@ -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" > 0.9.0.9029 < / span >
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.0.1 < / span >
< / span >
< / div >
@ -179,7 +179,7 @@
@@ -179,7 +179,7 @@
< h1 > How to conduct AMR analysis< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
< h4 class = "date" > 20 February 2020< / h4 >
< h4 class = "date" > 23 February 2020< / h4 >
< div class = "hidden name" > < code > AMR.Rmd< / code > < / div >
@ -188,7 +188,7 @@
@@ -188,7 +188,7 @@
< 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 20 February 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 23 February 2020.< / p >
< div id = "introduction" class = "section level1" >
< h1 class = "hasAnchor" >
< a href = "#introduction" class = "anchor" > < / a > Introduction< / h1 >
@ -219,21 +219,21 @@
@@ -219,21 +219,21 @@
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2020-02-20 < / td >
< td align = "center" > 2020-02-23 < / 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" > 2020-02-20 < / td >
< td align = "center" > 2020-02-23 < / 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" > 2020-02-20 < / td >
< td align = "center" > 2020-02-23 < / td >
< td align = "center" > efgh< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
@ -328,10 +328,10 @@
@@ -328,10 +328,10 @@
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td align = "center" > 2010-01-05 < / td >
< td align = "center" > F 4< / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > Streptococcus pneumoniae < / td >
< td align = "center" > 2014-10-31 < / td >
< td align = "center" > B 4< / td >
< td align = "center" > Hospital B < / td >
< td align = "center" > Staphylococcus aureus < / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
@ -339,59 +339,59 @@
@@ -339,59 +339,59 @@
< td align = "center" > M< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2012-08-23 < / td >
< td align = "center" > J5 < / td >
< td align = "center" > 2012-02-24 < / td >
< td align = "center" > E10 < / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > Streptococcus pneumoniae< / td >
< td align = "center" > S< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > R< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2016-06-20 < / td >
< td align = "center" > S 1< / td >
< td align = "center" > 2017-11-04 < / td >
< td align = "center" > G 1< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > Escherichia coli< / 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" > S< / td >
< td align = "center" > F< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2013-05 -08< / td >
< td align = "center" > J3 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > 2011-10 -08< / td >
< td align = "center" > V4 < / 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" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > F< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 2011-12-28 < / td >
< td align = "center" > T8 < / td >
< td align = "center" > 2016-02-16 < / td >
< td align = "center" > K6 < / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > Staphylococcus aureus< / td >
< td align = "center" > S< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > F< / td >
< td align = "center" > R< / td >
< td align = "center" > M< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 2016-11-05 < / td >
< td align = "center" > G9 < / td >
< td align = "center" > 2014-05-28 < / td >
< td align = "center" > N6 < / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > Escherichia coli< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > S< / td >
< td align = "center" > F< / td >
< / tr >
< / tbody >
< / table >
@ -423,16 +423,16 @@ Unique: 2</p>
@@ -423,16 +423,16 @@ Unique: 2</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > M< / td >
< td align = "right" > 10,402 < / td >
< td align = "right" > 52.0 1%< / td >
< td align = "right" > 10,402 < / td >
< td align = "right" > 52.0 1%< / td >
< td align = "right" > 10,361 < / td >
< td align = "right" > 51.8 1%< / td >
< td align = "right" > 10,361 < / td >
< td align = "right" > 51.8 1%< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > F< / td >
< td align = "right" > 9,598 < / td >
< td align = "right" > 47.99 %< / td >
< td align = "right" > 9,639 < / td >
< td align = "right" > 48.20 %< / td >
< td align = "right" > 20,000< / td >
< td align = "right" > 100.00%< / td >
< / tr >
@ -447,65 +447,7 @@ Unique: 2</p>
@@ -447,65 +447,7 @@ Unique: 2</p>
< span id = "cb12-2" > < a href = "#cb12-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" > mutate_at< / a > < / span > (< span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" > vars< / a > < / span > (AMX< span class = "op" > :< / span > GEN), as.rsi)< / span > < / code > < / pre > < / div >
< p > Finally, we will apply < a href = "http://www.eucast.org/expert_rules_and_intrinsic_resistance/" > EUCAST rules< / a > on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the < code > < a href = "../reference/eucast_rules.html" > eucast_rules()< / a > < / code > function can also apply additional rules, like forcing < help title = "ATC: J01CA01" > ampicillin< / help > = R when < help title = "ATC: J01CR02" > amoxicillin/clavulanic acid< / help > = R.< / p >
< p > Because the amoxicillin (column < code > AMX< / code > ) and amoxicillin/clavulanic acid (column < code > AMC< / code > ) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The < code > < a href = "../reference/eucast_rules.html" > eucast_rules()< / a > < / code > fixes this:< / p >
< div class = "sourceCode" id = "cb13" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb13-1" > < a href = "#cb13-1" > < / a > data < -< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/eucast_rules.html" > eucast_rules< / a > < / span > (data, < span class = "dt" > col_mo =< / span > < span class = "st" > "bacteria"< / span > )< / span >
< span id = "cb13-2" > < a href = "#cb13-2" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-3" > < a href = "#cb13-3" > < / a > < span class = "co" > # Other rules by this AMR package< / span > < / span >
< span id = "cb13-4" > < a href = "#cb13-4" > < / a > < span class = "co" > # Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)< / span > < / span >
< span id = "cb13-5" > < a href = "#cb13-5" > < / a > < span class = "co" > # Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)< / span > < / span >
< span id = "cb13-6" > < a href = "#cb13-6" > < / a > < span class = "co" > # Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,986 values changed)< / span > < / span >
< span id = "cb13-7" > < a href = "#cb13-7" > < / a > < span class = "co" > # Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (157 values changed)< / span > < / span >
< span id = "cb13-8" > < a href = "#cb13-8" > < / a > < span class = "co" > # Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)< / span > < / span >
< span id = "cb13-9" > < a href = "#cb13-9" > < / a > < span class = "co" > # Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)< / span > < / span >
< span id = "cb13-10" > < a href = "#cb13-10" > < / a > < span class = "co" > # Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)< / span > < / span >
< span id = "cb13-11" > < a href = "#cb13-11" > < / a > < span class = "co" > # Non-EUCAST: set trimethoprim/sulfa = S where trimethoprim = S (no changes)< / span > < / span >
< span id = "cb13-12" > < a href = "#cb13-12" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-13" > < a href = "#cb13-13" > < / a > < span class = "co" > # ----< / span > < / span >
< span id = "cb13-14" > < a href = "#cb13-14" > < / a > < span class = "co" > # Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)< / span > < / span >
< span id = "cb13-15" > < a href = "#cb13-15" > < / a > < span class = "co" > # http://eucast.org/< / span > < / span >
< span id = "cb13-16" > < a href = "#cb13-16" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-17" > < a href = "#cb13-17" > < / a > < span class = "co" > # EUCAST Clinical Breakpoints (v10.0, 2020)< / span > < / span >
< span id = "cb13-18" > < a href = "#cb13-18" > < / a > < span class = "co" > # Aerococcus sanguinicola (no changes)< / span > < / span >
< span id = "cb13-19" > < a href = "#cb13-19" > < / a > < span class = "co" > # Aerococcus urinae (no changes)< / span > < / span >
< span id = "cb13-20" > < a href = "#cb13-20" > < / a > < span class = "co" > # Anaerobic Gram-negatives (no changes)< / span > < / span >
< span id = "cb13-21" > < a href = "#cb13-21" > < / a > < span class = "co" > # Anaerobic Gram-positives (no changes)< / span > < / span >
< span id = "cb13-22" > < a href = "#cb13-22" > < / a > < span class = "co" > # Burkholderia pseudomallei (no changes)< / span > < / span >
< span id = "cb13-23" > < a href = "#cb13-23" > < / a > < span class = "co" > # Campylobacter coli (no changes)< / span > < / span >
< span id = "cb13-24" > < a href = "#cb13-24" > < / a > < span class = "co" > # Campylobacter jejuni (no changes)< / span > < / span >
< span id = "cb13-25" > < a href = "#cb13-25" > < / a > < span class = "co" > # Enterobacterales (Order) (no changes)< / span > < / span >
< span id = "cb13-26" > < a href = "#cb13-26" > < / a > < span class = "co" > # Enterococcus (no changes)< / span > < / span >
< span id = "cb13-27" > < a href = "#cb13-27" > < / a > < span class = "co" > # Haemophilus influenzae (no changes)< / span > < / span >
< span id = "cb13-28" > < a href = "#cb13-28" > < / a > < span class = "co" > # Kingella kingae (no changes)< / span > < / span >
< span id = "cb13-29" > < a href = "#cb13-29" > < / a > < span class = "co" > # Moraxella catarrhalis (no changes)< / span > < / span >
< span id = "cb13-30" > < a href = "#cb13-30" > < / a > < span class = "co" > # Pasteurella multocida (no changes)< / span > < / span >
< span id = "cb13-31" > < a href = "#cb13-31" > < / a > < span class = "co" > # Staphylococcus (no changes)< / span > < / span >
< span id = "cb13-32" > < a href = "#cb13-32" > < / a > < span class = "co" > # Streptococcus groups A, B, C, G (no changes)< / span > < / span >
< span id = "cb13-33" > < a href = "#cb13-33" > < / a > < span class = "co" > # Streptococcus pneumoniae (1,017 values changed)< / span > < / span >
< span id = "cb13-34" > < a href = "#cb13-34" > < / a > < span class = "co" > # Viridans group streptococci (no changes)< / span > < / span >
< span id = "cb13-35" > < a href = "#cb13-35" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-36" > < a href = "#cb13-36" > < / a > < span class = "co" > # EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)< / span > < / span >
< span id = "cb13-37" > < a href = "#cb13-37" > < / a > < span class = "co" > # Table 01: Intrinsic resistance in Enterobacteriaceae (1,297 values changed)< / span > < / span >
< span id = "cb13-38" > < a href = "#cb13-38" > < / a > < span class = "co" > # Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)< / span > < / span >
< span id = "cb13-39" > < a href = "#cb13-39" > < / a > < span class = "co" > # Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)< / span > < / span >
< span id = "cb13-40" > < a href = "#cb13-40" > < / a > < span class = "co" > # Table 04: Intrinsic resistance in Gram-positive bacteria (2,752 values changed)< / span > < / span >
< span id = "cb13-41" > < a href = "#cb13-41" > < / a > < span class = "co" > # Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)< / span > < / span >
< span id = "cb13-42" > < a href = "#cb13-42" > < / a > < span class = "co" > # Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)< / span > < / span >
< span id = "cb13-43" > < a href = "#cb13-43" > < / a > < span class = "co" > # Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)< / span > < / span >
< span id = "cb13-44" > < a href = "#cb13-44" > < / a > < span class = "co" > # Table 12: Interpretive rules for aminoglycosides (no changes)< / span > < / span >
< span id = "cb13-45" > < a href = "#cb13-45" > < / a > < span class = "co" > # Table 13: Interpretive rules for quinolones (no changes)< / span > < / span >
< span id = "cb13-46" > < a href = "#cb13-46" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-47" > < a href = "#cb13-47" > < / a > < span class = "co" > # -------------------------------------------------------------------------------< / span > < / span >
< span id = "cb13-48" > < a href = "#cb13-48" > < / a > < span class = "co" > # EUCAST rules affected 6,502 out of 20,000 rows, making a total of 8,209 edits< / span > < / span >
< span id = "cb13-49" > < a href = "#cb13-49" > < / a > < span class = "co" > # => added 0 test results< / span > < / span >
< span id = "cb13-50" > < a href = "#cb13-50" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-51" > < a href = "#cb13-51" > < / a > < span class = "co" > # => changed 8,209 test results< / span > < / span >
< span id = "cb13-52" > < a href = "#cb13-52" > < / a > < span class = "co" > # - 124 test results changed from S to I< / span > < / span >
< span id = "cb13-53" > < a href = "#cb13-53" > < / a > < span class = "co" > # - 4,743 test results changed from S to R< / span > < / span >
< span id = "cb13-54" > < a href = "#cb13-54" > < / a > < span class = "co" > # - 1,209 test results changed from I to S< / span > < / span >
< span id = "cb13-55" > < a href = "#cb13-55" > < / a > < span class = "co" > # - 356 test results changed from I to R< / span > < / span >
< span id = "cb13-56" > < a href = "#cb13-56" > < / a > < span class = "co" > # - 1,777 test results changed from R to S< / span > < / span >
< span id = "cb13-57" > < a href = "#cb13-57" > < / a > < span class = "co" > # -------------------------------------------------------------------------------< / span > < / span >
< span id = "cb13-58" > < a href = "#cb13-58" > < / a > < span class = "co" > # < / span > < / span >
< span id = "cb13-59" > < a href = "#cb13-59" > < / a > < span class = "co" > # Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.< / span > < / span > < / code > < / pre > < / div >
< div class = "sourceCode" id = "cb13" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb13-1" > < a href = "#cb13-1" > < / a > data < -< span class = "st" > < / span > < span class = "kw" > < a href = "../reference/eucast_rules.html" > eucast_rules< / a > < / span > (data, < span class = "dt" > col_mo =< / span > < span class = "st" > "bacteria"< / span > )< / span > < / code > < / pre > < / div >
< / div >
< div id = "adding-new-variables" class = "section level1" >
< h1 class = "hasAnchor" >
@ -529,9 +471,8 @@ Unique: 2</p>
@@ -529,9 +471,8 @@ Unique: 2</p>
< span id = "cb15-2" > < a href = "#cb15-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" > mutate< / a > < / span > (< span class = "dt" > first =< / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > first_isolate< / a > < / span > (.))< / span >
< span id = "cb15-3" > < a href = "#cb15-3" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `bacteria` as input for `col_mo`.< / span > < / span >
< span id = "cb15-4" > < a href = "#cb15-4" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `date` as input for `col_date`.< / span > < / span >
< span id = "cb15-5" > < a href = "#cb15-5" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `patient_id` as input for `col_patient_id`.< / span > < / span >
< span id = "cb15-6" > < a href = "#cb15-6" > < / a > < span class = "co" > # => Found 5,695 first isolates (28.5% of total)< / span > < / span > < / code > < / pre > < / div >
< p > So only 28.5% 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 >
< span id = "cb15-5" > < a href = "#cb15-5" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `patient_id` as input for `col_patient_id`.< / span > < / span > < / code > < / pre > < / div >
< p > So only 28.4% 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 = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb16-1" > < a href = "#cb16-1" > < / a > data_1st < -< span class = "st" > < / span > data < span class = "op" > %> %< / span > < span class = "st" > < / span > < / span >
< span id = "cb16-2" > < a href = "#cb16-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/filter.html" > filter< / a > < / span > (first < span class = "op" > ==< / span > < span class = "st" > < / span > < span class = "ot" > TRUE< / span > )< / span > < / code > < / pre > < / div >
< p > For future use, the above two syntaxes can be shortened with the < code > < a href = "../reference/first_isolate.html" > filter_first_isolate()< / a > < / code > function:< / p >
@ -541,7 +482,7 @@ Unique: 2</p>
@@ -541,7 +482,7 @@ Unique: 2</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 N 2, 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 Q 2, sorted on date:< / p >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > isolate< / th >
@ -557,8 +498,8 @@ Unique: 2</p>
@@ -557,8 +498,8 @@ Unique: 2</p>
< tbody >
< tr class = "odd" >
< td align = "center" > 1< / td >
< td align = "center" > 2010-02-09 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-02-26 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
@ -568,98 +509,98 @@ Unique: 2</p>
@@ -568,98 +509,98 @@ Unique: 2</p>
< / tr >
< tr class = "even" >
< td align = "center" > 2< / td >
< td align = "center" > 2010-03-0 2< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-03-25 < / td >
< td align = "center" > Q 2< / 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" > FALSE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 3< / td >
< td align = "center" > 2010-04-0 5< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-05-23 < / td >
< td align = "center" > Q 2< / 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 >
< / tr >
< tr class = "even" >
< td align = "center" > 4< / td >
< td align = "center" > 2010-05-19 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-05-24 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > I < / 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 = "odd" >
< td align = "center" > 5< / td >
< td align = "center" > 2010-07 -08< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-09 -08< / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > I < / 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" > 6< / td >
< td align = "center" > 2010-08-0 9< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-03-1 9< / td >
< td align = "center" > Q 2< / 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" > S< / td >
< td align = "center" > FALS E< / td >
< td align = "center" > TRU E< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 7< / td >
< td align = "center" > 2011-05-26 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-04-02 < / td >
< td align = "center" > Q 2< / 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" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 8< / td >
< td align = "center" > 2011-05-26 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-04-05 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 9< / td >
< td align = "center" > 2011-06-19 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-11-13 < / td >
< td align = "center" > Q 2< / 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" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 10< / td >
< td align = "center" > 2011-07-29 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-11-28 < / td >
< td align = "center" > Q 2< / 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 >
@ -676,9 +617,7 @@ Unique: 2</p>
@@ -676,9 +617,7 @@ Unique: 2</p>
< span id = "cb18-5" > < a href = "#cb18-5" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `bacteria` as input for `col_mo`.< / span > < / span >
< span id = "cb18-6" > < a href = "#cb18-6" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `date` as input for `col_date`.< / span > < / span >
< span id = "cb18-7" > < a href = "#cb18-7" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `patient_id` as input for `col_patient_id`.< / span > < / span >
< span id = "cb18-8" > < a href = "#cb18-8" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.< / span > < / span >
< span id = "cb18-9" > < a href = "#cb18-9" > < / a > < span class = "co" > # [Criterion] Inclusion based on key antibiotics, ignoring I< / span > < / span >
< span id = "cb18-10" > < a href = "#cb18-10" > < / a > < span class = "co" > # => Found 15,096 first weighted isolates (75.5% of total)< / span > < / span > < / code > < / pre > < / div >
< span id = "cb18-8" > < a href = "#cb18-8" > < / a > < span class = "co" > # < / span > < span class = "al" > NOTE< / span > < span class = "co" > : Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.< / span > < / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th align = "center" > isolate< / th >
@ -695,8 +634,8 @@ Unique: 2</p>
@@ -695,8 +634,8 @@ Unique: 2</p>
< tbody >
< tr class = "odd" >
< td align = "center" > 1< / td >
< td align = "center" > 2010-02-09 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-02-26 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
@ -707,23 +646,23 @@ Unique: 2</p>
@@ -707,23 +646,23 @@ Unique: 2</p>
< / tr >
< tr class = "even" >
< td align = "center" > 2< / td >
< td align = "center" > 2010-03-0 2< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-03-25 < / td >
< td align = "center" > Q 2< / 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" > FALSE< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 3< / td >
< td align = "center" > 2010-04-0 5< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-05-23 < / td >
< td align = "center" > Q 2< / 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 >
@ -731,11 +670,11 @@ Unique: 2</p>
@@ -731,11 +670,11 @@ Unique: 2</p>
< / tr >
< tr class = "even" >
< td align = "center" > 4< / td >
< td align = "center" > 2010-05-19 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-05-24 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R < / td >
< td align = "center" > I < / 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 >
@ -743,83 +682,83 @@ Unique: 2</p>
@@ -743,83 +682,83 @@ Unique: 2</p>
< / tr >
< tr class = "odd" >
< td align = "center" > 5< / td >
< td align = "center" > 2010-07 -08< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2010-09 -08< / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > I < / 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 = "even" >
< td align = "center" > 6< / td >
< td align = "center" > 2010-08-0 9< / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-03-1 9< / td >
< td align = "center" > Q 2< / 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" > S< / td >
< td align = "center" > FALS E< / td >
< td align = "center" > TRU E< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td align = "center" > 7< / td >
< td align = "center" > 2011-05-26 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-04-02 < / td >
< td align = "center" > Q 2< / 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" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > TRUE< / td >
< td align = "center" > TRUE< / td >
< td align = "center" > FALSE< / td >
< td align = "center" > FALSE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 8< / td >
< td align = "center" > 2011-05-26 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-04-05 < / td >
< td align = "center" > Q 2< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > R< / td >
< td align = "center" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > R< / 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 = "odd" >
< td align = "center" > 9< / td >
< td align = "center" > 2011-06-19 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-11-13 < / td >
< td align = "center" > Q 2< / 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" > S < / td >
< td align = "center" > S< / td >
< td align = "center" > FALSE< / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td align = "center" > 10< / td >
< td align = "center" > 2011-07-29 < / td >
< td align = "center" > N 2< / td >
< td align = "center" > 2011-11-28 < / td >
< td align = "center" > Q 2< / 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 >
< td align = "center" > FALSE< / td >
< td align = "center" > TRU E< / td >
< td align = "center" > FALS E< / td >
< / tr >
< / tbody >
< / table >
< p > Instead of 2, now 9 isolates are flagged. In total, 75.5% of all isolates are marked โfirst weightedโ - 47.0 % 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 7 isolates are flagged. In total, 74.8% of all isolates are marked โfirst weightedโ - 46.4 % 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 = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb19-1" > < a href = "#cb19-1" > < / a > data_1st < -< span class = "st" > < / span > data < span class = "op" > %> %< / span > < span class = "st" > < / span > < / span >
< span id = "cb19-2" > < a href = "#cb19-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/first_isolate.html" > filter_first_weighted_isolate< / a > < / span > ()< / span > < / code > < / pre > < / div >
< p > So we end up with 15,096 isolates for analysis.< / p >
< p > So we end up with 14,960 isolates for analysis.< / p >
< p > We can remove unneeded columns:< / p >
< div class = "sourceCode" id = "cb20" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb20-1" > < a href = "#cb20-1" > < / a > data_1st < -< span class = "st" > < / span > data_1st < span class = "op" > %> %< / span > < span class = "st" > < / span > < / span >
< span id = "cb20-2" > < a href = "#cb20-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/select.html" > select< / a > < / span > (< span class = "op" > -< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/c.html" > c< / a > < / span > (first, keyab))< / span > < / code > < / pre > < / div >
@ -827,7 +766,6 @@ Unique: 2</p>
@@ -827,7 +766,6 @@ Unique: 2</p>
< div class = "sourceCode" id = "cb21" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb21-1" > < a href = "#cb21-1" > < / a > < span class = "kw" > < a href = "https://rdrr.io/r/utils/head.html" > head< / a > < / span > (data_1st)< / span > < / code > < / pre > < / div >
< table class = "table" >
< thead > < tr class = "header" >
< th > < / th >
< th align = "center" > date< / th >
< th align = "center" > patient_id< / th >
< th align = "center" > hospital< / th >
@ -844,30 +782,28 @@ Unique: 2</p>
@@ -844,30 +782,28 @@ Unique: 2</p>
< / tr > < / thead >
< tbody >
< tr class = "odd" >
< td > 1< / td >
< td align = "center" > 2010-01-05 < / td >
< td align = "center" > F4 < / td >
< td align = "center" > Hospital A < / td >
< td align = "center" > B_ STRPT_PNMN < / td >
< td align = "center" > 2014-10-3 1< / td >
< td align = "center" > B4 < / td >
< td align = "center" > Hospital B < / 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" > M< / 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 > 6< / td >
< td align = "center" > 2016-11-05< / td >
< td align = "center" > G9< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > 2012-02-24< / td >
< td align = "center" > E10< / td >
< td align = "center" > Hospital B< / 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" > I< / td >
< td align = "center" > S< / td >
< td align = "center" > S< / td >
< td align = "center" > M< / td >
< td align = "center" > Gram-negative< / td >
@ -876,14 +812,13 @@ Unique: 2</p>
@@ -876,14 +812,13 @@ Unique: 2</p>
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td > 7< / td >
< td align = "center" > 2016-05-20< / td >
< td align = "center" > A10< / td >
< td align = "center" > Hospital D< / td >
< td align = "center" > 2017-11-04< / td >
< td align = "center" > G1< / td >
< td align = "center" > Hospital B< / 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" > M< / td >
< td align = "center" > Gram-negative< / td >
@ -892,10 +827,9 @@ Unique: 2</p>
@@ -892,10 +827,9 @@ Unique: 2</p>
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td > 9< / td >
< td align = "center" > 2015-10-02< / td >
< td align = "center" > R3< / td >
< td align = "center" > Hospital C< / td >
< td align = "center" > 2011-10-08< / td >
< td align = "center" > V4< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_ESCHR_COLI< / td >
< td align = "center" > R< / td >
< td align = "center" > S< / td >
@ -908,35 +842,33 @@ Unique: 2</p>
@@ -908,35 +842,33 @@ Unique: 2</p>
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "odd" >
< td > 10< / td >
< td align = "center" > 2016-03-04< / td >
< td align = "center" > B10< / 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" > 2016-02-16< / td >
< td align = "center" > K6< / td >
< td align = "center" > Hospital D< / 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" > Gram-negative< / td >
< td align = "center" > Escherichia < / td >
< td align = "center" > coli < / td >
< td align = "center" > Gram-posi tive< / td >
< td align = "center" > Staphylococcus < / td >
< td align = "center" > aureus < / td >
< td align = "center" > TRUE< / td >
< / tr >
< tr class = "even" >
< td > 11< / td >
< td align = "center" > 2013-09-10< / td >
< td align = "center" > P4< / td >
< td align = "center" > Hospital B< / td >
< td align = "center" > B_KLBSL_PNMN< / td >
< td align = "center" > R< / td >
< td align = "center" > 2014-05-28< / td >
< td align = "center" > N6< / td >
< td align = "center" > Hospital C< / 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-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 >
@ -958,8 +890,8 @@ Unique: 2</p>
@@ -958,8 +890,8 @@ Unique: 2</p>
< div class = "sourceCode" id = "cb23" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb23-1" > < a href = "#cb23-1" > < / a > data_1st < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/cleaner/man/freq.html" > freq< / a > < / span > (genus, species)< / span > < / code > < / pre > < / div >
< p > < strong > Frequency table< / strong > < / p >
< p > Class: character< br >
Length: 15,096 < br >
Available: 15,096 (100%, NA: 0 = 0%)< br >
Length: 14,960 < br >
Available: 14,960 (100%, NA: 0 = 0%)< br >
Unique: 4< / p >
< p > Shortest: 16< br >
Longest: 24< / p >
@ -976,33 +908,33 @@ Longest: 24</p>
@@ -976,33 +908,33 @@ Longest: 24</p>
< tr class = "odd" >
< td align = "left" > 1< / td >
< td align = "left" > Escherichia coli< / td >
< td align = "right" > 7,491 < / td >
< td align = "right" > 49.62 %< / td >
< td align = "right" > 7,491 < / td >
< td align = "right" > 49.62 %< / td >
< td align = "right" > 7,397 < / td >
< td align = "right" > 49.45 %< / td >
< td align = "right" > 7,397 < / td >
< td align = "right" > 49.45 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 2< / td >
< td align = "left" > Staphylococcus aureus< / td >
< td align = "right" > 3,729 < / td >
< td align = "right" > 24.70 %< / td >
< td align = "right" > 11,22 0< / td >
< td align = "right" > 74.32 %< / td >
< td align = "right" > 3,685 < / td >
< td align = "right" > 24.63 %< / td >
< td align = "right" > 11,082 < / td >
< td align = "right" > 74.08 %< / td >
< / tr >
< tr class = "odd" >
< td align = "left" > 3< / td >
< td align = "left" > Streptococcus pneumoniae< / td >
< td align = "right" > 2,340 < / td >
< td align = "right" > 15.50 %< / td >
< td align = "right" > 13,560 < / td >
< td align = "right" > 89.83 %< / td >
< td align = "right" > 2,361 < / td >
< td align = "right" > 15.78 %< / td >
< td align = "right" > 13,443 < / td >
< td align = "right" > 89.86 %< / td >
< / tr >
< tr class = "even" >
< td align = "left" > 4< / td >
< td align = "left" > Klebsiella pneumoniae< / td >
< td align = "right" > 1,536 < / td >
< td align = "right" > 10.17 %< / td >
< td align = "right" > 15,096 < / td >
< td align = "right" > 1,517 < / td >
< td align = "right" > 10.14 %< / td >
< td align = "right" > 14,960 < / td >
< td align = "right" > 100.00%< / td >
< / tr >
< / tbody >
@ -1014,7 +946,7 @@ Longest: 24</p>
@@ -1014,7 +946,7 @@ Longest: 24</p>
< p > The functions < code > < a href = "../reference/proportion.html" > resistance()< / a > < / code > and < code > < a href = "../reference/proportion.html" > susceptibility()< / a > < / code > can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions < code > < a href = "../reference/proportion.html" > proportion_S()< / a > < / code > , < code > < a href = "../reference/proportion.html" > proportion_SI()< / a > < / code > , < code > < a href = "../reference/proportion.html" > proportion_I()< / a > < / code > , < code > < a href = "../reference/proportion.html" > proportion_IR()< / a > < / code > and < code > < a href = "../reference/proportion.html" > proportion_R()< / a > < / code > can be used to determine the proportion of a specific antimicrobial outcome.< / 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 = "cb24" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb24-1" > < a href = "#cb24-1" > < / a > data_1st < span class = "op" > %> %< / span > < span class = "st" > < / span > < span class = "kw" > < a href = "../reference/proportion.html" > resistance< / a > < / span > (AMX)< / span >
< span id = "cb24-2" > < a href = "#cb24-2" > < / a > < span class = "co" > # [1] 0.468137 3< / span > < / span > < / code > < / pre > < / div >
< span id = "cb24-2" > < a href = "#cb24-2" > < / a > < span class = "co" > # [1] 0.4635695 < / span > < / span > < / code > < / 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 = "cb25" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < span id = "cb25-1" > < a href = "#cb25-1" > < / a > data_1st < span class = "op" > %> %< / span > < span class = "st" > < / span > < / span >
< span id = "cb25-2" > < a href = "#cb25-2" > < / a > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/group_by.html" > group_by< / a > < / span > (hospital) < span class = "op" > %> %< / span > < span class = "st" > < / span > < / span >
@ -1027,19 +959,19 @@ Longest: 24</p>
@@ -1027,19 +959,19 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.4648446 < / td >
< td align = "center" > 0.4490022 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.4689223 < / td >
< td align = "center" > 0.4746786 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.4656180 < / td >
< td align = "center" > 0.4505104 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.4734787 < / td >
< td align = "center" > 0.4760039 < / td >
< / tr >
< / tbody >
< / table >
@ -1057,23 +989,23 @@ Longest: 24</p>
@@ -1057,23 +989,23 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Hospital A< / td >
< td align = "center" > 0.4648446 < / td >
< td align = "center" > 4537 < / td >
< td align = "center" > 0.4490022 < / td >
< td align = "center" > 4510 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital B< / td >
< td align = "center" > 0.4689223 < / td >
< td align = "center" > 526 1< / td >
< td align = "center" > 0.4746786 < / td >
< td align = "center" > 5134 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Hospital C< / td >
< td align = "center" > 0.4656180 < / td >
< td align = "center" > 222 5< / td >
< td align = "center" > 0.4505104 < / td >
< td align = "center" > 2253 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Hospital D< / td >
< td align = "center" > 0.4734787 < / td >
< td align = "center" > 307 3< / td >
< td align = "center" > 0.4760039 < / td >
< td align = "center" > 306 3< / td >
< / tr >
< / tbody >
< / table >
@ -1093,27 +1025,27 @@ Longest: 24</p>
@@ -1093,27 +1025,27 @@ Longest: 24</p>
< tbody >
< tr class = "odd" >
< td align = "center" > Escherichia< / td >
< td align = "center" > 0.9255106 < / td >
< td align = "center" > 0.8972100 < / td >
< td align = "center" > 0.9937 25 8< / td >
< td align = "center" > 0.9251048 < / td >
< td align = "center" > 0.8952278 < / td >
< td align = "center" > 0.9928349 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Klebsiella< / td >
< td align = "center" > 0.9199219 < / td >
< td align = "center" > 0.8932292 < / td >
< td align = "center" > 0.9934896 < / td >
< td align = "center" > 0.9169413 < / td >
< td align = "center" > 0.9083718 < / td >
< td align = "center" > 0.9947264 < / td >
< / tr >
< tr class = "odd" >
< td align = "center" > Staphylococcus< / td >
< td align = "center" > 0.9187450 < / td >
< td align = "center" > 0.9133816 < / td >
< td align = "center" > 0.992491 3< / td >
< td align = "center" > 0.9305292 < / td >
< td align = "center" > 0.9158752 < / td >
< td align = "center" > 0.9937585 < / td >
< / tr >
< tr class = "even" >
< td align = "center" > Streptococcus< / td >
< td align = "center" > 0.6128205 < / td >
< td align = "center" > 0.6027107 < / td >
< td align = "center" > 0.0000000< / td >
< td align = "center" > 0.6128205 < / td >
< td align = "center" > 0.6027107 < / td >
< / tr >
< / tbody >
< / table >