@ -31,7 +31,7 @@
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9135 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9136 < / small >
< button class = "navbar-toggler" type = "button" data-bs-toggle = "collapse" data-bs-target = "#navbar" aria-controls = "navbar" aria-expanded = "false" aria-label = "Toggle navigation" >
@ -90,7 +90,7 @@
website update since they are based on randomly created values and the
page was written in < a href = "https://rmarkdown.rstudio.com/" class = "external-link" > R
Markdown< / a > . However, the methodology remains unchanged. This page was
generated on 28 January 2025.< / p >
generated on 31 January 2025.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -146,21 +146,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2025-01-28 < / td >
< td align = "center" > 2025-01-31 < / td >
< td align = "center" > abcd< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2025-01-28 < / td >
< td align = "center" > 2025-01-31 < / td >
< td align = "center" > abcd< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2025-01-28 < / td >
< td align = "center" > 2025-01-31 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -262,53 +262,54 @@ user input can be used:</p>
< p > Now we can thus clean our data:< / p >
< div class = "sourceCode" id = "cb5" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data< / span > < span class = "op" > $< / span > < span class = "va" > bacteria< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data< / span > < span class = "op" > $< / span > < span class = "va" > bacteria< / span > , info < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> mo_uncertainties() to review these uncertainties, or use< / span > < / span >
< span > < span class = "co" > #> add_custom_microorganisms() to add custom entries.< / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > mo_uncertainties()< / span > < span style = "color: #0000BB;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > add_custom_microorganisms()< / span > < span style = "color: #0000BB;" > < / span > < / span > < / span > < / > < / pre > < / div >
< p > Apparently, there was some uncertainty about the translation to
taxonomic codes. Let’ < / p >
< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/as.mo.html" > mo_uncertainties< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Matching scores are based on the resemblance between the input and the full< / span > < / span >
< span > < span class = "co" > #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > > taxonomic name, and the pathogenicity in humans. See < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > ?mo_matching_score< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > Colour keys: < / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.000-0.549 < / span > < span style = "color: #080808; background-color: #FFD787;" > 0.550-0.649 < / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.650-0.749 < / span > < span style = "color: #080808; background-color: #5FD7AF;" > 0.750-1.000 < / span > < / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> --------------------------------------------------------------------------------< / span > < / span >
< span > < span class = "co" > #> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Enterococcus crotali (0.650), Escherichia coli coli< / span > < / span >
< span > < span class = "co" > #> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii< / span > < / span >
< span > < span class = "co" > #> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591 ),< / span > < / span >
< span > < span class = "co" > #> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae< / span > < / span >
< span > < span class = "co" > #> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae< / span > < / span >
< span > < span class = "co" > #> dissolvens (0.565 )< / span > < / span >
< span > < span class = "co" > #> --------------------------------------------------------------------------------< / span > < / span >
< span > < span class = "co" > #> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella < / span > < / span >
< span > < span class = "co" > #> pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis< / span > < / span >
< span > < span class = "co" > #> (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500 ),< / span > < / span >
< span > < span class = "co" > #> Kingella potus (0.400), Kluyveromyces pseudotropicale (0.386 ),< / span > < / span >
< span > < span class = "co" > #> Kluyveromyces pseudotropicalis (0.363), Kosakonia pseudosacchari< / span > < / span >
< span > < span class = "co" > #> (0.361), and Kluyveromyces pseudotropicalis pseudotropicalis (0.361 )< / span > < / span >
< span > < span class = "co" > #> --------------------------------------------------------------------------------< / span > < / span >
< span > < span class = "co" > #> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus < / span > < / span >
< span > < span class = "co" > #> argenteus (0.625), Staphylococcus aureus anaerobius (0.625 ),< / span > < / span >
< span > < span class = "co" > #> Staphylococcus auricularis (0.615), Salmonella Aurelianis (0.595 ),< / span > < / span >
< span > < span class = "co" > #> Salmonella Aarhus (0.588), Salmonella Amounderness (0.587 ),< / span > < / span >
< span > < span class = "co" > #> Staphylococcus argensis (0.587), Streptococcus australis (0.587 ), and< / span > < / span >
< span > < span class = "co" > #> Salmonella choleraesuis arizonae (0.562 )< / span > < / span >
< span > < span class = "co" > #> --------------------------------------------------------------------------------< / span > < / span >
< span > < span class = "co" > #> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus < / span > < / span >
< span > < span class = "co" > #> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545 ),< / span > < / span >
< span > < span class = "co" > #> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans< / span > < / span >
< span > < span class = "co" > #> (0.533), Staphylococcus pseudintermedius (0.532), Serratia < / span > < / span >
< span > < span class = "co" > #> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus< / span > < / span >
< span > < span class = "co" > #> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus < / span > < / span >
< span > < span class = "co" > #> periodonticum (0.519 )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #B2B2B2;" > < / span > < / span > < / span >
< span > < span class = "co" > #> "E. coli" -> < span style = "font-weight: bold; font-style: italic;" > < / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.688< / span > < / span > < / span >
< span > < span class = "co" > #> Also matched: < span style = "font-style: italic;" > Enterococcus crotali< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.650< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.643< / span > ), < span style = "font-style: italic;" > Escherichia coli expressing< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.611< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.600< / span > ), < span style = "font-style: italic;" > Enterococcus columbae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.595< / span > ), < span style = "font-style: italic;" > Enterococcus camelliae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.591< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Enterococcus casseliflavus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.577< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.571< / span > ), < span style = "font-style: italic;" > Enterobacter cloacae< / span > complex< span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.571< / span > ), and < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> dissolvens< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.565< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #B2B2B2;" > < / span > < / span > < / span >
< span > < span class = "co" > #> "K. pneumoniae" -> < span style = "font-weight: bold; font-style: italic;" > < / span > < span style = "color: #080808; background-color: #5FD7AF;" > 0.786< / span > < / span > < / span >
< span > < span class = "co" > #> Also matched: < span style = "font-style: italic;" > Klebsiella pneumoniae ozaenae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.707< / span > ), < span style = "font-style: italic;" > Klebsiella< / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> pneumoniae pneumoniae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.688< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.658< / span > ), < span style = "font-style: italic;" > Klebsiella pasteurii< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.500< / span > ), < span style = "font-style: italic;" > Klebsiella planticola< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.500< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Kingella potus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.400< / span > ), < span style = "font-style: italic;" > Kluyveromyces pseudotropicale< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.386< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Kluyveromyces pseudotropicalis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.363< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.361< / span > ), and < span style = "font-style: italic;" > Kluyveromyces pseudotropicalis pseudotropicalis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.361< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #B2B2B2;" > < / span > < / span > < / span >
< span > < span class = "co" > #> "S. aureus" -> < span style = "font-weight: bold; font-style: italic;" > < / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.690< / span > < / span > < / span >
< span > < span class = "co" > #> Also matched: < span style = "font-style: italic;" > Staphylococcus aureus aureus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.643< / span > ), < span style = "font-style: italic;" > Staphylococcus< / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> argenteus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.625< / span > ), < span style = "font-style: italic;" > Staphylococcus aureus anaerobius< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.625< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Staphylococcus auricularis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.615< / span > ), < span style = "font-style: italic;" > Salmonella< / span > Aurelianis< span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.595< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Salmonella< / span > Aarhus< span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.588< / span > ), < span style = "font-style: italic;" > Salmonella< / span > Amounderness< span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.587< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Staphylococcus argensis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.587< / span > ), < span style = "font-style: italic;" > Streptococcus australis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.587< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Salmonella choleraesuis arizonae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.562< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #B2B2B2;" > < / span > < / span > < / span >
< span > < span class = "co" > #> "S. pneumoniae" -> < span style = "font-weight: bold; font-style: italic;" > < / span > < span style = "color: #080808; background-color: #5FD7AF;" > 0.750< / span > < / span > < / span >
< span > < span class = "co" > #> Also matched: < span style = "font-style: italic;" > Streptococcus pseudopneumoniae< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFFF87;" > 0.700< / span > ), < span style = "font-style: italic;" > Streptococcus< / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> phocae salmonis< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFD787;" > 0.552< / span > ), < span style = "font-style: italic;" > Serratia proteamaculans quinovora< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.545< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "font-style: italic;" > Streptococcus pseudoporcinus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.536< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.533< / span > ), < span style = "font-style: italic;" > Staphylococcus pseudintermedius< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.532< / span > ), < span style = "font-style: italic;" > Serratia< / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > > proteamaculans proteamaculans< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.526< / span > ), < span style = "font-style: italic;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> pasteurianus< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.526< / span > ), < span style = "font-style: italic;" > Salmonella< / span > Portanigra< span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.524< / span > ), and < span style = "font-style: italic;" > Streptococcus< / span > < / span > < / span >
< span > < span class = "co" > < span style = "font-style: italic;" > #> periodonticum< / span > < span style = "color: #0000BB;" > (< / span > < span style = "color: #080808; background-color: #FFAFAF;" > 0.519< / span > < / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Only the first 10 other matches of each record are shown. Run< / span > < / span >
< span > < span class = "co" > #> print(mo_uncertainties(), n = ...) to view more entries, or save< / span > < / span >
< span > < span class = "co" > #> mo_uncertainties() to an object. < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > < span style = "color: #0000BB;" > > Only the first 10 other matches of each record are shown. Run< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > print(mo_uncertainties(), n = ...)< / span > < span style = "color: #0000BB;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > mo_uncertainties()< / span > < span style = "color: #0000BB;" > to an object.< / span > < / span > < / span > < / code > < / pre > < / div >
< p > That’ < / p >
< / div >
< div class = "section level3" >
@ -338,16 +339,16 @@ dplyr:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 3,000 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J3 A 2012-11-21 B_ESCHR_COLI R I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R7 A 2018-04-03 B_KLBSL_PNMN R I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > P3 A 2014-09-19 B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > P10 A 2015-12-10 B_ESCHR_COLI S I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B7 A 2015-03-02 B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > W3 A 2018-03-31 B_STPHY_AURS R S R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > J8 A 2016-06-14 B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > M3 A 2015-10-25 B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > J3 A 2019-06-19 B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > G6 A 2015-04-27 B_STPHY_AURS S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J3 A 2012-11-21 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R7 A 2018-04-03 < span style = "color: #949494;" > B_< / span > KLBSL< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > P3 A 2014-09-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > P10 A 2015-12-10 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B7 A 2015-03-02 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > W3 A 2018-03-31 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > J8 A 2016-06-14 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > M3 A 2015-10-25 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > J3 A 2019-06-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > G6 A 2015-04-27 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< p > This is basically it for the cleaning, time to start the data
inclusion.< / p >
@ -395,14 +396,14 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
< div class = "sourceCode" id = "cb8" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data< / span > < span class = "op" > < -< / span > < span class = "va" > our_data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > first < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/first_isolate.html" > first_isolate< / a > < / span > < span class = "op" > (< / span > info < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ 365 days < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> of 2 < / span > < / span >
< span > < span class = "co" > #> => Found 2,724 'phenotype-based' first isolates (90.8% of total where a< / span > < / span >
< span > < span class = "co" > #> microbial ID was available)< / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BB0000;" > ℹ < / span > < span style = "color: #BB0000; font-weight: bold;" > 365 days< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; font-weight: bold;" > bacteria< / span > < span style = "color: #0000BB;" > ' as input for < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > col_mo< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; font-weight: bold;" > date< / span > < span style = "color: #0000BB;" > ' as input for < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > col_date< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; font-weight: bold;" > patient_id< / span > < span style = "color: #0000BB;" > ' as input for < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > col_patient_id< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BB0000;" > ℹ < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #BB0000;" > #> of 2< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #080808;" > => Found < / span > < span style = "color: #080808; font-weight: bold;" > 2,724 'phenotype-based' first isolates< / span > < span style = "color: #080808;" > < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #080808;" > > microbial ID was available)< / span > < / span > < / span > < / > < / pre > < / div >
< p > So only 91% is suitable for resistance analysis! We can now filter on
it with the < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter()< / a > < / code > function, also from the
< code > dplyr< / code > package:< / p >
@ -420,16 +421,16 @@ like:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,724 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J3 A 2012-11-21 B_ESCHR_COLI R I S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R7 A 2018-04-03 B_KLBSL_PNMN R I S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > P3 A 2014-09-19 B_ESCHR_COLI R S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > W3 A 2018-03-31 B_STPHY_AURS R S R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > G6 A 2015-04-27 B_STPHY_AURS S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J3 A 2012-11-21 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R7 A 2018-04-03 < span style = "color: #949494;" > B_< / span > KLBSL< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > P3 A 2014-09-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > P10 A 2015-12-10 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B7 A 2015-03-02 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > W3 A 2018-03-31 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > M3 A 2015-10-25 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > J3 A 2019-06-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > G6 A 2015-04-27 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > P4 A 2011-06-21 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< p > Time for the analysis.< / p >
< / div >
@ -519,39 +520,39 @@ in:</p>
< div class = "sourceCode" id = "cb14" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > aminoglycosides()< / span > < span style = "color: #0000BB;" > using column '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,724 × < / span > < / span > < / span >
< span > < span class = "co" > #> date GEN < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > 2012-11-21 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > 2018-04-03 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > 2014-09-19 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > 2015-12-10 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 2015-03-02 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2018-03-31 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2015-10-25 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2019-06-19 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2015-04-27 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2011-06-21 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > 2012-11-21 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > 2018-04-03 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > 2014-09-19 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > 2015-12-10 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 2015-03-02 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2018-03-31 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2015-10-25 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2019-06-19 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2015-04-27 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2011-06-21 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > , < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (amoxicillin/clavulanic acid)< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > betalactams()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > > (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,724 × < / span > < / span > < / span >
< span > < span class = "co" > #> bacteria AMX AMC < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > B_ESCHR_COLI R I < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B_KLBSL_PNMN R I < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > B_ESCHR_COLI R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > B_ESCHR_COLI S I < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > B_STPHY_AURS R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_STPHY_AURS S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > < span style = "color: #949494;" > B_< / span > KLBSL< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
@ -559,73 +560,73 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,724 × < / span > < / span > < / span >
< span > < span class = "co" > #> bacteria AMX AMC CIP GEN < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > B_ESCHR_COLI R I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B_KLBSL_PNMN R I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > B_ESCHR_COLI S I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > B_STPHY_AURS R S R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_STPHY_AURS S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > < span style = "color: #949494;" > B_< / span > KLBSL< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > # filtering using AB selectors is also possible:< / span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/any.html" class = "external-link" > any< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > aminoglycosides()< / span > < span style = "color: #0000BB;" > using column '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 981 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J5 A 2017-12-25 B_STRPT_PNMN R S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > X1 A 2017-07-04 B_STPHY_AURS R S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > B3 A 2016-07-24 B_ESCHR_COLI S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > V7 A 2012-04-03 B_ESCHR_COLI S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > C9 A 2017-03-23 B_ESCHR_COLI S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > R1 A 2018-06-10 B_STPHY_AURS S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > S2 A 2013-07-19 B_STRPT_PNMN S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > P5 A 2019-03-09 B_STPHY_AURS S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > Q8 A 2019-08-10 B_STPHY_AURS S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > K5 A 2013-03-15 B_STRPT_PNMN S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > J5 A 2017-12-25 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > X1 A 2017-07-04 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > B3 A 2016-07-24 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > V7 A 2012-04-03 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > C9 A 2017-03-23 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > R1 A 2018-06-10 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > S2 A 2013-07-19 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > P5 A 2019-03-09 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > Q8 A 2019-08-10 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > K5 A 2013-03-15 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/all.html" class = "external-link" > all< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (amoxicillin/clavulanic acid)< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > betalactams()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > > (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 462 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B6 A 2016-11-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > I7 A 2015-08-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > N3 A 2014-12-29 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > # even works in base R (since R 3.0):< / span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > [< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/all.html" class = "external-link" > all< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > ==< / span > < span class = "st" > "R"< / span > < span class = "op" > )< / span > , < span class = "op" > ]< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (amoxicillin/clavulanic acid)< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > betalactams()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > > (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 462 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B6 A 2016-11-20 B_ESCHR_COLI R R R R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > N3 A 2014-12-29 B_STRPT_PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B6 A 2016-11-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > I7 A 2015-08-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > N3 A 2014-12-29 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level3" >
@ -666,16 +667,16 @@ like:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,000 × < / span > < / span > < / span >
< span > < span class = "co" > #> date patient age gender ward mo PEN OXA FLC AMX < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > 2002-01-02 A77334 65 F Clinical < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > 2002-01-03 A77334 65 F Clinical < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > 2002-01-07 067927 45 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > 2002-01-07 067927 45 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 2002-01-13 067927 45 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2002-01-13 067927 45 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2002-01-14 462729 78 M Clinical < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2002-01-14 462729 78 M Clinical < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2002-01-16 067927 45 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2002-01-17 858515 79 F ICU < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > EPDR < span style = "color: #080808; background-color: #FFAFAF;" > R < / span > < span style = "color: #B2B2B2;" > NA< / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #B2B2B2;" > NA< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < sir> , AMP < sir> , TZP < sir> , CZO < sir> , FEP < sir> ,< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # CXM < sir> , FOX < sir> , CTX < sir> , CAZ < sir> , CRO < sir> , GEN < sir> ,< / span > < / span > < / span >
@ -693,9 +694,9 @@ previously mentioned antibiotic class selectors:</p>
< div class = "sourceCode" id = "cb16" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > aminoglycosides()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > TOB< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (tobramycin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMK< / span > < span style = "color: #0000BB;" > ' (amikacin), and '< / span > < span style = "color: #0000BB; font-weight: bold;" > KAN< / span > < span style = "color: #0000BB;" > ' (kanamycin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > carbapenems()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > IPM< / span > < span style = "color: #0000BB;" > ' (imipenem) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > MEM< / span > < span style = "color: #0000BB;" > ' (meropenem)< / span > < / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "16%" >
@ -823,8 +824,8 @@ language to be Spanish using the <code>language</code> argument:</p>
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > ,< / span >
< span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "st" > "es"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > aminoglycosides()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > TOB< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (tobramycin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMK< / span > < span style = "color: #0000BB;" > ' (amikacin), and '< / span > < span style = "color: #0000BB; font-weight: bold;" > KAN< / span > < span style = "color: #0000BB;" > ' (kanamycin)< / span > < / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "20%" >
@ -947,9 +948,9 @@ argument must be used. This can be any column in the data, or e.g.
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "../reference/antimicrobial_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "ward"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > aminoglycosides()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > TOB< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (tobramycin), '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMK< / span > < span style = "color: #0000BB;" > ' (amikacin), and '< / span > < span style = "color: #0000BB; font-weight: bold;" > KAN< / span > < span style = "color: #0000BB;" > ' (kanamycin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #EEEEEE;" > carbapenems()< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > IPM< / span > < span style = "color: #0000BB;" > ' (imipenem) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > MEM< / span > < span style = "color: #0000BB;" > ' (meropenem)< / span > < / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "13%" >
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