@ -38,7 +38,7 @@
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 1.8.2.9147 < / small >
< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 1.8.2.9148 < / 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" >
@ -187,7 +187,7 @@
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 26 February 2023.< / p >
generated on 11 March 2023.< / p >
< div class = "section level2" >
< h2 id = "introduction" > Introduction< a class = "anchor" aria-label = "anchor" href = "#introduction" > < / a >
< / h2 >
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2023-02-26 < / td >
< td align = "center" > 2023-03-11 < / td >
< td align = "center" > abcd< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2023-02-26 < / td >
< td align = "center" > 2023-03-11 < / td >
< td align = "center" > abcd< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2023-02-26 < / td >
< td align = "center" > 2023-03-11 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -427,11 +427,11 @@ page.</p>
dplyr:< / p >
< div class = "sourceCode" id = "cb7" > < 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 = "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 >
< span > < / span >
< span > < span class = "co" > # method 2, let the AMR package determine the eligible 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 = "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_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is_sir_eligible< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # result:< / span > < / span >
@ -592,7 +592,7 @@ impression, as it comes with support for the new <code>mo</code> and
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" >
< 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 >
< code class = "sourceCode R" > < span > < span class = "va" > our_data< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "../reference/count.html" > count< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > < span class = "op" > )< / span > , sort < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 4 × < / span > < / span > < / span >
< span > < span class = "co" > #> `mo_name(bacteria)` n< / span > < / span >
@ -602,7 +602,7 @@ microorganisms:</p>
< 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 = "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 = "va" > our_data_1st< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span >
< span > < span class = "fu" > < a href = "../reference/count.html" > count< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > bacteria< / span > < span class = "op" > )< / span > , sort < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> < span style = "color: #949494;" > # A tibble: 4 × < / span > < / span > < / span >
< span > < span class = "co" > #> `mo_name(bacteria)` n< / span > < / span >
@ -788,7 +788,8 @@ antibiograms:</p>
< / table >
< 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" > our_data_1st< / span > ,< / span >
< span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > < spanclass = "op" > )< / span > < / span > < / code > < / pre > < / div >
< span > ab_transform < span class = "op" > =< / span > < span class = "st" > "name"< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "28%" >
@ -841,8 +842,9 @@ antibiograms:</p>
< / table >
< div class = "sourceCode" id = "cb17" > < 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" > our_data_1st< / 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 > < spanclass = "op" > )< / span > < span class = "co" > # support for 20 languages< / span > < / span > < / code > < / pre > < / div >
< 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 >
< span > < span class = "op" > )< / span > < span class = "co" > # support for 20 languages< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< colgroup >
< col width = "27%" >
@ -896,7 +898,8 @@ antibiograms:</p>
< div class = "sourceCode" id = "cb18" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # combined:< / span > < / span >
< span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / 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" > "AMC+GEN"< / span > < span class = "op" > )< / span > < spanclass = "op" > )< / span > < / span > < / code > < / pre > < / div >
< 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" > "AMC+GEN"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > Pathogen (N min-max)< / th >
@ -938,12 +941,14 @@ antibiograms:</p>
< div class = "sourceCode" id = "cb19" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # for a syndromic antibiogram, we must fake some clinical conditions:< / span > < / span >
< span > < span class = "va" > our_data_1st< / span > < span class = "op" > $< / span > < span class = "va" > condition< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" class = "external-link" > sample< / a > < / span > < 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" > "Cardial"< / span > , < span class = "st" > "Respiratory"< / span > , < span class = "st" > "Rheumatic"< / span > < span class = "op" > )< / span > ,< / span >
< span > size < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/nrow.html" class = "external-link" > nrow< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > < span class = "op" > )< / span > ,< / span >
< span > replace < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span >
< span > size < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/nrow.html" class = "external-link" > nrow< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > < span class = "op" > )< / span > ,< / span >
< span > replace < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < / span >
< span > < span class = "op" > )< / span > < / span >
< span > < / span >
< span > < span class = "co" > # syndromic:< / span > < / span >
< span > < span class = "fu" > < a href = "../reference/antibiogram.html" > antibiogram< / a > < / span > < span class = "op" > (< / span > < span class = "va" > our_data_1st< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > < spanclass = "op" > )< / span > < / span > < / code > < / pre > < / div >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > < / span >
< span > < span class = "op" > )< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "left" > Syndromic Group< / th >
@ -957,119 +962,120 @@ antibiograms:</p>
< tr class = "odd" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > E. coli< / em > (43 1-43 1)< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 54 < / td >
< td align = "right" > 57 < / td >
< td align = "right" > 63 < / td >
< em > E. coli< / em > (40 1-40 1)< / td >
< td align = "right" > 67 < / td >
< td align = "right" > 61 < / td >
< td align = "right" > 59 < / td >
< td align = "right" > 65 < / td >
< / tr >
< tr class = "even" >
< td align = "left" > Respiratory< / td >
< td align = "left" >
< em > E. coli< / em > (396-396 )< / td >
< td align = "right" > 64 < / td >
< td align = "right" > 61 < / td >
< td align = "right" > 58 < / td >
< td align = "right" > 63 < / td >
< em > E. coli< / em > (403-403 )< / td >
< td align = "right" > 60 < / td >
< td align = "right" > 55 < / td >
< td align = "right" > 54 < / td >
< td align = "right" > 59 < / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Rheumatic< / td >
< td align = "left" >
< em > E. coli< / em > (423-423 )< / td >
< em > E. coli< / em > (446-446 )< / td >
< td align = "right" > 65< / td >
< td align = "right" > 59< / td >
< td align = "right" > 60< / td >
< td align = "right" > 58 < / td >
< td align = "right" > 63< / td >
< td align = "right" > 64 < / td >
< / tr >
< tr class = "even" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > K. pneumoniae< / em > (105-105 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 54< / td >
< td align = "right" > 59< / td >
< em > K. pneumoniae< / em > (99-99 )< / td >
< td align = "right" > 65 < / td >
< td align = "right" > 61< / td >
< td align = "right" > 60< / td >
< td align = "right" > 59< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Respiratory< / td >
< td align = "left" >
< em > K. pneumoniae< / em > (110-110)< / td >
< td align = "right" > 62< / td >
< td align = "right" > 49< / td >
< td align = "right" > 56< / td >
< td align = "right" > 60< / td >
< td align = "right" > 54< / td >
< td align = "right" > 55< / td >
< td align = "right" > 63< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Rheumatic< / td >
< td align = "left" >
< em > K. pneumoniae< / em > (101 -101 )< / td >
< td align = "right" > 66 < / td >
< td align = "right" > 50 < / td >
< em > K. pneumoniae< / em > (107 -107 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 49 < / td >
< td align = "right" > 61< / td >
< td align = "right" > 62< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > S. aureus< / em > (235-235)< / td >
< td align = "right" > 64< / td >
< td align = "right" > 55< / td >
< td align = "right" > 61< / td >
< td align = "right" > 57< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Respiratory< / td >
< td align = "left" >
< em > S. aureus< / em > (208-208)< / td >
< td align = "right" > 62< / td >
< td align = "right" > 61< / td >
< td align = "right" > 57< / td >
< td align = "right" > 65< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Rheumatic< / td >
< td align = "left" >
< em > S. aureus< / em > (218-218)< / td >
< td align = "right" > 67< / td >
< td align = "right" > 55< / td >
< td align = "right" > 53< / td >
< td align = "right" > 67< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > S. pneumoniae< / em > (132-132)< / td >
< td align = "right" > 62< / td >
< td align = "right" > 56< / td >
< td align = "right" > 62< / td >
< td align = "right" > 68< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > S. aureus< / em > (225-225)< / td >
< td align = "right" > 66< / td >
< td align = "right" > 57< / td >
< td align = "right" > 53< / td >
< td align = "right" > 61< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Respiratory< / td >
< td align = "left" >
< em > S. aureus < / em > (217-21 7)< / td >
< em > S. pneumoniae < / em > (137-13 7)< / td >
< td align = "right" > 60< / td >
< td align = "right" > 55 < / td >
< td align = "right" > 54 < / td >
< td align = "right" > 61< / td >
< td align = "right" > 61< / td >
< td align = "right" > 64< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Rheumatic< / td >
< td align = "left" >
< em > S. aureus< / em > (219-219)< / td >
< td align = "right" > 67< / td >
< td align = "right" > 58< / td >
< td align = "right" > 58< / td >
< td align = "right" > 64< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Cardial< / td >
< td align = "left" >
< em > S. pneumoniae< / em > (152-152)< / td >
< td align = "right" > 67< / td >
< td align = "right" > 57< / td >
< td align = "right" > 64< / td >
< td align = "right" > 63< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Respiratory< / td >
< td align = "left" >
< em > S. pneumoniae< / em > (122-122)< / td >
< td align = "right" > 67< / td >
< td align = "right" > 57< / td >
< td align = "right" > 64< / td >
< td align = "right" > 67< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Rheumatic< / td >
< td align = "left" >
< em > S. pneumoniae< / em > (125-125 )< / td >
< td align = "right" > 5 7< / td >
< td align = "right" > 53 < / td >
< td align = "right" > 50 < / td >
< td align = "right" > 67 < / td >
< em > S. pneumoniae< / em > (130-130 )< / td >
< td align = "right" > 70 < / td >
< td align = "right" > 58 < / td >
< td align = "right" > 56 < / td >
< td align = "right" > 68 < / td >
< / tr >
< / tbody >
< / table >
< div class = "sourceCode" id = "cb20" > < 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" > our_data_1st< / span > ,< / span >
< span > < span class = "co" > # you can use AB selectors here as well:< / 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" > penicillins< / a > < / span > < span class = "op" > (< / 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 >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > # you can use AB selectors here as well:< / 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" > penicillins< / a > < / span > < span class = "op" > (< / 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 >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < / span >
< span > < span class = "op" > )< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span >
< span > < span class = "co" > #> (amoxicillin/clavulanic acid)< / span > < / span >
< span > < span class = "co" > #> ℹ < / span > < / span > < / code > < / pre > < / div >
@ -1084,55 +1090,56 @@ antibiograms:</p>
< tbody >
< tr class = "odd" >
< td align = "left" > Cardial< / td >
< td align = "left" > Gram-negative (536-536 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 54 < / td >
< td align = "right" > 62 < / td >
< td align = "left" > Gram-negative (500-500 )< / td >
< td align = "right" > 66 < / td >
< td align = "right" > 61 < / td >
< td align = "right" > 64 < / td >
< / tr >
< tr class = "even" >
< td align = "left" > Respiratory< / td >
< td align = "left" > Gram-negative (506-506 )< / td >
< td align = "right" > 63 < / td >
< td align = "left" > Gram-negative (513-513 )< / td >
< td align = "right" > 60 < / td >
< td align = "right" > 54< / td >
< td align = "right" > 59< / td >
< td align = "right" > 63< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Rheumatic< / td >
< td align = "left" > Gram-negative (524-524 )< / td >
< td align = "left" > Gram-negative (553-553 )< / td >
< td align = "right" > 65< / td >
< td align = "right" > 58 < / td >
< td align = "right" > 62 < / td >
< td align = "right" > 57 < / td >
< td align = "right" > 64 < / td >
< / tr >
< tr class = "even" >
< td align = "left" > Cardial< / td >
< td align = "left" > Gram-positive (37 7-37 7)< / td >
< td align = "right" > 67 < / td >
< td align = "right" > 57 < / td >
< td align = "right" > 62 < / td >
< td align = "left" > Gram-positive (36 7-36 7)< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 55 < / td >
< td align = "right" > 61 < / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Respiratory< / td >
< td align = "left" > Gram-positive (339-339 )< / td >
< td align = "left" > Gram-positive (345-345 )< / td >
< td align = "right" > 61< / td >
< td align = "right" > 58< / td >
< td align = "right" > 63< / td >
< td align = "right" > 56< / td >
< td align = "right" > 65< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Rheumatic< / td >
< td align = "left" > Gram-positive (344 -344 )< / td >
< td align = "right" > 63 < / td >
< td align = "left" > Gram-positive (348 -348 )< / td >
< td align = "right" > 68 < / td >
< td align = "right" > 56< / td >
< td align = "right" > 65 < / td >
< td align = "right" > 67 < / td >
< / tr >
< / tbody >
< / table >
< div class = "sourceCode" id = "cb21" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span > < span class = "co" > # WISCA: < / span > < / span >
< code class = "sourceCode R" > < span > < span class = "co" > # WISCA:< / span > < / span >
< span > < span class = "co" > # (we lack some details, but it could contain a filter on e.g. > 65 year-old males)< / span > < / span >
< 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" > our_data_1st< / 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" > "AMC+GEN"< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < span class = "op" > )< / 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" > "AMC+GEN"< / span > < span class = "op" > )< / span > ,< / span >
< span > syndromic_group < span class = "op" > =< / span > < span class = "st" > "condition"< / span > ,< / span >
< span > mo_transform < span class = "op" > =< / span > < span class = "st" > "gramstain"< / span > < / span >
< span > < span class = "op" > )< / span > < / span >
< span > < span class = "va" > wisca< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
@ -1145,45 +1152,45 @@ antibiograms:</p>
< tbody >
< tr class = "odd" >
< td align = "left" > Cardial< / td >
< td align = "left" > Gram-negative (536-536 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 75 < / td >
< td align = "right" > 75 < / td >
< td align = "left" > Gram-negative (500-500 )< / td >
< td align = "right" > 66 < / td >
< td align = "right" > 77 < / td >
< td align = "right" > 77 < / td >
< / tr >
< tr class = "even" >
< td align = "left" > Respiratory< / td >
< td align = "left" > Gram-negative (506-506 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 77 < / td >
< td align = "right" > 75 < / td >
< td align = "left" > Gram-negative (513-513 )< / td >
< td align = "right" > 60 < / td >
< td align = "right" > 72 < / td >
< td align = "right" > 71 < / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Rheumatic< / td >
< td align = "left" > Gram-negative (524-524 )< / td >
< td align = "left" > Gram-negative (553-553 )< / td >
< td align = "right" > 65< / td >
< td align = "right" > 78< / td >
< td align = "right" > 76< / td >
< td align = "right" > 75< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Cardial< / td >
< td align = "left" > Gram-positive (37 7-37 7)< / td >
< td align = "right" > 67 < / td >
< td align = "right" > 78 < / td >
< td align = "left" > Gram-positive (36 7-36 7)< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 79 < / td >
< td align = "right" > 75< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Respiratory< / td >
< td align = "left" > Gram-positive (339-339 )< / td >
< td align = "right" > 63 < / td >
< td align = "right" > 77< / td >
< td align = "left" > Gram-positive (345-345 )< / td >
< td align = "right" > 61 < / td >
< td align = "right" > 76< / td >
< td align = "right" > 73< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Rheumatic< / td >
< td align = "left" > Gram-positive (344 -344 )< / td >
< td align = "right" > 63 < / td >
< td align = "left" > Gram-positive (348 -348 )< / td >
< td align = "right" > 68 < / td >
< td align = "right" > 77< / td >
< td align = "right" > 76 < / td >
< td align = "right" > 79 < / td >
< / tr >
< / tbody >
< / table >
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