@ -39,7 +39,7 @@
@@ -39,7 +39,7 @@
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.3.0.9006 < / span >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.3.0.9015 < / span >
< / span >
< / div >
@ -79,7 +79,7 @@
@@ -79,7 +79,7 @@
< a href = "../articles/datasets.html" >
< span class = "fa fa-database" > < / span >
Download our reference d ata sets for own use
Data sets for download / own use
< / a >
< / li >
< li >
@ -193,7 +193,7 @@
@@ -193,7 +193,7 @@
< h1 data-toc-skip > How to conduct AMR analysis< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
< h4 class = "date" > 21 August 2020< / h4 >
< h4 class = "date" > 03 September 2020< / h4 >
< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" > < code > vignettes/AMR.Rmd< / code > < / a > < / small >
< div class = "hidden name" > < code > AMR.Rmd< / code > < / div >
@ -202,7 +202,7 @@
@@ -202,7 +202,7 @@
< p > < strong > Note:< / strong > values on this page will change with every website update since they are based on randomly created values and the page was written in < a href = "https://rmarkdown.rstudio.com/" > R Markdown< / a > . However, the methodology remains unchanged. This page was generated on 21 August 2020.< / p >
< p > < strong > Note:< / strong > values on this page will change with every website update since they are based on randomly created values and the page was written in < a href = "https://rmarkdown.rstudio.com/" > R Markdown< / a > . However, the methodology remains unchanged. This page was generated on 03 September 2020.< / p >
< div id = "introduction" class = "section level1" >
< h1 class = "hasAnchor" >
< a href = "#introduction" class = "anchor" > < / a > Introduction< / h1 >
@ -233,21 +233,21 @@
@@ -233,21 +233,21 @@
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2020-08-21 < / td >
< td align = "center" > 2020-09-03 < / 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" > 2020-08-21 < / td >
< td align = "center" > 2020-09-03 < / 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" > 2020-08-21 < / td >
< td align = "center" > 2020-09-03 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -361,66 +361,66 @@
@@ -361,66 +361,66 @@
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2011-03-20 < / td >
< td align = "center" > W2 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > Streptococcus pneumoniae < / td >
< td align = "center" > 2014-05-29 < / td >
< td align = "center" > B4 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Escherichia coli < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R < / td >
< td align = "center" > F < / td >
< td align = "center" > S < / td >
< td align = "center" > M < / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2011-12-03 < / td >
< td align = "center" > X9 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Klebsiella pneumoniae < / td >
< td align = "center" > R < / td >
< td align = "center" > I < / td >
< td align = "center" > 2017-04-19 < / td >
< td align = "center" > S1 < / td >
< td align = "center" > Hospital C < / td >
< td align = "center" > Staphylococcus aureus < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > F< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2012-11-11< / td >
< td align = "center" > A5< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > Staphylococcus aureus< / td >
< td align = "center" > S< / td >
< td align = "center" > 2017-04-21< / td >
< td align = "center" > L3< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2012-09-03< / td >
< td align = "center" > Y3< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
< td align = "center" > 2011-01-19< / td >
< td align = "center" > A7< / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > Staphylococcus aureus< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > F< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2012-11-19 < / td >
< td align = "center" > I3 < / td >
< td align = "center" > Hospital C < / td >
< td align = "center" > 2011-01-24 < / td >
< td align = "center" > H10 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2015-06-05 < / td >
< td align = "center" > Q7 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Escherichia coli < / td >
< td align = "center" > S < / td >
< td align = "center" > 2011-01-31 < / td >
< td align = "center" > T9 < / td >
< td align = "center" > Hospital C < / td >
< td align = "center" > Streptococcus pneumoniae < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -459,16 +459,16 @@ Longest: 1</p>
@@ -459,16 +459,16 @@ Longest: 1</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > M< / td >
< td align = "right" > 10,358 < / td >
< td align = "right" > 51.79 %< / td >
< td align = "right" > 10,358 < / td >
< td align = "right" > 51.79 %< / td >
< td align = "right" > 10,409 < / td >
< td align = "right" > 52.05 %< / td >
< td align = "right" > 10,409 < / td >
< td align = "right" > 52.05 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > F< / td >
< td align = "right" > 9,642 < / td >
< td align = "right" > 48.21 %< / td >
< td align = "right" > 9,591 < / td >
< td align = "right" > 47.96 %< / td >
< td align = "right" > 20,000< / td >
< td align = "right" > 100.00%< / td >
< / tr >
@ -518,7 +518,7 @@ Longest: 1</p>
@@ -518,7 +518,7 @@ Longest: 1</p>
< span class = "co" > # NOTE: Using column `date` as input for `col_date`.< / span >
< span class = "co" > # NOTE: Using column `patient_id` as input for `col_patient_id`.< / span >
< / pre > < / div >
< p > So only 28.3 % is suitable for resistance analysis! We can now filter on it with the < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" > filter()< / a > < / code > function, also from the < code > dplyr< / code > package:< / p >
< p > So only 28.6 % is suitable for resistance analysis! We can now filter on it with the < code > < a href = "https://dplyr.tidyverse.org/reference/filter.html" > filter()< / a > < / code > function, also from the < code > dplyr< / code > package:< / p >
< div class = "sourceCode" id = "cb16" > < pre class = "downlit" >
< span class = "kw" > data_1st< / span > < span class = "op" > < -< / span > < span class = "kw" > data< / span > < span class = "op" > %> %< / span >
< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" > filter< / a > < / span > (< span class = "kw" > first< / span > < span class = "op" > ==< / span > < span class = "fl" > TRUE< / span > )
@ -532,7 +532,7 @@ Longest: 1</p>
@@ -532,7 +532,7 @@ Longest: 1</p>
< div id = "first-weighted-isolates" class = "section level2" >
< h2 class = "hasAnchor" >
< a href = "#first-weighted-isolates" class = "anchor" > < / a > First < em > weighted< / em > isolates< / h2 >
< p > We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient C 8, sorted on date:< / p >
< p > We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient M 8, sorted on date:< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > isolate< / th >
@ -548,21 +548,21 @@ Longest: 1</p>
@@ -548,21 +548,21 @@ Longest: 1</p>
< tbody >
< tr class = "odd" >
< td align = "center" > 1< / td >
< td align = "center" > 2010-01-13 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-01-28 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2< / td >
< td align = "center" > 2010-02-19 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-05-23 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -570,10 +570,10 @@ Longest: 1</p>
@@ -570,10 +570,10 @@ Longest: 1</p>
< / tr >
< tr class = "odd" >
< td align = "center" > 3< / td >
< td align = "center" > 2010-03-12 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-07-11 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -581,30 +581,30 @@ Longest: 1</p>
@@ -581,30 +581,30 @@ Longest: 1</p>
< / tr >
< tr class = "even" >
< td align = "center" > 4< / td >
< td align = "center" > 2010-03-25 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-10-01 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 5< / td >
< td align = "center" > 2010-04-28 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-12-02 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 6< / td >
< td align = "center" > 2010-07-22 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-12-23 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -614,8 +614,8 @@ Longest: 1</p>
@@ -614,8 +614,8 @@ Longest: 1</p>
< / tr >
< tr class = "odd" >
< td align = "center" > 7< / td >
< td align = "center" > 2010-12-05 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-01-16 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -625,33 +625,33 @@ Longest: 1</p>
@@ -625,33 +625,33 @@ Longest: 1</p>
< / tr >
< tr class = "even" >
< td align = "center" > 8< / td >
< td align = "center" > 2011-01-18 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-03-14 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 9< / td >
< td align = "center" > 2011-05-24 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-04-02 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > I < / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 10< / td >
< td align = "center" > 2011-06-2 4< / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-04-05 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
@ -686,34 +686,34 @@ Longest: 1</p>
@@ -686,34 +686,34 @@ Longest: 1</p>
< tbody >
< tr class = "odd" >
< td align = "center" > 1< / td >
< td align = "center" > 2010-01-13 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-01-28 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2< / td >
< td align = "center" > 2010-02-19 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-05-23 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< td align = "center" > FALS E< / td >
< td align = "center" > TRU E< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 3< / td >
< td align = "center" > 2010-03-12 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-07-11 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -722,32 +722,32 @@ Longest: 1</p>
@@ -722,32 +722,32 @@ Longest: 1</p>
< / tr >
< tr class = "even" >
< td align = "center" > 4< / td >
< td align = "center" > 2010-03-25 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-10-01 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > FALSE< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 5< / td >
< td align = "center" > 2010-04-28 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-12-02 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 6< / td >
< td align = "center" > 2010-07-22 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2010-12-23 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -758,8 +758,8 @@ Longest: 1</p>
@@ -758,8 +758,8 @@ Longest: 1</p>
< / tr >
< tr class = "odd" >
< td align = "center" > 7< / td >
< td align = "center" > 2010-12-05 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-01-16 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -770,11 +770,11 @@ Longest: 1</p>
@@ -770,11 +770,11 @@ Longest: 1</p>
< / tr >
< tr class = "even" >
< td align = "center" > 8< / td >
< td align = "center" > 2011-01-18 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-03-14 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
@ -782,23 +782,23 @@ Longest: 1</p>
@@ -782,23 +782,23 @@ Longest: 1</p>
< / tr >
< tr class = "odd" >
< td align = "center" > 9< / td >
< td align = "center" > 2011-05-24 < / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-04-02 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > I < / td >
< td align = "center" > R < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< td align = "center" > TRU E< / td >
< td align = "center" > FALS E< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 10< / td >
< td align = "center" > 2011-06-2 4< / td >
< td align = "center" > C 8< / td >
< td align = "center" > 2011-04-05 < / td >
< td align = "center" > M 8< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > R < / td >
< td align = "center" > R < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
@ -806,13 +806,13 @@ Longest: 1</p>
@@ -806,13 +806,13 @@ Longest: 1</p>
< / tr >
< / tbody >
< / table >
< p > Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked โfirst weightedโ - 50.1 % more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.< / p >
< p > Instead of 2, now 8 isolates are flagged. In total, 79.1% of all isolates are marked โfirst weightedโ - 50.5 % more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.< / p >
< p > As with < code > < a href = "../reference/first_isolate.html" > filter_first_isolate()< / a > < / code > , thereโs a shortcut for this new algorithm too:< / p >
< div class = "sourceCode" id = "cb19" > < pre class = "downlit" >
< span class = "kw" > data_1st< / span > < span class = "op" > < -< / span > < span class = "kw" > data< / span > < span class = "op" > %> %< / span >
< span class = "fu" > < a href = "../reference/first_isolate.html" > filter_first_weighted_isolate< / a > < / span > ()
< / pre > < / div >
< p > So we end up with 15,686 isolates for analysis.< / p >
< p > So we end up with 15,813 isolates for analysis.< / p >
< p > We can remove unneeded columns:< / p >
< div class = "sourceCode" id = "cb20" > < pre class = "downlit" >
< span class = "kw" > data_1st< / span > < span class = "op" > < -< / span > < span class = "kw" > data_1st< / span > < span class = "op" > %> %< / span >
@ -857,63 +857,63 @@ Longest: 1</p>
@@ -857,63 +857,63 @@ Longest: 1</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "center" > 2011-03-20< / td >
< td align = "center" > W2< / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_STRPT_PNMN< / td >
< td align = "left" > 2< / td >
< td align = "center" > 2017-04-19< / td >
< td align = "center" > S1< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > B_STPHY_AURS< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > F< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Strept ococcus< / td >
< td align = "center" > pneumoni ae< / td >
< td align = "center" > Staphyl ococcus< / td >
< td align = "center" > aur eus < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 3< / td >
< td align = "center" > 2012-11-11< / td >
< td align = "center" > A5< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > B_STPHY_AURS< / td >
< td align = "center" > R< / td >
< td align = "center" > 2017-04-21< / td >
< td align = "center" > L3< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > Staphylococcus < / td >
< td align = "center" > aureus < / td >
< td align = "center" > Gram-nega tive< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 4< / td >
< td align = "center" > 2012-09-03< / td >
< td align = "center" > Y3< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > 2011-01-19< / td >
< td align = "center" > A7< / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_STPHY_AURS< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > F< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Staphylococcus< / td >
< td align = "center" > aureus< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 5< / td >
< td align = "center" > 2012-11-19 < / td >
< td align = "center" > I3 < / td >
< td align = "center" > Hospital C < / td >
< td align = "center" > 2011-01-24 < / td >
< td align = "center" > H10 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Escherichia< / td >
@ -921,35 +921,35 @@ Longest: 1</p>
@@ -921,35 +921,35 @@ Longest: 1</p>
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 8< / td >
< td align = "center" > 2013-11-06< / td >
< td align = "center" > B1< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_KLBSL_PNMN< / td >
< td align = "left" > 6< / td >
< td align = "center" > 2011-01-31< / td >
< td align = "center" > T9< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > B_STRPT_PNMN< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Klebsiella< / td >
< td align = "center" > R< / td >
< td align = "center" > F< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Streptococcus< / td >
< td align = "center" > pneumoniae< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 9< / td >
< td align = "center" > 2017-01-21< / td >
< td align = "center" > U3< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > B_KLBSL_PNMN< / td >
< td align = "left" > 7< / td >
< td align = "center" > 2012-12-27< / td >
< td align = "center" > Q9< / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > F< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Klebsiell a< / td >
< td align = "center" > pneumoniae < / td >
< td align = "center" > Escherichi a< / td >
< td align = "center" > coli < / td >
< td align = "center" > TRUE< / td >
< / tr >
< / tbody >
@ -975,8 +975,8 @@ Longest: 1</p>
@@ -975,8 +975,8 @@ Longest: 1</p>
< / pre > < / div >
< p > < strong > Frequency table< / strong > < / p >
< p > Class: character< br >
Length: 15,686 < br >
Available: 15,686 (100%, NA: 0 = 0%)< br >
Length: 15,813 < br >
Available: 15,813 (100%, NA: 0 = 0%)< br >
Unique: 4< / p >
< p > Shortest: 16< br >
Longest: 24< / p >
@ -993,33 +993,33 @@ Longest: 24</p>
@@ -993,33 +993,33 @@ Longest: 24</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > Escherichia coli< / td >
< td align = "right" > 7,774 < / td >
< td align = "right" > 49.56 %< / td >
< td align = "right" > 7,774 < / td >
< td align = "right" > 49.56 %< / td >
< td align = "right" > 7,901 < / td >
< td align = "right" > 49.97 %< / td >
< td align = "right" > 7,901 < / td >
< td align = "right" > 49.97 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Staphylococcus aureus< / td >
< td align = "right" > 3,952 < / td >
< td align = "right" > 25.19 %< / td >
< td align = "right" > 11,726 < / td >
< td align = "right" > 74.75 %< / td >
< td align = "right" > 3,946 < / td >
< td align = "right" > 24.95 %< / td >
< td align = "right" > 11,84 7< / td >
< td align = "right" > 74.92 %< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > Streptococcus pneumoniae< / td >
< td align = "right" > 2,367 < / td >
< td align = "right" > 15.09 %< / td >
< td align = "right" > 14,093 < / td >
< td align = "right" > 89.84 %< / td >
< td align = "right" > 2,394 < / td >
< td align = "right" > 15.14 %< / td >
< td align = "right" > 14,241 < / td >
< td align = "right" > 90.06 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > Klebsiella pneumoniae< / td >
< td align = "right" > 1,593 < / td >
< td align = "right" > 10.16 %< / td >
< td align = "right" > 15,686 < / td >
< td align = "right" > 1,572 < / td >
< td align = "right" > 9.94 %< / td >
< td align = "right" > 15,813 < / td >
< td align = "right" > 100.00%< / td >
< / tr >
< / tbody >
@ -1048,50 +1048,50 @@ Longest: 24</p>
@@ -1048,50 +1048,50 @@ Longest: 24</p>
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > AMX< / td >
< td align = "center" > 3685 < / td >
< td align = "center" > 3774 < / td >
< td align = "center" > 257< / td >
< td align = "center" > 3832 < / td >
< td align = "center" > 7774 < / td >
< td align = "center" > 3870 < / td >
< td align = "center" > 7901 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > E. coli< / td >
< td align = "center" > AMC< / td >
< td align = "center" > 6104 < / td >
< td align = "center" > 275 < / td >
< td align = "center" > 1395 < / td >
< td align = "center" > 7774 < / td >
< td align = "center" > 6189 < / td >
< td align = "center" > 306 < / td >
< td align = "center" > 1406 < / td >
< td align = "center" > 7901 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > CIP< / td >
< td align = "center" > 5979 < / td >
< td align = "center" > 6042 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 1795 < / td >
< td align = "center" > 7774 < / td >
< td align = "center" > 1859 < / td >
< td align = "center" > 7901 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > E. coli< / td >
< td align = "center" > GEN< / td >
< td align = "center" > 6986 < / td >
< td align = "center" > 7094 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 78 8< / td >
< td align = "center" > 7774 < / td >
< td align = "center" > 807 < / td >
< td align = "center" > 7901 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > AMX< / td >
< td align = "center" > 0< / td >
< td align = "center" > 0< / td >
< td align = "center" > 1593 < / td >
< td align = "center" > 1593 < / td >
< td align = "center" > 1572 < / td >
< td align = "center" > 1572 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > AMC< / td >
< td align = "center" > 1269 < / td >
< td align = "center" > 57 < / td >
< td align = "center" > 26 7< / td >
< td align = "center" > 1593 < / td >
< td align = "center" > 1245 < / td >
< td align = "center" > 56 < / td >
< td align = "center" > 271 < / td >
< td align = "center" > 1572 < / td >
< / tr >
< / tbody >
< / table >
@ -1116,34 +1116,34 @@ Longest: 24</p>
@@ -1116,34 +1116,34 @@ Longest: 24</p>
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > CIP< / td >
< td align = "center" > 5979 < / td >
< td align = "center" > 6042 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 1795 < / td >
< td align = "center" > 7774 < / td >
< td align = "center" > 1859 < / td >
< td align = "center" > 7901 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > CIP< / td >
< td align = "center" > 1213 < / td >
< td align = "center" > 1182 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 38 0< / td >
< td align = "center" > 1593 < / td >
< td align = "center" > 39 0< / td >
< td align = "center" > 1572 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > S. aureus< / td >
< td align = "center" > CIP< / td >
< td align = "center" > 3003 < / td >
< td align = "center" > 2966 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 949 < / td >
< td align = "center" > 3952 < / td >
< td align = "center" > 980 < / td >
< td align = "center" > 3946 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > S. pneumoniae< / td >
< td align = "center" > CIP< / td >
< td align = "center" > 1820 < / td >
< td align = "center" > 1834 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 547 < / td >
< td align = "center" > 2367 < / td >
< td align = "center" > 560 < / td >
< td align = "center" > 2394 < / td >
< / tr >
< / tbody >
< / table >
@ -1156,7 +1156,7 @@ Longest: 24</p>
@@ -1156,7 +1156,7 @@ Longest: 24</p>
< p > As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (< code > < a href = "../reference/proportion.html" > proportion_R()< / a > < / code > , equal to < code > < a href = "../reference/proportion.html" > resistance()< / a > < / code > ) and susceptibility as the proportion of S and 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 = "cb28" > < pre class = "downlit" >
< span class = "kw" > data_1st< / span > < span class = "op" > %> %< / span > < span class = "fu" > < a href = "../reference/proportion.html" > resistance< / a > < / span > (< span class = "kw" > AMX< / span > )
< span class = "co" > # [1] 0.5350631 < / span >
< span class = "co" > # [1] 0.5330424 < / span >
< / pre > < / div >
< p > Or can be used in conjuction with < code > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" > group_by()< / a > < / code > and < code > < a href = "https://dplyr.tidyverse.org/reference/summarise.html" > summarise()< / a > < / code > , both from the < code > dplyr< / code > package:< / p >
< div class = "sourceCode" id = "cb29" > < pre class = "downlit" >
@ -1173,19 +1173,19 @@ Longest: 24</p>
@@ -1173,19 +1173,19 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.5338783 < / td >
< td align = "center" > 0.5262478 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.5368875 < / td >
< td align = "center" > 0.5401022 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.5367068 < / td >
< td align = "center" > 0.5257556 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.5322422 < / td >
< td align = "center" > 0.5357938 < / td >
< / tr >
< / tbody >
< / table >
@ -1206,23 +1206,23 @@ Longest: 24</p>
@@ -1206,23 +1206,23 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.5338783 < / td >
< td align = "center" > 4649 < / td >
< td align = "center" > 0.5262478 < / td >
< td align = "center" > 4648 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.5368875 < / td >
< td align = "center" > 5571 < / td >
< td align = "center" > 0.5401022 < / td >
< td align = "center" > 5673 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.5367068 < / td >
< td align = "center" > 2411 < / td >
< td align = "center" > 0.5257556 < / td >
< td align = "center" > 2349 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.5322422 < / td >
< td align = "center" > 3055 < / td >
< td align = "center" > 0.5357938 < / td >
< td align = "center" > 3143 < / td >
< / tr >
< / tbody >
< / table >
@ -1245,27 +1245,27 @@ Longest: 24</p>
@@ -1245,27 +1245,27 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Escherichia< / td >
< td align = "center" > 0.8205557 < / td >
< td align = "center" > 0.8986365 < / td >
< td align = "center" > 0.9855930 < / td >
< td align = "center" > 0.8220478 < / td >
< td align = "center" > 0.8978610 < / td >
< td align = "center" > 0.9860777 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Klebsiella< / td >
< td align = "center" > 0.83 2391 7< / td >
< td align = "center" > 0.8901444 < / td >
< td align = "center" > 0.9855 618 < / td >
< td align = "center" > 0.8276081 < / td >
< td align = "center" > 0.9001272 < / td >
< td align = "center" > 0.986005 1< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Staphylococcus< / td >
< td align = "center" > 0.8276822 < / td >
< td align = "center" > 0.921 052 6< / td >
< td align = "center" > 0.9868421 < / td >
< td align = "center" > 0.8335023 < / td >
< td align = "center" > 0.9206792 < / td >
< td align = "center" > 0.9878358 < / td >