@ -38,7 +38,7 @@
< 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 = "" > 2.0.0.9019 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.0.0.9020 < / 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" >
@ -118,28 +118,28 @@
< / li >
< li class = "nav-item dropdown" >
< a href = "#" class = "nav-link dropdown-toggle" data-bs-toggle = "dropdown" role = "button" aria-expanded = "false" aria-haspopup = "true" id = "dropdown--with-other-pkgs" >
< span class = "fa fa-circles-overlap " > < / span >
< span class = "fa fa-layer-plus " > < / span >
With other pkgs
< / a >
< div class = "dropdown-menu" aria-labelledby = "dropdown--with-other-pkgs" >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap " > < / span >
< span class = "fa fa-layer-plus " > < / span >
AMR & dplyr/tidyverse
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap " > < / span >
< span class = "fa fa-layer-plus " > < / span >
AMR & data.table
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap " > < / span >
< span class = "fa fa-layer-plus " > < / span >
AMR & tidymodels
< / a >
< a class = "dropdown-item" href = "../articles/other_pkg.html" >
< span class = "fa fa-circles-overlap " > < / span >
< span class = "fa fa-layer-plus " > < / span >
AMR & base R
< / a >
@ -204,7 +204,7 @@
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 May 2023.< / p >
generated on 26 May 2023.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2023-05-24 < / td >
< td align = "center" > 2023-05-26 < / 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" > 2023-05-24 < / td >
< td align = "center" > 2023-05-26 < / 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" > 2023-05-24 < / td >
< td align = "center" > 2023-05-26 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -347,7 +347,7 @@ supports all kinds of input:</p>
< span > < span class = "co" > #> [1] B_KLBSL_PNMN< / span > < / span >
< span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "KLPN"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Class 'mo'< / span > < / span >
< span > < span class = "co" > #> [1] B_BCLLS_THRN_KRST < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> [1] B_KLBSL_PNMN < / span > < / span > < / code > < / pre > < / div >
< p > The first character in above codes denote their taxonomic kingdom,
such as Bacteria (B), Fungi (F), and Protozoa (P).< / p >
< p > The < code > AMR< / code > package also contain functions to directly
@ -388,37 +388,35 @@ 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: Entero bacter cowanii (0.60 0), Eubacterium combesii < / span > < / span >
< span > < span class = "co" > #> (0.600 ), Eggerthia catenaformis (0.59 1), Eu bacterium callanderi < / 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 ), Entero bacter cloacae < / span > < / span >
< span > < span class = "co" > #> cloacae (0.57 1), Ehrlichia canis (0.567), and Enterobacter cloacae < / span > < / span >
< span > < span class = "co" > #> dissolvens (0.565)< / span > < / span >
< span > < span class = "co" > #> Also matched: Eu bacterium alactolyticum (0.62 0), Erwinia herbicola < / span > < / span >
< span > < span class = "co" > #> (0.618 ), Campylobacter coli (0.61 1), Entero bacter cowanii (0.600), < / span > < / span >
< span > < span class = "co" > #> Eubacterium combesii (0.600), Enterococcus faecalis (0.595 ), Eggerthia < / span > < / span >
< span > < span class = "co" > #> catenaformis (0.591 ), Enterocloster aldensi s (0.591 ), Eu bacterium < / span > < / span >
< span > < span class = "co" > #> callanderi (0.59 1), and Rhodococcus corallinus (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: Klebsiell a pneumoniae ozaenae (0.707 ), Klebsiella < / span > < / span >
< span > < span class = "co" > #> pneumoniae pneumoniae (0.68 8), 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), Kosakonia pseudosacchari (0.361), Kaistella < / span > < / span >
< span > < span class = "co" > #> palustris (0.333 ), Kocuria palustris (0.333 ), and Kocuria pelophila < / span > < / span >
< span > < span class = "co" > #> (0.333 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Nocardi a pneumoniae (0.763 ), Chlamydia pneumoniae < / span > < / span >
< span > < span class = "co" > #> (0.750), Mycoplasma pneumoniae (0.73 8), Klebsiella quasi pneumoniae< / span > < / span >
< span > < span class = "co" > #> (0.731), Chlamydophila pneumoniae (0.708), Streptococcus pneumoniae < / span > < / span >
< span > < span class = "co" > #> (0.708), Klebsiella pneumoniae ozaenae (0.707), Mycoplasmoides < / span > < / span >
< span > < span class = "co" > #> pneumoniae (0.700 ), Klebsiella pneumoniae pneumoniae (0.688 ), and< / span > < / span >
< span > < span class = "co" > #> Haemophilus pleuropneumoniae (0.679 )< / 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" > #> Streptomyces argenteol us (0.483 ), Streptomyces aureus (0.474), < / span > < / span >
< span > < span class = "co" > #> Streptomyces azure us (0.467 ), Streptomyces aureorectus (0.444), < / span > < / span >
< span > < span class = "co" > #> Streptomyces auratu s (0.433 ), Streptomyces aurantiogriseus (0.429), and < / span > < / span >
< span > < span class = "co" > #> Streptomyces aureocirculatu s (0.429 )< / span > < / span >
< span > < span class = "co" > #> Staphylococcus capitis urealytic us (0.618 ), Staphylococcus capitis < / span > < / span >
< span > < span class = "co" > #> ureolytic us (0.618 ), Staphylococcus intermedius (0.615), Salmonella < / span > < / span >
< span > < span class = "co" > #> choleraesuis choleraesui s (0.611 ), Staphylococcus sciuri lentus < / span > < / span >
< span > < span class = "co" > #> (0.607), Salmonella Reubeuss (0.605), and Schaalia turicensi s (0.605 )< / 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 pseudo pneumoniae (0.70 0), Serrat ia< / span > < / span >
< span > < span class = "co" > #> proteamaculans quinovora (0.545), Streptococcus ps eudoporcinus (0.536 ),< / span > < / span >
< span > < span class = "co" > #> Staphylococcus pseudintermedius (0.532), Serratia proteamaculans < / span > < / span >
< span > < span class = "co" > #> proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas < / span > < / span >
< span > < span class = "co" > #> paucimobilis (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" > #> "S. pneumoniae" -> Nocardia pneumoniae (B_NOCRD _PNMN, 0.763 )< / span > < / span >
< span > < span class = "co" > #> Also matched: Chlamydia pneumoniae (0.75 0), Streptococcus pneumon iae < / span > < / span >
< span > < span class = "co" > #> (0.750), Klebsiella pneumoniae (0.738), Mycoplasma pn eumoniae (0.738 ),< / span > < / span >
< span > < span class = "co" > #> Chlamydophila pneumoniae (0.708), Mycoplasmoides pneumoniae (0.700), < / span > < / span >
< span > < span class = "co" > #> Streptococcus pseudopneumoniae (0.700), Haemophilus pleuropneumoniae < / span > < / span >
< span > < span class = "co" > #> (0.679), Klebsiella pneumoniae ozaenae (0.672), and Actinobacillus < / span > < / span >
< span > < span class = "co" > #> pleuropneumoniae (0.661) < / 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 >
@ -515,8 +513,8 @@ 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 2,626 'phenotype-based' first isolates (87.6 % within scop e and < / span > < / span >
< span > < span class = "co" > #> 87.5% of total where a microbial ID was available)< / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> => Found 2,637 'phenotype-based' first isolates (87.9 % of total wher e a< / span > < / span >
< span > < span class = "co" > #> microbial ID was available)< / span > < / span > < / code > < / pre > < / div >
< p > So only 88% 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 >
@ -527,11 +525,11 @@ 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 2 626 isolates for analysis. Now our data looks
< p > So we end up with 2 637 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: 2,626 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,637 × < / 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 >
@ -544,7 +542,7 @@ like:</p>
< 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: #949494;" > # ℹ 16 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 27 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< p > Time for the analysis.< / p >
< / div >
< / div >
@ -557,29 +555,29 @@ 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:2626 Length:2626 Min. :2011-01-01 < / span > < / span >
< span > < span class = "co" > #> Class :character Class :character 1st Qu.:2013-04-14 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-05 < / span > < / span >
< span > < span class = "co" > #> Mean :2015-06-15 < / span > < / span >
< span > < span class = "co" > #> Length:2637 Length:2637 Min. :2011-01-01 < / span > < / span >
< span > < span class = "co" > #> Class :character Class :character 1st Qu.:2013-04-13 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-04 < / span > < / span >
< span > < span class = "co" > #> Mean :2015-06-14 < / span > < / span >
< span > < span class = "co" > #> 3rd Qu.:2017-08-23 < / span > < / span >
< span > < span class = "co" > #> Max. :2020-01-01 < / 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 %R :43.2% (n=113 4) %R :36.1 % (n=947 ) < / span > < / span >
< span > < span class = "co" > #> Unique:4 %SI :56.8% (n=1492 ) %SI :63.9 % (n=167 9) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI - %S :41.1% (n=1080 ) - %S :52.7% (n=1383 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS - %I :15.7 % (n=412) - %I :11.3% (n=296 ) < / span > < / span >
< span > < span class = "co" > #> #3 :B_STRPT _PNMN < / span > < / span >
< span > < span class = "co" > #> < NA> :0 %R :43.2% (n=1140 ) %R :35.9 % (n=948 ) < / span > < / span >
< span > < span class = "co" > #> Unique:5 %SI :56.8% (n=1497 ) %SI :64.1 % (n=168 9) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI - %S :41.1% (n=1085 ) - %S :52.7% (n=1391 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS - %I :15.6 % (n=412) - %I :11.3% (n=298 ) < / span > < / span >
< span > < span class = "co" > #> #3 :B_KLBSL _PNMN < / 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" > #> %R :42.0 % (n=1102 ) %R :37.0 % (n=971 ) TRUE:2626 < / span > < / span >
< span > < span class = "co" > #> %SI :58.0 % (n=1524 ) %SI :63.0 % (n=165 5) < / span > < / span >
< span > < span class = "co" > #> - %S :51.9 % (n=1362 ) - %S :59.9 % (n=157 4) < / span > < / span >
< span > < span class = "co" > #> - %I : 6.2 % (n=162) - %I : 3.1% (n=81) < / span > < / span >
< span > < span class = "co" > #> %R :41.9 % (n=1105 ) %R :36.9 % (n=972 ) TRUE:2637 < / span > < / span >
< span > < span class = "co" > #> %SI :58.1 % (n=153 2) %SI :63.1 % (n=166 5) < / span > < / span >
< span > < span class = "co" > #> - %S :52.0 % (n=1370 ) - %S :60.1 % (n=158 4) < / span > < / span >
< span > < span class = "co" > #> - %I : 6.1 % (n=162) - %I : 3.1% (n=81) < / span > < / span >
< span > < span class = "co" > #> < / 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: 2,626 < / span > < / span >
< span > < span class = "co" > #> Rows: 2,637 < / 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", "J8", "M3", "J3", "G6", "P4"…< / 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 >
@ -594,7 +592,7 @@ 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 1808 4 3 3 3 < / span > < / span >
< span > < span class = "co" > #> 260 3 1814 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" >
@ -606,23 +604,25 @@ 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;" > 3< / span > Streptococcus pneumoniae 4 26< / 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;" > 3< / span > Klebsiella pneumoniae 3 26< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Streptococcus pneumoniae 275 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > Nocardia pneumoniae 151< / 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 > 250< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 661< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Streptococcus pneumoniae 399 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 316 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Klebsiella pneumoniae 316 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Streptococcus pneumoniae 267 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > Nocardia pneumoniae 143< / 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 >
@ -634,7 +634,7 @@ 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: 2,626 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,637 × < / 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 >
@ -647,13 +647,13 @@ in:</p>
< 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: #949494;" > # ℹ 16 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 27 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: 2,626 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,637 × < / 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 >
@ -666,11 +666,11 @@ in:</p>
< 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: #949494;" > # ℹ 16 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 27 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: 2,626 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,637 × < / 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 >
@ -683,26 +683,26 @@ in:</p>
< 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: #949494;" > # ℹ 16 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 27 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: 971 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 972 × < / 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;" > 1< / span > J5 A 2017-12-25 B_NOCRD _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;" > 7< / span > S2 A 2013-07-19 B_NOCRD _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: #949494;" > # ℹ 1 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > K5 A 2013-03-15 B_NOCRD _PNMN S S S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 2 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 >
@ -711,12 +711,12 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 471 × < / 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;" > 1< / span > M7 A 2013-07-22 B_NOCRD _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 > I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > N3 A 2014-12-29 B_STRPT _PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > N3 A 2014-12-29 B_NOCRD _PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
@ -730,12 +730,12 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 471 × < / 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;" > 1< / span > M7 A 2013-07-22 B_NOCRD _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 > I7 A 2015-08-19 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > N3 A 2014-12-29 B_STRPT _PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > N3 A 2014-12-29 B_NOCRD _PNMN R R R S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > C5 A 2015-08-30 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
@ -1352,7 +1352,7 @@ 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] 0.4318355 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> [1] 0.4323094 < / 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" >
@ -1364,7 +1364,7 @@ own:</p>
< 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 0.343< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B 0.569< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > C 0.375 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > C 0.378 < / span > < / span > < / code > < / pre > < / div >
< hr >
< p > < em > Author: Dr. < / em > < / p >
< / div >
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