@ -29,7 +29,7 @@
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9112 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9116 < / 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" >
@ -87,7 +87,7 @@
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 09 December 2024.< / p >
generated on 13 December 2024.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2024-12-09 < / td >
< td align = "center" > 2024-12-13 < / 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" > 2024-12-09 < / td >
< td align = "center" > 2024-12-13 < / 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" > 2024-12-09 < / td >
< td align = "center" > 2024-12-13 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -690,9 +690,26 @@ previously mentioned antibiotic class selectors:</p>
< div class = "sourceCode" id = "cb16" > < 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 For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> ℹ The function aminoglycosides() should be used inside a dplyr verb or < / span > < / span >
< span > < span class = "co" > #> data.frame call, e.g.: < / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(column_a, column_b, aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % filter(any(aminoglycosides() == "R"))< / span > < / span >
< span > < span class = "co" > #> • your_data[, aminoglycosides()]< / span > < / span >
< span > < span class = "co" > #> • your_data[, c("column_a", "column_b", aminoglycosides())]< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Now returning a vector of all possible antimicrobials that< / span > < / span >
< span > < span class = "co" > #> aminoglycosides() can select.< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> data.frame call, e.g.:< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(carbapenems())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(column_a, column_b, carbapenems())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % filter(any(carbapenems() == "R"))< / span > < / span >
< span > < span class = "co" > #> • your_data[, carbapenems()]< / span > < / span >
< span > < span class = "co" > #> • your_data[, c("column_a", "column_b", carbapenems())]< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Now returning a vector of all possible antimicrobials that carbapenems()< / span > < / span >
< span > < span class = "co" > #> can select.< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "16%" >
@ -820,8 +837,16 @@ language to be Spanish using the <code>language</code> argument:</p>
< 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 >
< span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > ,< / span >
< span > language < span class = "op" > =< / span > < span class = "st" > "es"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)< / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> ℹ The function aminoglycosides() should be used inside a dplyr verb or < / span > < / span >
< span > < span class = "co" > #> data.frame call, e.g.:< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(column_a, column_b, aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % filter(any(aminoglycosides() == "R"))< / span > < / span >
< span > < span class = "co" > #> • your_data[, aminoglycosides()]< / span > < / span >
< span > < span class = "co" > #> • your_data[, c("column_a", "column_b", aminoglycosides())]< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Now returning a vector of all possible antimicrobials that< / span > < / span >
< span > < span class = "co" > #> aminoglycosides() can select.< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "20%" >
@ -944,9 +969,26 @@ argument must be used. This can be any column in the data, or e.g.
< 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 >
< span > < span class = "co" > #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' < / span > < / span >
< span > < span class = "co" > #> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) < / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span > < / code > < / pre > < / div >
< span > < span class = "co" > #> ℹ The function aminoglycosides() should be used inside a dplyr verb or < / span > < / span >
< span > < span class = "co" > #> data.frame call, e.g.: < / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(column_a, column_b, aminoglycosides())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % filter(any(aminoglycosides() == "R"))< / span > < / span >
< span > < span class = "co" > #> • your_data[, aminoglycosides()]< / span > < / span >
< span > < span class = "co" > #> • your_data[, c("column_a", "column_b", aminoglycosides())]< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Now returning a vector of all possible antimicrobials that< / span > < / span >
< span > < span class = "co" > #> aminoglycosides() can select.< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> data.frame call, e.g.:< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(carbapenems())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % select(column_a, column_b, carbapenems())< / span > < / span >
< span > < span class = "co" > #> • your_data %> % filter(any(carbapenems() == "R"))< / span > < / span >
< span > < span class = "co" > #> • your_data[, carbapenems()]< / span > < / span >
< span > < span class = "co" > #> • your_data[, c("column_a", "column_b", carbapenems())]< / span > < / span >
< span > < span class = "co" > #> < / span > < / span >
< span > < span class = "co" > #> Now returning a vector of all possible antimicrobials that carbapenems()< / span > < / span >
< span > < span class = "co" > #> can select.< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "13%" >
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