@ -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" > 1.7.1.9013 < / span >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.7.1.9014 < / span >
< / span >
< / div >
@ -193,7 +193,7 @@
@@ -193,7 +193,7 @@
< h1 data-toc-skip > How to conduct AMR data analysis< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
< h4 class = "date" > 04 July 2021< / h4 >
< h4 class = "date" > 06 July 2021< / 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 04 July 2021.< / 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 06 July 2021.< / 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" > 2021-07-04 < / td >
< td align = "center" > 2021-07-06 < / 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" > 2021-07-04 < / td >
< td align = "center" > 2021-07-06 < / 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" > 2021-07-04 < / td >
< td align = "center" > 2021-07-06 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -344,32 +344,32 @@
@@ -344,32 +344,32 @@
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2016-09-28 < / td >
< td align = "center" > A1 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > 2016-02-04 < / td >
< td align = "center" > V9 < / 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" > M < / td >
< td align = "center" > S < / td >
< td align = "center" > F < / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2012-09-28 < / td >
< td align = "center" > J9 < / td >
< td align = "center" > 2011-09-24 < / td >
< td align = "center" > D2 < / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > Streptococcus pneumoniae< / 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" > M< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2011-10-02 < / td >
< td align = "center" > S7 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Klebsiella pneumoniae < / td >
< td align = "center" > 2014-06-20 < / td >
< td align = "center" > Z9 < / 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 >
@ -377,9 +377,9 @@
@@ -377,9 +377,9 @@
< td align = "center" > F< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2016-11-15 < / td >
< td align = "center" > U6 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > 2018-01-01 < / td >
< td align = "center" > P4 < / td >
< td align = "center" > Hospital C < / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
@ -388,26 +388,26 @@
@@ -388,26 +388,26 @@
< td align = "center" > F< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2016-12-08 < / td >
< td align = "center" > B10 < / td >
< td align = "center" > 2014-12-14 < / td >
< td align = "center" > W2 < / td >
< td align = "center" > Hospital A< / 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" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > F< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2010-05-10< / td >
< td align = "center" > M2< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > 2016-07-27< / td >
< td align = "center" > R6< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > Staphylococcus aureus< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > M < / td >
< td align = "center" > F < / td >
< / tr >
< / tbody >
< / table >
@ -441,16 +441,16 @@ Longest: 1</p>
@@ -441,16 +441,16 @@ Longest: 1</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > M< / td >
< td align = "right" > 10,434 < / td >
< td align = "right" > 52.17 %< / td >
< td align = "right" > 10,434 < / td >
< td align = "right" > 52.17 %< / td >
< td align = "right" > 10,365 < / td >
< td align = "right" > 51.83 %< / td >
< td align = "right" > 10,365 < / td >
< td align = "right" > 51.83 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > F< / td >
< td align = "right" > 9,56 6< / td >
< td align = "right" > 47.83 %< / td >
< td align = "right" > 9,635 < / td >
< td align = "right" > 48.18 %< / td >
< td align = "right" > 20,000< / td >
< td align = "right" > 100.00%< / td >
< / tr >
@ -505,9 +505,9 @@ Longest: 1</p>
@@ -505,9 +505,9 @@ Longest: 1</p>
< span class = "co" > # โน Using column 'patient_id' as input for `col_patient_id`.< / span >
< span class = "co" > # Basing inclusion on all antimicrobial results, using a points threshold of< / span >
< span class = "co" > # 2< / span >
< span class = "co" > # => Found 10,702 first weighted isolates (phenotype-based, 53.5 % of total< / span >
< span class = "co" > # => Found 10,656 first weighted isolates (phenotype-based, 53.3 % of total< / span >
< span class = "co" > # where a microbial ID was available)< / span > < / code > < / pre > < / div >
< p > So only 53.5 % 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 53.3 % 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 >
< div class = "sourceCode" id = "cb15" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "va" > data_1st< / span > < span class = "op" > < -< / span > < span class = "va" > data< / span > < span class = "op" > %> %< / span >
< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" > 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 > < / code > < / pre > < / div >
@ -515,7 +515,7 @@ Longest: 1</p>
@@ -515,7 +515,7 @@ Longest: 1</p>
< div class = "sourceCode" id = "cb16" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "va" > data_1st< / span > < span class = "op" > < -< / span > < span class = "va" > data< / span > < span class = "op" > %> %< / span >
< span class = "fu" > < a href = "../reference/first_isolate.html" > filter_first_isolate< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / code > < / pre > < / div >
< p > So we end up with 10,702 isolates for analysis. Now our data looks like:< / p >
< p > So we end up with 10,656 isolates for analysis. Now our data looks like:< / p >
< div class = "sourceCode" id = "cb17" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "fu" > < a href = "https://rdrr.io/r/utils/head.html" > head< / a > < / span > < span class = "op" > (< / span > < span class = "va" > data_1st< / span > < span class = "op" > )< / span > < / code > < / pre > < / div >
< table class = "table" >
@ -531,7 +531,7 @@ Longest: 1</p>
@@ -531,7 +531,7 @@ Longest: 1</p>
< col width = "3%" >
< col width = "6%" >
< col width = "11%" >
< col width = "12 %" >
< col width = "13 %" >
< col width = "9%" >
< col width = "5%" >
< / colgroup >
@ -553,99 +553,99 @@ Longest: 1</p>
@@ -553,99 +553,99 @@ Longest: 1</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "left" > 1 < / td >
< td align = "center" > 2016-09-28 < / td >
< td align = "center" > A1 < / td >
< td align = "left" > 2 < / td >
< td align = "center" > 2011-09-24 < / td >
< td align = "center" > D2 < / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_ESCHR_COLI < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / 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" > R< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-nega tive< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2 < / td >
< td align = "center" > 2012-09-28 < / td >
< td align = "center" > J 9< / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > B_STRPT_PNMN < / td >
< td align = "left" > 3 < / td >
< td align = "center" > 2014-06-20 < / td >
< td align = "center" > Z 9< / 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" > R < / td >
< td align = "center" > M < / td >
< td align = "center" > S < / td >
< td align = "center" > F < / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Streptococcus < / td >
< td align = "center" > pneumoni ae< / td >
< td align = "center" > < em > Staphylococcus< / em > < / td >
< td align = "center" > aur eus < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 5< / td >
< td align = "center" > 2016-12-08< / td >
< td align = "center" > B10< / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "left" > 6< / td >
< td align = "center" > 2016-07-27< / td >
< td align = "center" > R6< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_STPHY_AURS< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > M < / td >
< td align = "center" > Gram-nega tive< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > F < / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > < em > Staphylococcus< / em > < / td >
< td align = "center" > aureus < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 7< / td >
< td align = "center" > 2015-04-29 < / td >
< td align = "center" > W8 < / td >
< td align = "center" > 2011-07-24 < / td >
< td align = "center" > W2 < / td >
< td align = "center" > Hospital A< / 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" > R< / td >
< td align = "center" > F< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > < em > Escherichia< / em > < / td >
< td align = "center" > coli< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 8 < / td >
< td align = "center" > 2010-06-19 < / td >
< td align = "center" > Q5 < / td >
< td align = "left" > 9 < / td >
< td align = "center" > 2012-01-12 < / td >
< td align = "center" > K9 < / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > B_STPHY_AURS < / 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" > S< / td >
< td align = "center" > F < / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > Staphylococcus < / td >
< td align = "center" > aureus < / td >
< td align = "center" > M < / td >
< td align = "center" > Gram-nega tive< / td >
< td align = "center" > < em > Escherichia< / em > < / td >
< td align = "center" > coli < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 9< / td >
< td align = "center" > 2010-08-20< / td >
< td align = "center" > A8< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "left" > 11< / td >
< td align = "center" > 2013-03-11< / td >
< td align = "center" > B6< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > B_KLBSL_PNMN< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > < em > Klebsiella< / em > < / td >
< td align = "center" > pneumoniae < / td >
< td align = "center" > TRUE< / td >
< / tr >
< / tbody >
@ -669,8 +669,8 @@ Longest: 1</p>
@@ -669,8 +669,8 @@ Longest: 1</p>
< code class = "sourceCode R" > < span class = "va" > data_1st< / span > < span class = "op" > %> %< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/cleaner/man/freq.html" > freq< / a > < / span > < span class = "op" > (< / span > < span class = "va" > genus< / span > , < span class = "va" > species< / span > < span class = "op" > )< / span > < / code > < / pre > < / div >
< p > < strong > Frequency table< / strong > < / p >
< p > Class: character< br >
Length: 10,702 < br >
Available: 10,702 (100.0%, NA: 0 = 0.0%)< br >
Length: 10,656 < br >
Available: 10,656 (100.0%, NA: 0 = 0.0%)< br >
Unique: 4< / p >
< p > Shortest: 16< br >
Longest: 24< / p >
@ -687,33 +687,33 @@ Longest: 24</p>
@@ -687,33 +687,33 @@ Longest: 24</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > Escherichia coli< / td >
< td align = "right" > 4,661 < / td >
< td align = "right" > 43.55 %< / td >
< td align = "right" > 4,661 < / td >
< td align = "right" > 43.55 %< / td >
< td align = "right" > 4,664 < / td >
< td align = "right" > 43.77 %< / td >
< td align = "right" > 4,664 < / td >
< td align = "right" > 43.77 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Staphylococcus aureus< / td >
< td align = "right" > 2,69 7< / td >
< td align = "right" > 25.20 %< / td >
< td align = "right" > 7,358 < / td >
< td align = "right" > 68.75 %< / td >
< td align = "right" > 2,730 < / td >
< td align = "right" > 25.6 2%< / td >
< td align = "right" > 7,394 < / td >
< td align = "right" > 69.39 %< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > Streptococcus pneumoniae< / td >
< td align = "right" > 2,145 < / td >
< td align = "right" > 20.0 4%< / td >
< td align = "right" > 9,503 < / td >
< td align = "right" > 88.80 %< / td >
< td align = "right" > 2,093 < / td >
< td align = "right" > 19.6 4%< / td >
< td align = "right" > 9,487 < / td >
< td align = "right" > 89.03 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > Klebsiella pneumoniae< / td >
< td align = "right" > 1,19 9< / td >
< td align = "right" > 11.2 0%< / td >
< td align = "right" > 10,702 < / td >
< td align = "right" > 1,16 9< / td >
< td align = "right" > 10.97 %< / td >
< td align = "right" > 10,656 < / td >
< td align = "right" > 100.00%< / td >
< / tr >
< / tbody >
@ -732,14 +732,14 @@ Longest: 24</p>
@@ -732,14 +732,14 @@ Longest: 24</p>
< col width = "9%" >
< col width = "9%" >
< col width = "9%" >
< col width = "11 %" >
< col width = "10 %" >
< col width = "3%" >
< col width = "3%" >
< col width = "3%" >
< col width = "3%" >
< col width = "6%" >
< col width = "11%" >
< col width = "11 %" >
< col width = "13 %" >
< col width = "9%" >
< col width = "5%" >
< / colgroup >
@ -760,23 +760,38 @@ Longest: 24</p>
@@ -760,23 +760,38 @@ Longest: 24</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2016-09-28 < / td >
< td align = "center" > A1 < / td >
< td align = "center" > 2011-09-24 < / td >
< td align = "center" > D2 < / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_ESCHR_COLI < / td >
< td align = "center" > S < / td >
< td align = "center" > S < / 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" > R< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2011-07-24< / td >
< td align = "center" > W2< / 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" > S< / 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" > < em > Escherichia< / em > < / td >
< td align = "center" > coli< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2012-09-28< / td >
< td align = "center" > J9< / td >
< tr class = "odd " >
< td align = "center" > 2011-03-17 < / td >
< td align = "center" > D5 < / td >
< td align = "center" > Hospital A< / td >
< td align = "center" > B_STRPT_PNMN< / td >
< td align = "center" > S< / td >
@ -785,67 +800,52 @@ Longest: 24</p>
@@ -785,67 +800,52 @@ Longest: 24</p>
< td align = "center" > R< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Streptococcus< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd " >
< td align = "center" > 2015-04-29 < / td >
< td align = "center" > W8 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > B_ESCHR_COLI < / td >
< td align = "center" > R < / td >
< tr class = "even " >
< td align = "center" > 2011-06-13 < / td >
< td align = "center" > X10 < / td >
< td align = "center" > Hospital D < / td >
< td align = "center" > B_STRPT_PNMN < / 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-nega tive< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even " >
< td align = "center" > 2017-02-20 < / td >
< td align = "center" > P2 < / td >
< td align = "center" > Hospital C < / td >
< tr class = "odd " >
< td align = "center" > 2010-04-12 < / td >
< td align = "center" > Z4 < / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > B_STRPT_PNMN< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > R < / 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" > Streptococcus< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2010-09-14< / td >
< td align = "center" > T8< / td >
< td align = "center" > Hospital A< / 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" > F< / td >
< td align = "center" > Gram-negative< / td >
< td align = "center" > Escherichia< / td >
< td align = "center" > coli< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2011-01-26 < / td >
< td align = "center" > K8 < / td >
< td align = "center" > 2017-02-25< / td >
< td align = "center" > B5< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_STRPT_PNMN< / td >
< td align = "center" > S < / td >
< td align = "center" > S < / td >
< td align = "center" > I< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-positive< / td >
< td align = "center" > Streptococcus< / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > pneumoniae< / td >
< td align = "center" > TRUE< / td >
< / tr >
@ -868,52 +868,52 @@ Longest: 24</p>
@@ -868,52 +868,52 @@ Longest: 24</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > < em > E. coli< / em > < / td >
< td align = "center" > AMX< / td >
< td align = "center" > 2209 < / td >
< td align = "center" > 123 < / td >
< td align = "center" > 232 9< / td >
< td align = "center" > 4661 < / td >
< td align = "center" > 2180 < / td >
< td align = "center" > 145 < / td >
< td align = "center" > 233 9< / td >
< td align = "center" > 4664 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > E. coli< / td >
< td align = "center" > < em > E. coli< / em > < / td >
< td align = "center" > AMC< / td >
< td align = "center" > 3406 < / td >
< td align = "center" > 165 < / td >
< td align = "center" > 1090 < / td >
< td align = "center" > 4661 < / td >
< td align = "center" > 3360 < / td >
< td align = "center" > 17 6< / td >
< td align = "center" > 1128 < / td >
< td align = "center" > 4664 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > < em > E. coli< / em > < / td >
< td align = "center" > CIP< / td >
< td align = "center" > 3416 < / td >
< td align = "center" > 3405 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 124 5< / td >
< td align = "center" > 4661 < / td >
< td align = "center" > 1259 < / td >
< td align = "center" > 4664 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > E. coli< / td >
< td align = "center" > < em > E. coli< / em > < / td >
< td align = "center" > GEN< / td >
< td align = "center" > 4086 < / td >
< td align = "center" > 407 8< / td >
< td align = "center" > 0< / td >
< td align = "center" > 575 < / td >
< td align = "center" > 4661 < / td >
< td align = "center" > 586 < / td >
< td align = "center" > 4664 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > < em > K. pneumoniae< / em > < / td >
< td align = "center" > AMX< / td >
< td align = "center" > 0< / td >
< td align = "center" > 0< / td >
< td align = "center" > 119 9< / td >
< td align = "center" > 119 9< / td >
< td align = "center" > 116 9< / td >
< td align = "center" > 116 9< / td >
< / tr >
< tr class = "even" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > < em > K. pneumoniae< / em > < / td >
< td align = "center" > AMC< / td >
< td align = "center" > 933 < / td >
< td align = "center" > 3 9< / td >
< td align = "center" > 227 < / td >
< td align = "center" > 119 9< / td >
< td align = "center" > 924 < / td >
< td align = "center" > 4 9< / td >
< td align = "center" > 196 < / td >
< td align = "center" > 116 9< / td >
< / tr >
< / tbody >
< / table >
@ -934,36 +934,36 @@ Longest: 24</p>
@@ -934,36 +934,36 @@ Longest: 24</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > E. coli< / td >
< td align = "center" > < em > E. coli< / em > < / td >
< td align = "center" > GEN< / td >
< td align = "center" > 4086 < / td >
< td align = "center" > 407 8< / td >
< td align = "center" > 0< / td >
< td align = "center" > 575 < / td >
< td align = "center" > 4661 < / td >
< td align = "center" > 586 < / td >
< td align = "center" > 4664 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > K. pneumoniae< / td >
< td align = "center" > < em > K. pneumoniae< / em > < / td >
< td align = "center" > GEN< / td >
< td align = "center" > 1068 < / td >
< td align = "center" > 1042 < / td >
< td align = "center" > 0< / td >
< td align = "center" > 131 < / td >
< td align = "center" > 119 9< / td >
< td align = "center" > 127 < / td >
< td align = "center" > 116 9< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > S. aureus< / td >
< td align = "center" > < em > S. aureus< / em > < / td >
< td align = "center" > GEN< / td >
< td align = "center" > 2407 < / td >
< td align = "center" > 244 0< / td >
< td align = "center" > 0< / td >
< td align = "center" > 290< / td >
< td align = "center" > 269 7< / td >
< td align = "center" > 2730 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > S. pneumoniae< / td >
< td align = "center" > < em > S. pneumoniae< / em > < / td >
< td align = "center" > GEN< / td >
< td align = "center" > 0< / td >
< td align = "center" > 0< / td >
< td align = "center" > 2145 < / td >
< td align = "center" > 2145 < / td >
< td align = "center" > 2093 < / td >
< td align = "center" > 2093 < / td >
< / tr >
< / tbody >
< / table >
@ -977,7 +977,7 @@ Longest: 24</p>
@@ -977,7 +977,7 @@ 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 = "cb26" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "va" > data_1st< / span > < 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 = "co" > # [1] 0.5418613 < / span > < / code > < / pre > < / div >
< span class = "co" > # [1] 0.5442005 < / span > < / code > < / pre > < / div >
< p > Or can be used in conjunction 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 = "cb27" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "va" > data_1st< / span > < span class = "op" > %> %< / span >
@ -991,19 +991,19 @@ Longest: 24</p>
@@ -991,19 +991,19 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.52767 30< / td >
< td align = "center" > 0.551 2301 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.5422819 < / td >
< td align = "center" > 0.5383792 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.5609308 < / td >
< td align = "center" > 0.5587121 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.5475970 < / td >
< td align = "center" > 0.5329877 < / td >
< / tr >
< / tbody >
< / table >
@ -1022,23 +1022,23 @@ Longest: 24</p>
@@ -1022,23 +1022,23 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.52767 30< / td >
< td align = "center" > 3180 < / td >
< td align = "center" > 0.551 2301 < / td >
< td align = "center" > 3211 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.5422819 < / td >
< td align = "center" > 3725 < / td >
< td align = "center" > 0.5383792 < / td >
< td align = "center" > 3739 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.5609308 < / td >
< td align = "center" > 1633 < / td >
< td align = "center" > 0.5587121 < / td >
< td align = "center" > 1584 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.5475970 < / td >
< td align = "center" > 2164 < / td >
< td align = "center" > 0.5329877 < / td >
< td align = "center" > 2122 < / td >
< / tr >
< / tbody >
< / table >
@ -1058,28 +1058,28 @@ Longest: 24</p>
@@ -1058,28 +1058,28 @@ Longest: 24</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > Escherichia< / td >
< td align = "center" > 0.7661446 < / td >
< td align = "center" > 0.8766359 < / td >
< td align = "center" > 0.9759708 < / td >
< td align = "center" > < em > Escherichia< / em > < / td >
< td align = "center" > 0.7581475 < / td >
< td align = "center" > 0.8743568 < / td >
< td align = "center" > 0.9762007 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Klebsiella< / td >
< td align = "center" > 0.8106756 < / td >
< td align = "center" > 0.8907423 < / td >
< td align = "center" > 0.9833194 < / td >
< td align = "center" > < em > Klebsiella< / em > < / td >
< td align = "center" > 0.8323353 < / td >
< td align = "center" > 0.8913601 < / td >
< td align = "center" > 0.9760479 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Staphylococcus< / td >
< td align = "center" > 0.7942158 < / td >
< td align = "center" > 0.8924731 < / td >
< td align = "center" > 0.9818317 < / td >
< td align = "center" > < em > Staphylococcus< / em > < / td >
< td align = "center" > 0.7945055 < / td >
< td align = "center" > 0.8937729 < / td >
< td align = "center" > 0.9831502 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Streptococcus< / td >
< td align = "center" > 0.5501166 < / td >
< td align = "center" > < em > Streptococcus< / em > < / td >
< td align = "center" > 0.5351171 < / td >
< td align = "center" > 0.0000000< / td >
< td align = "center" > 0.5501166 < / td >
< td align = "center" > 0.5351171 < / td >
< / tr >
< / tbody >
< / table >
@ -1104,23 +1104,23 @@ Longest: 24</p>
@@ -1104,23 +1104,23 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "left" > Hospital A< / td >
< td align = "right" > 52.8 %< / td >
< td align = "right" > 26 .0%< / td >
< td align = "right" > 55.1 %< / td >
< td align = "right" > 27 .0%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Hospital B< / td >
< td align = "right" > 54.2 %< / td >
< td align = "right" > 26.5 %< / td >
< td align = "right" > 53.8 %< / td >
< td align = "right" > 26.2 %< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > Hospital C< / td >
< td align = "right" > 56.1 %< / td >
< td align = "right" > 26 .7%< / td >
< td align = "right" > 55.9 %< / td >
< td align = "right" > 27 .7%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > Hospital D< / td >
< td align = "right" > 54.8 %< / td >
< td align = "right"