@ -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 = "" > 2.1.0.9001 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.0.9002 < / 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" >
@ -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 20 July 2023.< / p >
generated on 20 October 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" > 2023-07 -20< / td >
< td align = "center" > 2023-1 0-20< / 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" > 2023-07 -20< / td >
< td align = "center" > 2023-1 0-20< / 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" > 2023-07 -20< / td >
< td align = "center" > 2023-1 0-20< / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -515,9 +515,9 @@ 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 2,626 '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 >
< p > So only 88 % is suitable for resistance analysis! We can now filter on
< span > < span class = "co" > #> => Found 2,712 'phenotype-based' first isolates (90.4% of total wher e 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
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" >
@ -527,11 +527,11 @@ 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 2 712 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: 2,712 × < / 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 >
@ -539,12 +539,12 @@ like:</p>
< 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;" > 6< / span > J8 A 2016-06-14 B_ESCHR_COLI R S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > M 3 A 2015-10-25 B_ESCHR_COLI R S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > J3 A 2019 -06-19 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > G6 A 2015 -04 -27 B_STPHY_AURS S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > P4 A 2011 -06-21 B_ESCHR_COLI S S S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 616 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< 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 > J 3 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;" > 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 702 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< p > Time for the analysis.< / p >
< / div >
< / div >
@ -557,44 +557,44 @@ 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" > #> 3rd Qu.:2017-08-23 < / span > < / span >
< span > < span class = "co" > #> Max. :2020-01-01 < / span > < / span >
< span > < span class = "co" > #> Length:2712 Length:2712 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" > #> 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 %R :43.2 % (n=1134 ) %R :36.1% (n=94 7) < / span > < / span >
< span > < span class = "co" > #> Unique:4 %SI :56.8 % (n=1492 ) %SI :63.9% (n=1679 ) < / 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" > #> < NA> :0 %R :42.9 % (n=116 3) %R :36.1% (n=978 ) < / span > < / span >
< span > < span class = "co" > #> Unique:4 %SI :57.1 % (n=15 49) %SI :63.9% (n=1734 ) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI - %S :41.0 % (n=1112 ) - %S :52.0 % (n=1409 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS - %I :16.1 % (n=437 ) - %I :12.0 % (n=325 ) < / span > < / span >
< span > < span class = "co" > #> #3 :B_STRPT_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=97 1) TRUE:2626 < / span > < / span >
< span > < span class = "co" > #> %SI :58.0% (n=152 4) %SI :63.0 % (n=1655 ) < / span > < / span >
< span > < span class = "co" > #> - %S :51.9 % (n=1362 ) - %S :59.9 % (n=1574 ) < / span > < / span >
< span > < span class = "co" > #> - %I : 6.2 % (n=162 ) - %I : 3.1% (n=81 ) < / span > < / span >
< span > < span class = "co" > #> %R :42.0% (n=1138 ) %R :37.3 % (n=101 1) TRUE:2712 < / span > < / span >
< span > < span class = "co" > #> %SI :58.0% (n=157 4) %SI :62.7 % (n=1701 ) < / span > < / span >
< span > < span class = "co" > #> - %S :51.5 % (n=139 6) - %S :59.6 % (n=1616 ) < / span > < / span >
< span > < span class = "co" > #> - %I : 6.6 % (n=178 ) - %I : 3.1% (n=85 ) < / 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: 2,712 < / 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" > #> $ 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 >
< span > < span class = "co" > #> $ date < span style = "color: #949494; font-style: italic;" > < date> < / span > 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31…< / span > < / span >
< span > < span class = "co" > #> $ bacteria < span style = "color: #949494; font-style: italic;" > < mo> < / span > "B_ESCHR_COLI", "B_KLBSL_PNMN", "B_ESCHR_COLI", "B_ESCHR_COL…< / span > < / span >
< span > < span class = "co" > #> $ AMX < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, R, R, R, S, S, S, S, R, S, S, R, R, R, R, I , S ,…< / span > < / span >
< span > < span class = "co" > #> $ AMC < span style = "color: #949494; font-style: italic;" > < sir> < / span > I, I, I, S, S, S, S, S, S, S, S, S, S , S, S, S, S, R, S, R ,…< / span > < / span >
< span > < span class = "co" > #> $ AMX < span style = "color: #949494; font-style: italic;" > < sir> < / span > R, R, S, S, R, R, S, S, S, S, R, S, S, S, R, R, R, R, S , R ,…< / span > < / span >
< span > < span class = "co" > #> $ AMC < span style = "color: #949494; font-style: italic;" > < sir> < / span > I, I, I, S, S, S, S, S, S, S, S, S, I , S, S, S, S, R, S, S ,…< / span > < / span >
< span > < span class = "co" > #> $ CIP < span style = "color: #949494; font-style: italic;" > < sir> < / span > S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,…< / span > < / span >
< span > < span class = "co" > #> $ GEN < span style = "color: #949494; font-style: italic;" > < sir> < / span > S, S, S, S, S, S, S, S, S, S, S , R , S, S, S, S, S, S, S, S,…< / span > < / span >
< span > < span class = "co" > #> $ GEN < span style = "color: #949494; font-style: italic;" > < sir> < / span > S, S, S, S, S, S, S, S, S, S, R , S , S, S, S, S, S, S, S, S,…< / span > < / span >
< span > < span class = "co" > #> $ first < span style = "color: #949494; font-style: italic;" > < lgl> < / span > TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…< / span > < / span >
< span > < / span >
< 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 1852 4 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" >
@ -619,10 +619,10 @@ microorganisms:</p>
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 4 × < / 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;" > 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;" > 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 >
< / 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: 2,712 × < / 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 >
@ -642,18 +642,18 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > 2015-12-10 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > 2015-03-02 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 2018-03-31 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2016-06-14 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2015-10-25 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2019 -06-19 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2015 -04 -27 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2011 -06-21 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 616 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 6< / span > 2015-10-25 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > 2019-06-19 S < / span > < / span >
< 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 702 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: 2,712 × < / 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 >
@ -662,15 +662,15 @@ in:</p>
< 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;" > 6< / span > B_ESCHR_COLI R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI R S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_ESCHR_COLI S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_STPHY_AURS S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 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;" > 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 616 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 702 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: 2,712 × < / 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 >
@ -679,17 +679,17 @@ in:</p>
< 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;" > 6< / span > B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 7< / span > B_ESCHR_COLI R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > B_ESCHR_COLI S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > B_STPHY_AURS S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 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;" > 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 616 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 702 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: 97 1 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 1,01 1 × < / 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 >
@ -702,45 +702,45 @@ in:</p>
< 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 96 1 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 1,00 1 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: 471 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 483 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 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;" > 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 -08-3 0 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > W9 A 2013-10 -02 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 61 more rows< / span > < / 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 -03-2 0 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 >
< 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: 471 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 483 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 B_STRPT_PNMN R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > R10 A 2013-12-20 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > R7 A 2015-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > R8 A 2019-10-25 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 5< / span > 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;" > 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 -08-3 0 B_KLBSL_PNMN R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > W9 A 2013-10 -02 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 61 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< 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 -03-2 0 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 >
< / div >
< div class = "section level3" >
< h3 id = "generate-antibiograms" > Generate antibiograms< a class = "anchor" aria-label = "anchor" href = "#generate-antibiograms" > < / a >
@ -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] 0.4288348 < / 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" >
@ -1362,9 +1362,9 @@ 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 0.343 < / span > < / span >
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< 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;" > 1< / span > A 0.342 < / span > < / span >
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< hr >
< p > < em > Author: Dr. < / em > < / p >
< / div >
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