#' @param x vector of dates (class `Date` or `POSIXt`)
#' @param episode_days required episode length in days, can also be less than a day, see *Details*
#' @param ... arguments passed on to [as.POSIXct()]
#' @param ... currently not used
#' @details
#' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
"AMP" "Ampicillin" "standard_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"SAM" "Ampicillin/sulbactam" "high_dosage" "2 g + 1 g" 4 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 4 iv" 11
"SAM" "Ampicillin/sulbactam" "standard_dosage" "2 g + 1 g" 3 "iv" "" "(2 g ampicillin + 1 g sulbactam) x 3 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "or 0.5 g x 1 iv" "0.5 g x 1 oral or 0.5 g x 1 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 11
"AZM" "Azithromycin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 11
"ATM" "Aztreonam" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
"ATM" "Aztreonam" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"PEN" "Benzylpenicillin" "high_dosage" "1.2 g" 4 "iv" "" "1.2 g (2 MU) x 4-6 iv" 11
"PEN" "Benzylpenicillin" "standard_dosage" "0.6 g" 4 "iv" "" "0.6 g (1 MU) x 4 iv" 11
"CEC" "Cefaclor" "high_dosage" "1 g" 3 "oral" "" "1 g x 3 oral" 11
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "depending on species and/or infection type" "0.25-0.5 g x 3 oral depending on species and/or infection type" 11
"CEC" "Cefaclor" "standard_dosage" "0.25-0.5 g" 3 "oral" "" "0.25-0.5 g x 3 oral" 11
"CFR" "Cefadroxil" "standard_dosage" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
"CFR" "Cefadroxil" "uncomplicated_uti" "0.5-1 g" 2 "oral" "" "0.5-1 g x 2 oral" 11
"CZO" "Cefazolin" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"CZO" "Cefazolin" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"FEP" "Cefepime" "high_dosage" "2 g" 3 "iv" "" "2 g x 3 iv" 11
"FEP" "Cefepime" "standard_dosage" "1 g" 3 "iv" "or 2 g x 2 iv" "1 g x 3 iv or 2 g x 2 iv" 11
"FEP" "Cefepime" "standard_dosage" "2 g" 2 "iv" "" "2 g x 2 iv" 11
"FDC" "Cefiderocol" "standard_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 11
"CFM" "Cefixime" "standard_dosage" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 11
"CFM" "Cefixime" "uncomplicated_uti" "0.2-0.4 g" 2 "oral" "" "0.2-0.4 g x 2 oral" 11
@ -36,14 +37,14 @@
"CPD" "Cefpodoxime" "uncomplicated_uti" "0.1-0.2 g" 2 "oral" "" "0.1-0.2 g x 2 oral" 11
"CPT" "Ceftaroline" "high_dosage" "0.6 g" 3 "iv" "over 2 hours" "0.6 g x 3 iv over 2 hours" 11
"CPT" "Ceftaroline" "standard_dosage" "0.6 g" 2 "iv" "over 1 hour" "0.6 g x 2 iv over 1 hour" 11
"CAZ" "Ceftazidime" "high_dosage" "2 g" 3 "iv" "or 1 g x 6 iv" "2 g x 3 iv or 1 g x 6 iv" 11
"CAZ" "Ceftazidime" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 11
"CAZ" "Ceftazidime" "standard_dosage" "1 g" 3 "iv" "" "1 g x 3 iv" 11
"CZA" "Ceftazidime/avibactam" "standard_dosage" "2 g + 0.5 g" 3 "iv" "over 2 hours" "(2 g ceftazidime + 0.5 g avibactam) x 3 iv over 2 hours" 11
"CTB" "Ceftibuten" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 11
"BPR" "Ceftobiprole" "standard_dosage" "0.5 g" 3 "iv" "over 2 hours" "0.5 g x 3 iv over 2 hours" 11
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "1 g + 0.5 g" 3 "iv" "over 1 hour" "(1 g ceftolozane + 0.5 g tazobactam) x 3 iv over 1 hour" 11
"CZT" "Ceftolozane/tazobactam" "standard_dosage" "2 g + 1 g" 3 "iv" "over 1 hour" "(2 g ceftolozane + 1 g tazobactam) x 3 iv over 1 hour" 11
"CRO" "Ceftriaxone" "high_dosage" "2 g" 2 "iv" "or 4 g x 1 iv" "2 g x 2 iv or 4 g x 1 iv" 11
"CRO" "Ceftriaxone" "high_dosage" "4 g" 1 "iv" "" "4 g x 1 iv" 11
"CRO" "Ceftriaxone" "standard_dosage" "2 g" 1 "iv" "" "2 g x 1 iv" 11
"CXM" "Cefuroxime" "high_dosage" "1.5 g" 3 "iv" "" "1.5 g x 3 iv" 11
"CXM" "Cefuroxime" "standard_dosage" "0.75 g" 3 "iv" "" "0.75 g x 3 iv" 11
@ -52,70 +53,100 @@
"CXM" "Cefuroxime" "uncomplicated_uti" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"LEX" "Cephalexin" "standard_dosage" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"LEX" "Cephalexin" "uncomplicated_uti" "0.25-1 g" 2 "oral" "" "0.25-1 g x 2-3 oral" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "or 2 g x 4 iv" "2 g x 4 oral or 2 g x 4 iv" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "or 1 g x 4 iv" "1 g x 4 oral or 1 g x 4 iv" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "or 0.4 g x 3 iv" "0.75 g x 2 oral or 0.4 g x 3 iv" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "or 0.4 g x 2 iv" "0.5 g x 2 oral or 0.4 g x 2 iv" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "iv" "" "2 g x 4 iv" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"CHL" "Chloramphenicol" "high_dosage" "2 g" 4 "oral" "" "2 g x 4 oral" 11
"CHL" "Chloramphenicol" "standard_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 11
"CIP" "Ciprofloxacin" "high_dosage" "0.75 g" 2 "oral" "" "0.75 g x 2 oral" 11
"CIP" "Ciprofloxacin" "standard_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"CLR" "Clarithromycin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"CLR" "Clarithromycin" "standard_dosage" "0.25 g" 2 "oral" "" "0.25 g x 2 oral" 11
"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "or 0.9 g x 3 iv" "0.3 g x 4 oral or 0.9 g x 3 iv" 11
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "or 0.6 g x 3 iv" "0.3 g x 2 oral or 0.6 g x 3 iv" 11
"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "or 2 g x 6 iv" "1 g x 4 oral or 2 g x 6 iv" 11
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "or 1 g x 4 iv" "0.5 g x 4 oral or 1 g x 4 iv" 11
"CLI" "Clindamycin" "high_dosage" "0.9 g" 3 "iv" "" "0.9 g x 3 iv" 11
"CLI" "Clindamycin" "standard_dosage" "0.6 g" 3 "iv" "" "0.6 g x 3 iv" 11
"CLI" "Clindamycin" "high_dosage" "0.3 g" 4 "oral" "" "0.3 g x 4 oral" 11
"CLI" "Clindamycin" "standard_dosage" "0.3 g" 2 "oral" "" "0.3 g x 2 oral" 11
"CLO" "Cloxacillin" "high_dosage" "2 g" 6 "iv" "" "2 g x 6 iv" 11
"CLO" "Cloxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"CLO" "Cloxacillin" "high_dosage" "1 g" 4 "oral" "" "1 g x 4 oral" 11
"CLO" "Cloxacillin" "standard_dosage" "0.5 g" 4 "oral" "" "0.5 g x 4 oral" 11
"COL" "Colistin" "standard_dosage" "4.5 MU" 2 "iv" "loading dose of 9 MU" "4.5 MU x 2 iv with a loading dose of 9 MU" 11
"DAL" "Dalbavancin" "standard_dosage" "1 g" 1 "iv" "over 30 minutes on day 8" "1 g x 1 iv over 30 minutes on day 1 If needed, 0.5 g x 1 iv over 30 minutes on day 8" 11
"IPM" "Imipenem" "high_dosage" "1 g" 4 "iv" "over 30 minutes" "1 g x 4 iv over 30 minutes" 11
"IPM" "Imipenem" "standard_dosage" "0.5 g" 4 "iv" "over 30 minutes" "0.5 g x 4 iv over 30 minutes" 11
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
"IMR" "Imipenem/relebactam" "standard_dosage" "0.5 g + 0.25 g" 4 "iv" "over 30 minutes" "(0.5 g imipenem + 0.25 g relebactam) x 4 iv over 30 minutes" 11
"LMU" "Lefamulin" "standard_dosage" "0.15 g" 2 "iv" "or 0.6 g x 2 oral" "0.15 g x 2 iv or 0.6 g x 2 oral" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "or 0.5 g x 2 iv" "0.5 g x 2 oral or 0.5 g x 2 iv" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "or 0.5 g x 1 iv" "0.5 g x 1 oral or 0.5 g x 1 iv" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "or 0.6 g x 2 iv" "0.6 g x 2 oral or 0.6 g x 2 iv" 11
"LMU" "Lefamulin" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "iv" "" "0.5 g x 2 iv" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "iv" "" "0.5 g x 1 iv" 11
"LVX" "Levofloxacin" "high_dosage" "0.5 g" 2 "oral" "" "0.5 g x 2 oral" 11
"LVX" "Levofloxacin" "standard_dosage" "0.5 g" 1 "oral" "" "0.5 g x 1 oral" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "iv" "" "0.6 g x 2 iv" 11
"LNZ" "Linezolid" "standard_dosage" "0.6 g" 2 "oral" "" "0.6 g x 2 oral" 11
"MEM" "Meropenem" "high_dosage" "2 g" 3 "iv" "over 3 hours" "2 g x 3 iv over 3 hours" 11
"MEM" "Meropenem" "standard_dosage" "1 g" 3 "iv" "over 30 minutes" "1 g x 3 iv over 30 minutes" 11
"MEV" "Meropenem/vaborbactam" "standard_dosage" "2 g + 2 g" 3 "iv" "over 3 hours" "(2 g meropenem + 2 g vaborbactam) x 3 iv over 3 hours" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "or 0.5 g x 3 iv" "0.5 g x 3 oral or 0.5 g x 3 iv" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "or 0.4 g x 3 iv" "0.4 g x 3 oral or 0.4 g x 3 iv" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "iv" "" "0.5 g x 3 iv" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "iv" "" "0.4 g x 3 iv" 11
"MTR" "Metronidazole" "high_dosage" "0.5 g" 3 "oral" "" "0.5 g x 3 oral" 11
"MTR" "Metronidazole" "standard_dosage" "0.4 g" 3 "oral" "" "0.4 g x 3 oral" 11
"MNO" "Minocycline" "standard_dosage" "0.1 g" 2 "oral" "" "0.1 g x 2 oral" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "or 0.4 g x 1 iv" "0.4 g x 1 oral or 0.4 g x 1 iv" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "or 0.4 g x 2 iv" "0.4 g x 2 oral or 0.4 g x 2 iv" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "or 0.2 g x 2 iv" "0.2 g x 2 oral or 0.2 g x 2 iv" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "iv" "" "0.4 g x 1 iv" 11
"MFX" "Moxifloxacin" "standard_dosage" "0.4 g" 1 "oral" "" "0.4 g x 1 oral" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "iv" "" "0.4 g x 2 iv" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "iv" "" "0.2 g x 2 iv" 11
"OFX" "Ofloxacin" "high_dosage" "0.4 g" 2 "oral" "" "0.4 g x 2 oral" 11
"OFX" "Ofloxacin" "standard_dosage" "0.2 g" 2 "oral" "" "0.2 g x 2 oral" 11
"ORI" "Oritavancin" "standard_dosage" "1.2 g" 1 "iv" "" "1.2 g x 1 (single dose) iv over 3 hours" 11
"OXA" "Oxacillin" "high_dosage" "1 g" 6 "iv" "" "1 g x 6 iv" 11
"OXA" "Oxacillin" "standard_dosage" "1 g" 4 "iv" "" "1 g x 4 iv" 11
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "depending on species and/or infection type" "0.5-2 g x 3-4 oral depending on species and/or infection type" 11
"PHN" "Phenoxymethylpenicillin" "standard_dosage" "0.5-2 g" 3 "oral" "" "0.5-2 g x 3-4 oral" 11
"PIP" "Piperacillin" "high_dosage" "4 g" 4 "iv" "" "4 g x 4 iv by extended 3-hour infusion" 11
"PIP" "Piperacillin" "standard_dosage" "4 g" 4 "iv" "" "4 g x 4 iv" 11
"TZP" "Piperacillin/tazobactam" "high_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv by extended 3-hour infusion" 11
"TZP" "Piperacillin/tazobactam" "standard_dosage" "4 g + 0.5 g" 4 "iv" "" "(4 g piperacillin + 0.5 g tazobactam) x 4 iv or x 3 by extended 4-hour infusion" 11
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral" 11
"SXT" "Trimethoprim/sulfamethoxazole" "high_dosage" "0.24 g + 1.2 g" 2 "oral" "" "(0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 oral or (0.24 g trimethoprim + 1.2 g sulfamethoxazole) x 2 iv" 11
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"SXT" "Trimethoprim/sulfamethoxazole" "standard_dosage" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral or (0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 iv" 11
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"VAN" "Vancomycin" "standard_dosage" "0.5 g" 4 "iv" "or 1 g x 2 iv or 2 g x 1 by continuous infusion" "0.5 g x 4 iv or 1 g x 2 iv or 2 g x 1 by continuous infusion" 11
"SXT" "Trimethoprim/sulfamethoxazole" "uncomplicated_uti" "0.16 g + 0.8 g" 2 "oral" "" "(0.16 g trimethoprim + 0.8 g sulfamethoxazole) x 2 oral" 11
"VAN" "Vancomycin" "standard_dosage" "1 g" 2 "iv" "" "1 g x 2 iv or 2 g x 1 by continuous infusion" 11
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><ahref="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><ahref="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><ahref="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <ahref="./reference/microorganisms.html">all microorganisms</a> and <ahref="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<tableclass="table">
<thead><trclass="header">
<thalign="left">mo</th>
<thalign="left">bacteria</th>
<thalign="center">AMK</th>
<thalign="center">GEN</th>
<thalign="center">KAN</th>
@ -256,6 +256,24 @@ Since you are one of our users, we would like to know how you use the package an
<li>Loading the package (i.e., <code><ahref="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before</li>
<li>Loading the package (i.e., <code><ahref="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (increased with ~3 MB)</li>
</ul>
</div>
</div>
@ -615,7 +615,7 @@
<p>Making this package independent of especially the tidyverse (e.g.packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
<p>Negative effects of this change are:</p>
<ul>
<li>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><ahref="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
<li><del>All functions from the <code>mo_*</code> family (like <code><ahref="../reference/mo_property.html">mo_name()</a></code> and <code><ahref="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
@ -952,7 +952,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<spanclass="co">#> invalid microorganism code, NA generated</span></code></pre></div>
<p>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.</p>
</li>
<li><p>Function <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">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://rdrr.io/pkg/cleaner/man/freq.html">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>
<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>
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
</ul>
</div>
@ -1221,7 +1221,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>The <code><ahref="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
@ -1246,7 +1246,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
<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>
@ -1487,7 +1487,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
@ -1588,7 +1588,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
<li><p>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</p></li>
<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>
</li>
<li><p>Check for <code><ahref="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
@ -1621,7 +1621,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><ahref="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
<li>
<p>AI improvements for <code>as.mo</code>:</p>
@ -1789,13 +1789,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
@ -1869,13 +1869,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<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://rdrr.io/pkg/cleaner/man/freq.html">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://rdrr.io/r/graphics/hist.html">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://rdrr.io/pkg/cleaner/man/freq.html">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>
<p>A <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 135 observations and 9 variables:</p><ul>
<p>A <ahref='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 169 observations and 9 variables:</p><ul>
<li><p><code>ab</code><br/> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>name</code><br/> Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>type</code><br/> Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"</p></li>
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
\title{Data Set with Treatment Dosages as Defined by EUCAST}
\format{
A \link{data.frame} with 135 observations and 9 variables:
A \link{data.frame} with 169 observations and 9 variables:
\itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{name}\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO
