@ -39,7 +39,7 @@
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9029 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9031 < / 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" >
@ -205,7 +205,7 @@
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 1 2 May 2024.< / p >
generated on 20 May 2024.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -261,21 +261,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2024-05-1 2< / td >
< td align = "center" > 2024-05-20 < / 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" > 2024-05-1 2< / td >
< td align = "center" > 2024-05-20 < / 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" > 2024-05-1 2< / td >
< td align = "center" > 2024-05-20 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -318,8 +318,9 @@ have extracted from their laboratory systems:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > M3 A 2015-10-25 E. coli R S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > J3 A 2019-06-19 E. coli S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > G6 A 2015-04-27 S. aureus S S S S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb3" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < / span >
< span > < span class = "co" > # we will use 'our_data' as the data set name for this tutorial< / span > < / span >
< span > < span class = "va" > our_data< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates_unclean< / span > < / span > < / code > < / pre > < / div >
< p > For AMR data analysis, we would like the microorganism column to
@ -336,17 +337,20 @@ included data were retrieved on 11 Dec 2022.</p>
< p > The codes of the AMR packages that come from < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > are
short, but still human readable. More importantly, < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code >
supports all kinds of input:< / p >
< div class = "sourceCode" id = "cb3 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb4 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Klebsiella pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Class 'mo'< / span > < / span >
< 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" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] B_KLBSL_PNMN< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb5 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Class 'mo'< / span > < / span >
< 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" > "KLEPNE"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] B_KLBSL_PNMN< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "KLEPNE"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Class 'mo'< / span > < / span >
< 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" > #> [1] B_KLBSL_PNMN< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb7" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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_KLBSL_PNMN< / span > < / span > < / code > < / pre > < / div >
< p > The first character in above codes denote their taxonomic kingdom,
@ -356,33 +360,38 @@ retrieve taxonomic properties, such as the name, genus, species, family,
order, and even Gram-stain. They all start with < code > mo_< / code > and
they use < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > internally, so that still any arbitrary
user input can be used:< / p >
< div class = "sourceCode" id = "cb4 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb8 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_family< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] "Enterobacteriaceae"< / span > < / span >
< span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > < span class = "op " > ( < / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] "Klebsiella"< / span > < / span >
< span > < span class = "fu " > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > ) < / span > < / span >
< span > < span class = "co" > #> [1] "pneumoniae"< / span > < / span >
< span > < / span >
< span > < span class = "co" > #> [1] "Enterobacteriaceae"< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb9 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co " > #> [1] "Klebsiella"< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb10" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / > < / span >
< span > < span class = "co" > #> [1] "pneumoniae"< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb11" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < / span >
< span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_gramstain< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Klebsiella pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] "Gram-negative"< / span > < / span >
< span > < / span >
< span > < span class = "co" > #> [1] "Gram-negative"< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb12" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < / span >
< span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_ref< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] "Trevisan, 1887"< / span > < / span >
< span > < / span >
< span > < span class = "co" > #> [1] "Trevisan, 1887"< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb13" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < / span >
< span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_snomed< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "K. pneumoniae"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [[1]]< / span > < / span >
< span > < span class = "co" > #> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" < / span > < / span >
< span > < span class = "co" > #> [5] "56415008" "714315002" "713926009"< / span > < / span > < / code > < / pre > < / div >
< p > Now we can thus clean our data:< / p >
< div class = "sourceCode" id = "cb5 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb14 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data< / span > < span class = "op" > $< / span > < span class = "va" > bacteria< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data< / span > < span class = "op" > $< / span > < span class = "va" > bacteria< / span > , info < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> mo_uncertainties() to review these uncertainties, or use< / span > < / span >
< span > < span class = "co" > #> add_custom_microorganisms() to add custom entries.< / span > < / span > < / code > < / pre > < / div >
< p > Apparently, there was some uncertainty about the translation to
taxonomic codes. Let’ < / p >
< div class = "sourceCode" id = "cb6 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb15 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/as.mo.html" > mo_uncertainties< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> Matching scores are based on the resemblance between the input and the full< / span > < / span >
< span > < span class = "co" > #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.< / span > < / span >
@ -439,7 +448,7 @@ diffusion values, read more about that on the <code><a href="../reference/as.sir
page.< / p >
< p > For now, we will just clean the SIR columns in our data using
dplyr:< / p >
< div class = "sourceCode" id = "cb7 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb16 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # method 1, be explicit about the columns:< / span > < / span >
< span > < span class = "va" > our_data< / span > < span class = "op" > < -< / span > < span class = "va" > our_data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > < span class = "op" > :< / span > < span class = "va" > GEN< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span >
@ -507,7 +516,7 @@ analysis, but the default phenotype-based method is in any case the
method to properly correct for most duplicate isolates. Read more about
the methods on the < code > < a href = "../reference/first_isolate.html" > first_isolate()< / a > < / code > page.< / p >
< p > The outcome of the function can easily be added to our data:< / p >
< div class = "sourceCode" id = "cb8 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb17 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data< / span > < span class = "op" > < -< / span > < span class = "va" > our_data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > first < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/first_isolate.html" > first_isolate< / a > < / span > < span class = "op" > (< / span > info < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
@ -521,16 +530,16 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
< 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" >
< div class = "sourceCode" id = "cb18 " > < 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 = "https://dplyr.tidyverse.org/reference/filter.html" class = "external-link" > filter< / a > < / span > < span class = "op" > (< / span > < span class = "va" > first< / span > < span class = "op" > ==< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > For future use, the above two syntaxes can be shortened:< / p >
< div class = "sourceCode" id = "cb10 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb19 " > < 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 2 712 isolates for analysis. Now our data looks
like:< / p >
< div class = "sourceCode" id = "cb11 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb20 " > < 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: 2,712 × < / span > < / span > < / span >
< span > < span class = "co" > #> patient_id hospital date bacteria AMX AMC CIP GEN first< / span > < / span >
@ -555,7 +564,7 @@ like:</p>
< p > The base R < code > < a href = "https://rdrr.io/r/base/summary.html" class = "external-link" > summary()< / a > < / code > function gives a good first
impression, as it comes with support for the new < code > mo< / code > and
< code > sir< / code > classes that we now have in our data set:< / p >
< div class = "sourceCode" id = "cb1 2" > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb21 " > < 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:2712 Length:2712 Min. :2011-01-01 < / span > < / span >
@ -577,8 +586,9 @@ impression, as it comes with support for the new <code>mo</code> and
< span > < span class = "co" > #> %SI :58.0% (n=1574) %SI :62.7% (n=1701) < / span > < / span >
< span > < span class = "co" > #> - %S :51.5% (n=1396) - %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 = "co" > #> < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb22" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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: 2,712< / span > < / span >
< span > < span class = "co" > #> Columns: 9< / span > < / span >
@ -590,8 +600,9 @@ impression, as it comes with support for the new <code>mo</code> and
< 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, 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" > #> $ first < span style = "color: #949494; font-style: italic;" > < lgl> < / span > TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb23" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -604,7 +615,7 @@ impression, as it comes with support for the new <code>mo</code> and
< p > To just get an idea how the species are distributed, create a
frequency table with < code > < a href = "../reference/count.html" > count()< / a > < / code > based on the name of the
microorganisms:< / p >
< div class = "sourceCode" id = "cb13 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb24 " > < 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 >
@ -613,8 +624,9 @@ microorganisms:</p>
< 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 426< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 326< / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 4< / span > Klebsiella pneumoniae 326< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb25" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -631,7 +643,7 @@ microorganisms:</p>
< p > Using so-called antibiotic class selectors, you can select or filter
columns based on the antibiotic class that your antibiotic results are
in:< / p >
< div class = "sourceCode" id = "cb14 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb26 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/select.html" class = "external-link" > select< / a > < / span > < span class = "op" > (< / span > < span class = "va" > date< / span > , < span class = "fu" > < a href = "../reference/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 >
@ -648,8 +660,9 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > 2015-04-27 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > 2011-06-21 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > 2014-09-05 S < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb27" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -667,8 +680,9 @@ in:</p>
< 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 < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb28" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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: 2,712 × < / span > < / span > < / span >
@ -684,8 +698,9 @@ in:</p>
< 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 < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb29" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -703,8 +718,9 @@ 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 < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb30" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -722,8 +738,9 @@ in:</p>
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 8< / span > Q2 A 2019-09-22 B_ESCHR_COLI R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 9< / span > X7 A 2011-03-20 B_ESCHR_COLI R R S R TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #BCBCBC;" > 10< / span > V1 A 2018-08-07 B_STPHY_AURS R R S S TRUE < / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span >
< span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # ℹ < / span > < / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb31" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < 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 >
@ -776,7 +793,7 @@ failure</li>
function to create any of the above antibiogram types. For starters,
this is what the included < code > example_isolates< / code > data set looks
like:< / p >
< div class = "sourceCode" id = "cb15 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb32 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > example_isolates< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 2,000 × < / span > < / span > < / span >
< span > < span class = "co" > #> date patient age gender ward mo PEN OXA FLC AMX < / span > < / span >
@ -805,7 +822,7 @@ like:</p>
should be used. The < code > antibiotics< / code > argument in the
< code > < a href = "../reference/antibiogram.html" > antibiogram()< / a > < / code > function supports any (combination) of the
previously mentioned antibiotic class selectors:< / p >
< div class = "sourceCode" id = "cb16 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb33 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "../reference/antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
@ -932,7 +949,7 @@ Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian,
Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish,
Swedish, Turkish, or Ukrainian. In this next example, we force the
language to be Spanish using the < code > language< / code > argument:< / p >
< div class = "sourceCode" id = "cb17 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb34 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span >
< span > antibiotics < 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 >
@ -978,7 +995,7 @@ language to be Spanish using the <code>language</code> argument:</p>
< / h4 >
< p > To create a combined antibiogram, use antibiotic codes or names with
a plus < code > +< / code > character like this:< / p >
< div class = "sourceCode" id = "cb18 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb35 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > , < span class = "st" > "TZP+GEN"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
@ -1060,7 +1077,7 @@ a plus <code>+</code> character like this:</p>
< p > To create a syndromic antibiogram, the < code > syndromic_group< / code >
argument must be used. This can be any column in the data, or e.g.
< code > < a href = "https://rdrr.io/r/base/ifelse.html" class = "external-link" > ifelse()< / a > < / code > with calculations based on certain columns:< / p >
< div class = "sourceCode" id = "cb19 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb36 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/antibiotic_class_selectors.html" > aminoglycosides< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > , < span class = "fu" > < a href = "../reference/antibiotic_class_selectors.html" > carbapenems< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "ward"< / span > < span class = "op" > )< / span > < / span >
@ -1254,7 +1271,7 @@ Antibiogram) in which cases are predefined based on clinical or
demographic characteristics (e.g., endocarditis in 75+ females). This
next example is a simplification without clinical characteristics, but
just gives an idea of how a WISCA can be created:< / p >
< div class = "sourceCode" id = "cb20 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb37 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > wisca< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > example_isolates< / span > ,< / span >
< span > antibiotics < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "AMC"< / span > , < span class = "st" > "AMC+CIP"< / span > , < span class = "st" > "TZP"< / span > , < span class = "st" > "TZP+TOB"< / span > < span class = "op" > )< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > ,< / span >
@ -1322,7 +1339,7 @@ just gives an idea of how a WISCA can be created:</p>
< p > Antibiograms can be plotted using < code > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > autoplot()< / a > < / code > from the
< code > ggplot2< / code > packages, since this < code > AMR< / code > package
provides an extension to that function:< / p >
< div class = "sourceCode" id = "cb21 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb38 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "fu" > < a href = "https://ggplot2.tidyverse.org/reference/autoplot.html" class = "external-link" > autoplot< / a > < / span > < span class = "op" > (< / span > < span class = "va" > wisca< / span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< p > < img src = "AMR_files/figure-html/unnamed-chunk-10-1.png" width = "720" > < / p >
< p > To calculate antimicrobial resistance in a more sensible way, also by
@ -1351,12 +1368,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
I (< code > < a href = "../reference/proportion.html" > proportion_SI()< / a > < / code > , equal to
< code > < a href = "../reference/proportion.html" > susceptibility()< / a > < / code > ). These functions can be used on their
own:< / p >
< div class = "sourceCode" id = "cb22 " > < pre class = "downlit sourceCode r" >
< div class = "sourceCode" id = "cb39 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "../reference/proportion.html" > resistance< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMX< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> [1] 0.4288348< / span > < / span > < / code > < / pre > < / div >
< 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" >
< div class = "sourceCode" id = "cb40 " > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" class = "external-link" > group_by< / a > < / span > < span class = "op" > (< / span > < span class = "va" > hospital< / span > < span class = "op" > )< / 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/summarise.html" class = "external-link" > summarise< / a > < / span > < span class = "op" > (< / span > amoxicillin < span class = "op" > =< / 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 class = "op" > )< / span > < / span >
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