@ -29,7 +29,7 @@
< 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 = "" > 2.1.1.9080 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9081 < / 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" >
@ -95,7 +95,7 @@
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 24 September 2024.< / p >
generated on 29 September 2024.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -151,21 +151,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2024-09-24 < / td >
< td align = "center" > 2024-09-29 < / 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" > 2024-09-24 < / td >
< td align = "center" > 2024-09-29 < / 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" > 2024-09-24 < / td >
< td align = "center" > 2024-09-29 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -279,37 +279,35 @@ taxonomic codes. Let’
< 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: Escherichia coli co li (0.643 ), Escherichia coli< / span > < / span >
< span > < span class = "co" > #> expressing (0.611 ), Enterobacter cowanii (0.600 ), Eubacterium combesii < / span > < / span >
< span > < span class = "co" > #> (0.600 ), Eggerthia catenaformi s (0.591 ), Eu bacterium callander i< / span > < / span >
< span > < span class = "co" > #> (0.591 ), Enterocloster citroniae (0.587 ), Eubacterium cylindroides < / span > < / span >
< span > < span class = "co" > #> (0.583), Enterococcus casseliflavu s (0.577 ), and Enterobacter cloacae < / span > < / span >
< span > < span class = "co" > #> cloacae (0.571)< / span > < / span >
< span > < span class = "co" > #> Also matched: Enterococcus crota li (0.650 ), Escherichia coli coli< / span > < / span >
< span > < span class = "co" > #> (0.643 ), Escherichia coli expressing (0.611 ), Erwinia coffeiphila < / span > < / span >
< span > < span class = "co" > #> (0.605 ), Eubacterium coprostanoligene s (0.603 ), Entero bacter cowani i< / span > < / span >
< span > < span class = "co" > #> (0.600 ), Eubacterium combesii (0.600 ), Enterococcus columbae (0.595), < / span > < / span >
< span > < span class = "co" > #> Eggerthia catenaformi s (0.591 ), and Enterococcus camelliae (0.591) < / 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 pasteuri i (0.500 ), Klebsi ella planticola (0.500),< / span > < / span >
< span > < span class = "co" > #> King ella potus (0.4 00), 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" > #> (0.658), Kosakonia pseudosacchar i (0.542 ), Kaist ella palustris (0.500),< / span > < / span >
< span > < span class = "co" > #> Kaist ella polysaccharea (0.5 00), Kingella potus (0.500), Kingella < / span > < / span >
< span > < span class = "co" > #> pumchi (0.500), Klebsiella pasteurii (0.500), and Klebsiella planticola < / span > < / span >
< span > < span class = "co" > #> (0.500 )< / span > < / span >
< span > < span class = "co" > #> --------------------------------------------------------------------------------< / span > < / span >
< span > < span class = "co" > #> "S. aureus" -> Staphylococcu s aureus (B_STPHY _AURS, 0.690 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Staphylococcus aureu s aureus (0.643 ), Staphylococcus< / span > < / span >
< span > < span class = "co" > #> argenteus (0.625 ), Staphylococcus aureus anaerobi us (0.625 ), Salmonella < / span > < / span >
< span > < span class = "co" > #> Aurelianis (0.595), Salmonella Aarh us (0.588 ), Salmonella Amoundernes s< / span > < / span >
< span > < span class = "co" > #> (0.587 ), Selenomonas artemidi s (0.571 ), Salmonella choleraesui s< / span > < / span >
< span > < span class = "co" > #> arizonae (0.562 ), Streptococcus anginosus anginos us (0.561 ), and< / span > < / span >
< span > < span class = "co" > #> Salmonella Abaetetuba (0.548 )< / span > < / span >
< span > < span class = "co" > #> "S. aureus" -> Streptomyce s aureus (B_SMYCS _AURS, 0.711 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Streptomyce s az ureus (0.700 ), Staphylococcus aureus < / span > < / span >
< span > < span class = "co" > #> (0.690 ), Streptomyces aureorect us (0.667 ), Streptomyces albipurpureus < / span > < / span >
< span > < span class = "co" > #> (0.654), Streptomyces aurat us (0.650 ), Staphylococcus aureus aureu s< / span > < / span >
< span > < span class = "co" > #> (0.643 ), Streptomyces aurantiogriseu s (0.643 ), Streptomyce s< / span > < / span >
< span > < span class = "co" > #> aureocirculatus (0.643 ), Streptomyces aureoverticillat us (0.629 ), and< / span > < / span >
< span > < span class = "co" > #> Staphylococcus argenteus (0.625 )< / 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), Serratia < / span > < / span >
< span > < span class = "co" > #> proteamaculans quinovora (0.545 ), Streptococcus pseudoporcinus (0.536), < / span > < / span >
< span > < span class = "co" > #> Staphylococcus pseudintermedius (0.532 ), Serratia proteamaculans < / span > < / span >
< span > < span class = "co" > #> proteamaculans (0.52 6), Salmo nella Portanigra (0.524), Sphingomonas < / span > < / span >
< span > < span class = "co" > #> paucimobil is (0.520 ), Streptococcus pluranimalium (0.519), < / span > < / span >
< span > < span class = "co" > #> Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan < / span > < / span >
< span > < span class = "co" > #> (0.500)< / span > < / span >
< span > < span class = "co" > #> Also matched: Streptococcus pseudopneumoniae (0.700), Sphingomonas < / span > < / span >
< span > < span class = "co" > #> piscinae (0.619 ), Sphingomonas paeninsulae (0.604), Streptomyces < / span > < / span >
< span > < span class = "co" > #> pseudovenezuelae (0.603 ), Sphingomonas panaciterrae (0.600), < / span > < / span >
< span > < span class = "co" > #> Sphingobacterium pakistanense (0.58 6), Shewa nella pneumatophori < / span > < / span >
< span > < span class = "co" > #> (0.583), Sphingobacterium pakistanens is (0.583 ), Sphingomonas palmae < / span > < / span >
< span > < span class = "co" > #> (0.579), and Sphingomonas pseudosanguinis (0.571) < / 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 >
@ -348,11 +346,11 @@ dplyr:</p>
< 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;" > 6< / span > W3 A 2018-03-31 B_SMYCS _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;" > 10< / span > G6 A 2015-04-27 B_SMYCS _AURS S S S S < / 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 >
@ -406,9 +404,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
< 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 2,71 2 'phenotype-based' first isolates (90.4 % of total where a< / 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 >
< p > So only 90 % is suitable for resistance analysis! We can now filter on
< 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 >
< div class = "sourceCode" id = "cb9" > < pre class = "downlit sourceCode r" >
@ -418,24 +416,24 @@ it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" cl
< div class = "sourceCode" id = "cb10" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / 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 = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > So we end up with 2 71 2 isolates for analysis. Now our data looks
< p > So we end up with 2 724 isolates for analysis. Now our data looks
like:< / p >
< div class = "sourceCode" id = "cb11" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,71 2 × < / span > < / span > < / span >
< 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 > P10 A 2015-12-10 B_ESCHR_COLI S I S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > B7 A 2015-03-02 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > W3 A 2018-03-31 B_STPHY _AURS R S R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > W3 A 2018-03-31 B_SMYCS _AURS R S R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > M3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > J3 A 2019-06-19 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > G6 A 2015-04-27 B_STPHY _AURS S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > G6 A 2015-04-27 B_SMYCS _AURS S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > P4 A 2011-06-21 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > Z1 A 2014-09-05 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 02 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 14 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< p > Time for the analysis.< / p >
< / div >
< / div >
@ -448,29 +446,29 @@ impression, as it comes with support for the new <code>mo</code> and
< div class = "sourceCode" id = "cb12" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/summary.html" class = "external-link" > summary< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> patient_id hospital date < / span > < / span >
< span > < span class = "co" > #> Length:271 2 Length:271 2 Min. :2011-01-01 < / span > < / span >
< span > < span class = "co" > #> Class :character Class :character 1st Qu.:2013-05-03 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-16 < / span > < / span >
< span > < span class = "co" > #> Mean :2015-06-2 1 < / span > < / span >
< span > < span class = "co" > #> 3rd Qu.:2017-08-24 < / span > < / span >
< span > < span class = "co" > #> Length:2724 Length:2724 Min. :2011-01-01 < / span > < / span >
< span > < span class = "co" > #> Class :character Class :character 1st Qu.:2013-04-26 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-14 < / span > < / span >
< span > < span class = "co" > #> Mean :2015-06-18 < / span > < / span >
< span > < span class = "co" > #> 3rd Qu.:2017-08-21 < / span > < / span >
< span > < span class = "co" > #> Max. :2019-12-27 < / span > < / span >
< span > < span class = "co" > #> bacteria AMX AMC < / span > < / span >
< span > < span class = "co" > #> Class :mo Class:sir Class:sir < / span > < / span >
< span > < span class = "co" > #> < NA> :0 %S :41.0 % (n=111 2) %S :52.0 % (n=1409 ) < / span > < / span >
< span > < span class = "co" > #> Unique:4 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI %I :16.1% (n=437 ) %I :12.0 % (n=325 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS %R :42.9 % (n=1163 ) %R :36.1 % (n=978 ) < / span > < / span >
< span > < span class = "co" > #> < NA> :0 %S :41.4 % (n=1127 ) %S :52.2 % (n=1421 ) < / span > < / span >
< span > < span class = "co" > #> Unique:5 %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI %I :16.1% (n=438 ) %I :12.1 % (n=329 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS %R :42.5 % (n=1159 ) %R :35.8 % (n=974 ) < / span > < / span >
< span > < span class = "co" > #> #3 :B_STRPT_PNMN %NI : 0.0% (n=0) %NI : 0.0% (n=0) < / span > < / span >
< span > < span class = "co" > #> CIP GEN first < / span > < / span >
< span > < span class = "co" > #> Class:sir Class:sir Mode:logical < / span > < / span >
< span > < span class = "co" > #> %S :51.5 % (n=1396 ) %S :59.6 % (n=1616 ) TRUE:271 2 < / span > < / span >
< span > < span class = "co" > #> %S :51.7 % (n=1407 ) %S :59.9 % (n=1632 ) TRUE:2724 < / span > < / span >
< span > < span class = "co" > #> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) < / span > < / span >
< span > < span class = "co" > #> %I : 6.6 % (n=178) %I : 3.1% (n=85) < / span > < / span >
< span > < span class = "co" > #> %R :42.0 % (n=1138 ) %R :37.3 % (n=1011 ) < / span > < / span >
< span > < span class = "co" > #> %I : 6.5 % (n=178) %I : 3.1% (n=85) < / span > < / span >
< span > < span class = "co" > #> %R :41.8 % (n=1139 ) %R :37.0 % (n=1007 ) < / span > < / span >
< span > < span class = "co" > #> %NI : 0.0% (n=0) %NI : 0.0% (n=0)< / span > < / span >
< span > < / span >
< span > < span class = "fu" > < a href = "https://pillar.r-lib.org/reference/glimpse.html" class = "external-link" > glimpse< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Rows: 2,71 2< / span > < / span >
< span > < span class = "co" > #> Rows: 2,724 < / span > < / span >
< span > < span class = "co" > #> Columns: 9< / span > < / span >
< span > < span class = "co" > #> $ patient_id < span style = "color: #949494; font-style: italic;" > < chr> < / span > "J3", "R7", "P10", "B7", "W3", "M3", "J3", "G6", "P4", "Z1"…< / span > < / span >
< span > < span class = "co" > #> $ hospital < span style = "color: #949494; font-style: italic;" > < chr> < / span > "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A", "A",…< / span > < / span >
@ -485,7 +483,7 @@ impression, as it comes with support for the new <code>mo</code> and
< span > < span class = "co" > # number of unique values per column:< / span > < / span >
< span > < span class = "fu" > < a href = "https://rdrr.io/r/base/lapply.html" class = "external-link" > sapply< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > , < span class = "va" > n_distinct< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP < / span > < / span >
< span > < span class = "co" > #> 260 3 1852 4 3 3 3 < / span > < / span >
< span > < span class = "co" > #> 260 3 1853 5 3 3 3 < / span > < / span >
< span > < span class = "co" > #> GEN first < / span > < / span >
< span > < span class = "co" > #> 3 1< / span > < / span > < / code > < / pre > < / div >
< div class = "section level3" >
@ -497,23 +495,25 @@ microorganisms:</p>
< div class = "sourceCode" id = "cb13" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 = "../reference/count.html" > count< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > < span class = "op" > )< / span > , sort < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 4 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 5 × < / span > < / span > < / span >
< span > < span class = "co" > #> `mo_name(bacteria)` n< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > Escherichia coli < span style = "text-decoration: underline;" > 1< / span > 518< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 730 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 483 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Streptococcus pneumoniae 426< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 326< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > Streptomyces aureus 247< / 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 = "../reference/count.html" > count< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > < span class = "op" > )< / span > , sort < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 4 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 5 × < / span > < / span > < / span >
< span > < span class = "co" > #> `mo_name(bacteria)` n< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > Escherichia coli < span style = "text-decoration: underline;" > 1< / span > 319< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 67 6< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 45 6< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Streptococcus pneumoniae 400< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 317< / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 317< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > Streptomyces aureus 232< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level3" >
< h3 id = "select-and-filter-with-antibiotic-selectors" > Select and filter with antibiotic selectors< a class = "anchor" aria-label = "anchor" href = "#select-and-filter-with-antibiotic-selectors" > < / a >
@ -525,7 +525,7 @@ in:</p>
< 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/antibiotic_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: #949494;" > # A tibble: 2,71 2 × < / 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 >
@ -538,100 +538,100 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2015-04-27 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2011-06-21 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2014-09-05 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 02 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 14 more rows< / 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/antibiotic_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: #949494;" > # A tibble: 2,71 2 × < / 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 S I < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_STPHY _AURS R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_SMYCS _AURS R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > B_ESCHR_COLI R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_STPHY _AURS S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_SMYCS _AURS S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_ESCHR_COLI 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: #949494;" > # ℹ 02 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 14 more rows< / 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 = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,71 2 × < / 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 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 S I S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_STPHY _AURS R S R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > B_SMYCS _AURS R S R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_STPHY _AURS S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_SMYCS _AURS S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_ESCHR_COLI 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: #949494;" > # ℹ 02 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 14 more rows< / 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/antibiotic_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: #949494;" > # A tibble: 1,011 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 1,007 × < / 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;" > 2< / span > X1 A 2017-07-04 B_SMYCS _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;" > 6< / span > R1 A 2018-06-10 B_SMYCS _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;" > 8< / span > P5 A 2019-03-09 B_SMYCS _AURS S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > Q8 A 2019-08-10 B_SMYCS _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: #949494;" > # ℹ 1,001 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 997 more rows< / 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/antibiotic_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: #949494;" > # A tibble: 483 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 479 × < / 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;" > 2< / span > R10 A 2013-12-20 B_SMYCS _AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_SMYCS _AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_SMYCS _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: #949494;" > # ℹ 73 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > C5 A 2015 -08-3 0 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 69 more rows< / 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/antibiotic_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: #949494;" > # A tibble: 483 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 479 × < / 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;" > 2< / span > R10 A 2013-12-20 B_SMYCS _AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_SMYCS _AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_SMYCS _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: #949494;" > # ℹ 73 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > C5 A 2015 -08-3 0 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 69 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level3" >
< h3 id = "generate-antibiograms" > Generate antibiograms< a class = "anchor" aria-label = "anchor" href = "#generate-antibiograms" > < / a >
@ -1230,7 +1230,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:< / p >
< div class = "sourceCode" id = "cb22" > < 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 class = "fu" > < a href = "../reference/proportion.html" > resistance< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] 0.4288348 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> [1] 0.4254772 < / span > < / span > < / code > < / pre > < / div >
< p > Or can be used in conjunction with < code > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by()< / a > < / code > and
< code > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" class = "external-link" > summarise()< / a > < / code > , both from the < code > dplyr< / code > package:< / p >
< div class = "sourceCode" id = "cb23" > < pre class = "downlit sourceCode r" >
@ -1240,9 +1240,9 @@ own:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 3 × < / span > < / span > < / span >
< span > < span class = "co" > #> hospital amoxicillin< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < dbl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > A 0.342 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > A 0.336 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B 0.564< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > C 0.372 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > C 0.370 < / span > < / span > < / code > < / pre > < / div >
< hr >
< p > < em > Author: Dr. < / em > < / p >
< / div >
github-actions