><spanclass="va">antibiotic1</span><spanclass="op">:</span><spanclass="va">antibiotic25</span><spanclass="op">)</span>, <spanclass="va">as.rsi</span>, mo <spanclass="op">=</span><spanclass="st">"E. coli"</span><spanclass="op">)</span>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><spanclass="op">(</span><spanclass="va">antibiotic1</span><spanclass="op">:</span><spanclass="va">antibiotic25</span><spanclass="op">)</span>, <spanclass="va">as.rsi</span>, mo <spanclass="op">=</span><spanclass="va">.</span><spanclass="op">$</span><spanclass="va">mybacteria</span><spanclass="op">)</span></code></pre></div>
<spanclass="fu"><ahref="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at</a></span><spanclass="op">(</span><spanclass="fu"><ahref="https://rdrr.io/pkg/dplyr/man/vars.html">vars</a></span><spanclass="op">(</span><spanclass="va">antibiotic1</span><spanclass="op">:</span><spanclass="va">antibiotic25</span><spanclass="op">)</span>, <spanclass="va">as.rsi</span>, mo <spanclass="op">=</span><spanclass="va">.</span><spanclass="op">$</span><spanclass="va">mybacteria</span><spanclass="op">)</span></code></pre></div>
</li>
</li>
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as argument to <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as argument to <code><ahref="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
@ -786,10 +786,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
@ -958,7 +958,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co"># (run this on your own console, as this page does not support colour printing)</span>
<spanclass="co"># (run this on your own console, as this page does not support colour printing)</span>
<li><p>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></p></li>
<li><p>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></p></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>
<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>
@ -1436,7 +1436,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<spanclass="fu"><ahref="https://dplyr.tidyverse.org/reference/select.html">select</a></span><spanclass="op">(</span><spanclass="op">-</span><spanclass="va">count</span>, <spanclass="op">-</span><spanclass="va">cum_count</span><spanclass="op">)</span><spanclass="co"># only get item, percent, cum_percent</span></code></pre></div>
<spanclass="fu"><ahref="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><spanclass="op">(</span><spanclass="op">-</span><spanclass="va">count</span>, <spanclass="op">-</span><spanclass="va">cum_count</span><spanclass="op">)</span><spanclass="co"># only get item, percent, cum_percent</span></code></pre></div>
</li>
</li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
@ -1708,7 +1708,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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>
<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>
@ -1894,7 +1894,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<ul>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><ahref="https://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><ahref="https://rdrr.io/pkg/dplyr/man/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
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