@@ -30,7 +30,7 @@
< 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 = "" > 3.0.1.9026 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 3.0.1.9030 < / 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" >
@@ -91,7 +91,7 @@
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 06 March 2026.< / p >
generated on 07 March 2026.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2026-03-06 < / td >
< td align = "center" > 2026-03-07 < / 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" > 2026-03-06 < / td >
< td align = "center" > 2026-03-07 < / 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" > 2026-03-06 < / td >
< td align = "center" > 2026-03-07 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@@ -407,7 +407,7 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; font-weight: bold;" > patient_id< / span > < span style = "color: #0000BB;" > ' as input for < / span > < span style = "color: #0000BB; background-color: #444444;" > `col_patient_id`< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BB0000;" > ℹ < / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #BB0000;" > #> of 2< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BBBBBB;" > => Found < / span > < span style = "color: #BBBBBB; font-weight: bold;" > 2,730 'phenotype-based' first isolates< / span > < span style = "color: #BBBBBB;" > (91.0 % of total where a< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BBBBBB;" > => Found < / span > < span style = "color: #BBBBBB; font-weight: bold;" > 2,724 'phenotype-based' first isolates< / span > < span style = "color: #BBBBBB;" > (90.8 % of total where a< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #BBBBBB;" > #> microbial ID was available)< / span > < / span > < / span > < / code > < / pre > < / div >
< p > So only 91% is suitable for resistance analysis! We can now filter on
it with the < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter()< / a > < / code > function, also from the
@@ -419,11 +419,11 @@ 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 2 730 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: 2,730 × < / 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 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
@@ -436,7 +436,7 @@ like:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > J3 A 2019-06-19 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > G6 A 2015-04-27 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > P4 A 2011-06-21 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 20 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 >
@@ -449,29 +449,29 @@ 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:2730 Length:2730 Min. :2011-01-01 < / span > < / span >
< span > < span class = "co" > #> Class :character Class :character 1st Qu.:2013-04-06 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-04 < / 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.:2013-04-07 < / span > < / span >
< span > < span class = "co" > #> Mode :character Mode :character Median :2015-06-03 < / span > < / span >
< span > < span class = "co" > #> Mean :2015-06-09 < / span > < / span >
< span > < span class = "co" > #> 3rd Qu.:2017-08-14 < / span > < / span >
< span > < span class = "co" > #> 3rd Qu.:2017-08-11 < / 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 :40.1 % (n=1071 ) %S :51.1 % (n=1354 ) < / span > < / span >
< span > < span class = "co" > #> < NA> :0 %S :41.6 % (n=1133 ) %S :52.6 % (n=1432 ) < / 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 :17.0 % (n=453 ) %I :12.7 % (n=335 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS %R :42.9 % (n=1147 ) %R :36 .2% (n=959) < / span > < / span >
< span > < span class = "co" > #> #1 :B_ESCHR_COLI %I :16.4 % (n=446 ) %I :12.2 % (n=333 ) < / span > < / span >
< span > < span class = "co" > #> #2 :B_STPHY_AURS %R :42.0 % (n=1145 ) %R :35 .2% (n=959) < / 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 :52.2 % (n=1426 ) %S :60.7 % (n=165 6) TRUE:2730 < / span > < / span >
< span > < span class = "co" > #> %S :52.5 % (n=1431 ) %S :61.0 % (n=1661 ) 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 : 6.5% (n=178 ) %I : 3.0% (n=83 ) < / span > < / span >
< span > < span class = "co" > #> %R :41.2 % (n=1126 ) %R :36.3 % (n=99 1) < / span > < / span >
< span > < span class = "co" > #> %I : 6.5% (n=176 ) %I : 3.0% (n=82 ) < / span > < / span >
< span > < span class = "co" > #> %R :41.0 % (n=1117 ) %R :36.0 % (n=98 1) < / 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: 2,730 < / 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"< span style = "color: #949494;" > , < / span > "R7"< span style = "color: #949494;" > , < / span > "P3"< span style = "color: #949494;" > , < / span > "P10"< span style = "color: #949494;" > , < / span > "B7"< span style = "color: #949494;" > , < / span > "W3"< span style = "color: #949494;" > , < / span > "M3"< span style = "color: #949494;" > , < / span > "J3"< span style = "color: #949494;" > , < / span > "G6"< span style = "color: #949494;" > , < / span > "P4"…< / span > < / span >
< span > < span class = "co" > #> $ hospital < span style = "color: #949494; font-style: italic;" > < chr> < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > , < / span > "A"< span style = "color: #949494;" > ,< / span > …< / span > < / span >
@@ -486,7 +486,7 @@ 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 1854 4 4 4 3 < / span > < / span >
< span > < span class = "co" > #> 260 3 1854 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" >
@@ -511,9 +511,9 @@ 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 > 326 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 684 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Streptococcus pneumoniae 401 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > Escherichia coli < span style = "text-decoration: underline;" > 1< / span > 321 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > Staphylococcus aureus 682 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > Streptococcus pneumoniae 402 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 319< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level3" >
@@ -526,7 +526,7 @@ 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/antimicrobial_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #444444;" > `aminoglycosides()`< / span > < span style = "color: #0000BB;" > using column '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,730 × < / 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 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
@@ -539,13 +539,13 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2019-06-19 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2015-04-27 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2011-06-21 < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 20 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/antimicrobial_selectors.html" > betalactams< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #444444;" > `betalactams()`< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,730 × < / 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 > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < / span > < / span >
@@ -558,11 +558,11 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 20 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: 2,730 × < / 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 > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FFD787;" > I < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
@@ -575,13 +575,13 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 20 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/antimicrobial_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" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #444444;" > `aminoglycosides()`< / span > < span style = "color: #0000BB;" > using column '< / span > < span style = "color: #0000BB; font-weight: bold;" > GEN< / span > < span style = "color: #0000BB;" > ' (gentamicin)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 99 1 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 98 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 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
@@ -594,13 +594,13 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > P5 A 2019-03-09 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > Q8 A 2019-08-10 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > K5 A 2013-03-15 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 8 1 more rows< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 7 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/antimicrobial_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" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #444444;" > `betalactams()`< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 461 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 462 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
@@ -613,13 +613,13 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > 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: #949494;" > # ℹ 2 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/antimicrobial_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" > #> < span style = "color: #0000BB;" > ℹ < / span > < span style = "color: #0000BB; background-color: #444444;" > `betalactams()`< / span > < span style = "color: #0000BB;" > using columns '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMX< / span > < span style = "color: #0000BB;" > ' (amoxicillin) and '< / span > < span style = "color: #0000BB; font-weight: bold;" > AMC< / span > < span style = "color: #0000BB;" > '< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> (amoxicillin/clavulanic acid)< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 461 × < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 462 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < date> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < sir> < / span > < span style = "color: #949494; font-style: italic;" > < lgl> < / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > M7 A 2013-07-22 < span style = "color: #949494;" > B_< / span > STRPT< span style = "color: #949494;" > _< / span > PNMN < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
@@ -632,7 +632,7 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 < span style = "color: #949494;" > B_< / span > ESCHR< span style = "color: #949494;" > _< / span > COLI < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 < span style = "color: #949494;" > B_< / span > STPHY< span style = "color: #949494;" > _< / span > AURS < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #FF5F5F;" > R < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > < span style = "color: #080808; background-color: #5FD7AF;" > S < / span > TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 1 more rows< / span > < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ 2 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 >
@@ -1289,7 +1289,7 @@ own:</p>
< span > < span class = "co" > < span style = "color: #0000BB;" > #> category susceptible. Set the < / span > < span style = "color: #0000BB; background-color: #444444;" > `guideline`< / span > < span style = "color: #0000BB;" > argument or the < / span > < span style = "color: #0000BB; background-color: #444444;" > `AMR_guideline`< / span > < / span > < / span >
< span > < span class = "co" > < span style = "color: #0000BB;" > #> option to either "CLSI" or "EUCAST", see < / span > < span style = "color: #0000BB; background-color: #444444;" > `?AMR-options`< / span > < span style = "color: #0000BB;" > .< / span > < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #0000BB;" > ℹ < / span > < / span > < / span >
< span > < span class = "co" > #> [1] 0.4294272 < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> [1] 0.4203377 < / 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 = "cb24" > < pre class = "downlit sourceCode r" >
@@ -1299,8 +1299,8 @@ 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 0.341 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B 0.586 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 1< / span > A 0.340 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 2< / span > B 0.551 < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 3< / span > C 0.370< / span > < / span > < / code > < / pre > < / div >
< / div >
< div class = "section level3" >
github-actions