2019-01-11 20:37:23 +01:00
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --> < html lang = "en" >
< head >
< meta http-equiv = "Content-Type" content = "text/html; charset=UTF-8" >
< meta charset = "utf-8" >
< meta http-equiv = "X-UA-Compatible" content = "IE=edge" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
< title > Benchmarks • AMR (for R)< / title >
<!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "180x180" href = "../apple-touch-icon.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "120x120" href = "../apple-touch-icon-120x120.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "76x76" href = "../apple-touch-icon-76x76.png" >
< link rel = "apple-touch-icon" type = "image/png" sizes = "60x60" href = "../apple-touch-icon-60x60.png" >
<!-- jquery --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity = "sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin = "anonymous" > < / script > <!-- Bootstrap --> < link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity = "sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin = "anonymous" > < / script > <!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity = "sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin = "anonymous" >
<!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity = "sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin = "anonymous" > < / script > <!-- sticky kit --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity = "sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < link href = "../pkgdown.css" rel = "stylesheet" >
< script src = "../pkgdown.js" > < / script > <!-- docsearch --> < script src = "../docsearch.js" > < / script > < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity = "sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin = "anonymous" >
< link href = "../docsearch.css" rel = "stylesheet" >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity = "sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin = "anonymous" > < / script > < link href = "../extra.css" rel = "stylesheet" >
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "Benchmarks" >
< meta property = "og:description" content = "" >
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.png" >
< meta name = "twitter:card" content = "summary" >
<!-- mathjax --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity = "sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity = "sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin = "anonymous" > < / script > <!-- [if lt IE 9]>
< script src = "https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js" > < / script >
< script src = "https://oss.maxcdn.com/respond/1.4.2/respond.min.js" > < / script >
<![endif]-->
< / head >
< body >
< div class = "container template-article" >
< header > < div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
< div class = "container" >
< div class = "navbar-header" >
< button type = "button" class = "navbar-toggle collapsed" data-toggle = "collapse" data-target = "#navbar" aria-expanded = "false" >
< span class = "sr-only" > Toggle navigation< / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< span class = "icon-bar" > < / span >
< / button >
< span class = "navbar-brand" >
< a class = "navbar-link" href = "../index.html" > AMR (for R)< / a >
2019-03-27 11:22:36 +01:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Released version" > 0.6.0< / span >
2019-01-11 20:37:23 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
< li >
< a href = "../index.html" >
< span class = "fa fa-home" > < / span >
Home
< / a >
< / li >
< li class = "dropdown" >
< a href = "#" class = "dropdown-toggle" data-toggle = "dropdown" role = "button" aria-expanded = "false" >
< span class = "fa fa-question-circle" > < / span >
How to
< span class = "caret" > < / span >
< / a >
< ul class = "dropdown-menu" role = "menu" >
< li >
< a href = "../articles/AMR.html" >
< span class = "fa fa-directions" > < / span >
Conduct AMR analysis
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../articles/resistance_predict.html" >
2019-01-11 20:37:23 +01:00
< span class = "fa fa-dice" > < / span >
Predict antimicrobial resistance
< / a >
< / li >
2019-01-29 00:06:50 +01:00
< li >
< a href = "../articles/WHONET.html" >
< span class = "fa fa-globe-americas" > < / span >
Work with WHONET data
< / a >
< / li >
2019-02-14 15:18:17 +01:00
< li >
< a href = "../articles/SPSS.html" >
< span class = "fa fa-file-upload" > < / span >
Import data from SPSS/SAS/Stata
< / a >
< / li >
2019-01-11 20:37:23 +01:00
< li >
< a href = "../articles/EUCAST.html" >
< span class = "fa fa-exchange-alt" > < / span >
Apply EUCAST rules
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/mo_property.html" >
2019-01-11 20:37:23 +01:00
< span class = "fa fa-bug" > < / span >
Get properties of a microorganism
< / a >
< / li >
< li >
2019-02-14 10:23:51 +01:00
< a href = "../reference/atc_property.html" >
2019-01-11 20:37:23 +01:00
< span class = "fa fa-capsules" > < / span >
Get properties of an antibiotic
< / a >
< / li >
< li >
< a href = "../articles/freq.html" >
< span class = "fa fa-sort-amount-down" > < / span >
Create frequency tables
< / a >
< / li >
< li >
< a href = "../articles/G_test.html" >
< span class = "fa fa-clipboard-check" > < / span >
Use the G-test
< / a >
< / li >
< li >
< a href = "../articles/benchmarks.html" >
< span class = "fa fa-shipping-fast" > < / span >
Other: benchmarks
< / a >
< / li >
< / ul >
< / li >
< li >
< a href = "../reference/" >
< span class = "fa fa-book-open" > < / span >
Manual
< / a >
< / li >
< li >
< a href = "../authors.html" >
< span class = "fa fa-users" > < / span >
Authors
< / a >
< / li >
< li >
< a href = "../news/" >
< span class = "far fa far fa-newspaper" > < / span >
Changelog
< / a >
< / li >
< / ul >
< ul class = "nav navbar-nav navbar-right" >
< li >
< a href = "https://gitlab.com/msberends/AMR" >
< span class = "fab fa fab fa-gitlab" > < / span >
Source Code
< / a >
< / li >
< li >
< a href = "../LICENSE-text.html" >
< span class = "fa fa-book" > < / span >
Licence
< / a >
< / li >
< / ul >
< form class = "navbar-form navbar-right" role = "search" >
< div class = "form-group" >
< input type = "search" class = "form-control" name = "search-input" id = "search-input" placeholder = "Search..." aria-label = "Search for..." autocomplete = "off" >
< / div >
< / form >
< / div >
<!-- /.nav - collapse -->
< / div >
<!-- /.container -->
< / div >
<!-- /.navbar -->
< / header > < div class = "row" >
< div class = "col-md-9 contents" >
< div class = "page-header toc-ignore" >
< h1 > Benchmarks< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
2019-03-27 11:22:36 +01:00
< h4 class = "date" > 27 March 2019< / h4 >
2019-01-11 20:37:23 +01:00
< div class = "hidden name" > < code > benchmarks.Rmd< / code > < / div >
< / div >
2019-03-06 14:39:02 +01:00
< p > One of the most important features of this package is the complete microbial taxonomic database, supplied by the < a href = "http://catalogueoflife.org" > Catalogue of Life< / a > . We created a function < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > that transforms any user input value to a valid microbial ID by using intelligent rules combined with the taxonomic tree of Catalogue of Life.< / p >
2019-02-20 00:04:48 +01:00
< p > Using the < code > microbenchmark< / code > package, we can review the calculation performance of this function. Its function < code > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark()< / a > < / code > runs different input expressions independently of each other and measures their time-to-result.< / p >
2019-02-14 10:23:51 +01:00
< div class = "sourceCode" id = "cb1" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb1-1" title = "1" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/library" > library< / a > < / span > (microbenchmark)< / a >
< a class = "sourceLine" id = "cb1-2" title = "2" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/library" > library< / a > < / span > (AMR)< / a > < / code > < / pre > < / div >
2019-01-11 20:37:23 +01:00
< p > In the next test, we try to ‘ ’ < em > Staphylococcus aureus< / em > . The actual result is the same every time: it returns its MO code < code > B_STPHY_AUR< / code > (< em > B< / em > stands for < em > Bacteria< / em > , the taxonomic kingdom).< / p >
2019-03-06 14:39:02 +01:00
< p > But the calculation time differs a lot:< / p >
2019-02-20 00:04:48 +01:00
< div class = "sourceCode" id = "cb2" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb2-1" title = "1" > S.aureus < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "sau"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-2" title = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "stau"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "staaur"< / span > ),< / a >
2019-02-25 15:52:32 +01:00
< a class = "sourceLine" id = "cb2-4" title = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "STAAUR"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
2019-02-20 00:04:48 +01:00
< a class = "sourceLine" id = "cb2-7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
2019-02-22 22:12:10 +01:00
< a class = "sourceLine" id = "cb2-8" title = "8" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
2019-03-15 13:57:25 +01:00
< a class = "sourceLine" id = "cb2-9" title = "9" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (S.aureus, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 2< / span > )< / a >
2019-02-22 22:12:10 +01:00
< a class = "sourceLine" id = "cb2-10" title = "10" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
2019-03-18 14:29:41 +01:00
< a class = "sourceLine" id = "cb2-11" title = "11" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
2019-03-27 11:22:36 +01:00
< a class = "sourceLine" id = "cb2-12" title = "12" > < span class = "co" > #> as.mo("sau") 18.0 18.0 22 18.0 20.0 48 10< / span > < / a >
< a class = "sourceLine" id = "cb2-13" title = "13" > < span class = "co" > #> as.mo("stau") 48.0 48.0 76 67.0 92.0 150 10< / span > < / a >
< a class = "sourceLine" id = "cb2-14" title = "14" > < span class = "co" > #> as.mo("staaur") 18.0 18.0 24 19.0 22.0 62 10< / span > < / a >
< a class = "sourceLine" id = "cb2-15" title = "15" > < span class = "co" > #> as.mo("STAAUR") 18.0 18.0 23 18.0 20.0 61 10< / span > < / a >
< a class = "sourceLine" id = "cb2-16" title = "16" > < span class = "co" > #> as.mo("S. aureus") 29.0 29.0 35 29.0 30.0 76 10< / span > < / a >
< a class = "sourceLine" id = "cb2-17" title = "17" > < span class = "co" > #> as.mo("S. aureus") 29.0 29.0 37 29.0 30.0 79 10< / span > < / a >
< a class = "sourceLine" id = "cb2-18" title = "18" > < span class = "co" > #> as.mo("Staphylococcus aureus") 8.2 8.2 13 8.2 8.4 52 10< / span > < / a > < / code > < / pre > < / div >
2019-02-27 11:36:12 +01:00
< p > In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.< / p >
2019-02-25 15:52:32 +01:00
< p > To achieve this speed, the < code > as.mo< / code > function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of < em > Thermus islandicus< / em > (< code > B_THERMS_ISL< / code > ), a bug probably never found before in humans:< / p >
< div class = "sourceCode" id = "cb3" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb3-1" title = "1" > T.islandicus < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "theisl"< / span > ),< / a >
2019-03-15 13:57:25 +01:00
< a class = "sourceLine" id = "cb3-2" title = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "THEISL"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-3" title = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "T. islandicus"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-4" title = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "T. islandicus"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Thermus islandicus"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-6" title = "6" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb3-7" title = "7" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (T.islandicus, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 2< / span > )< / a >
2019-02-25 15:52:32 +01:00
< a class = "sourceLine" id = "cb3-8" title = "8" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
2019-03-15 13:57:25 +01:00
< a class = "sourceLine" id = "cb3-9" title = "9" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
2019-03-27 11:22:36 +01:00
< a class = "sourceLine" id = "cb3-10" title = "10" > < span class = "co" > #> as.mo("theisl") 460 460 500 510 510 560 10< / span > < / a >
< a class = "sourceLine" id = "cb3-11" title = "11" > < span class = "co" > #> as.mo("THEISL") 460 470 490 490 510 530 10< / span > < / a >
< a class = "sourceLine" id = "cb3-12" title = "12" > < span class = "co" > #> as.mo("T. islandicus") 74 74 84 75 78 120 10< / span > < / a >
< a class = "sourceLine" id = "cb3-13" title = "13" > < span class = "co" > #> as.mo("T. islandicus") 74 75 88 75 120 120 10< / span > < / a >
< a class = "sourceLine" id = "cb3-14" title = "14" > < span class = "co" > #> as.mo("Thermus islandicus") 73 73 84 74 75 130 10< / span > < / a > < / code > < / pre > < / div >
< p > That takes 7.6 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like < em > Thermus islandicus< / em > ) are almost fast - these are the most probable input from most data sets.< / p >
2019-02-25 15:52:32 +01:00
< p > In the figure below, we compare < em > Escherichia coli< / em > (which is very common) with < em > Prevotella brevis< / em > (which is moderately common) and with < em > Thermus islandicus< / em > (which is very uncommon):< / p >
2019-02-20 00:04:48 +01:00
< div class = "sourceCode" id = "cb4" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb4-1" title = "1" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/par" > par< / a > < / span > (< span class = "dt" > mar =< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "dv" > 5< / span > , < span class = "dv" > 16< / span > , < span class = "dv" > 4< / span > , < span class = "dv" > 2< / span > )) < span class = "co" > # set more space for left margin text (16)< / span > < / a >
< a class = "sourceLine" id = "cb4-2" title = "2" > < / a >
2019-02-25 15:52:32 +01:00
< a class = "sourceLine" id = "cb4-3" title = "3" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Thermus islandicus"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-4" title = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Prevotella brevis"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Escherichia coli"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "T. islandicus"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "P. brevis"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-8" title = "8" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. coli"< / span > ),< / a >
2019-03-15 13:57:25 +01:00
< a class = "sourceLine" id = "cb4-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > ),< / a >
2019-02-22 22:12:10 +01:00
< a class = "sourceLine" id = "cb4-10" title = "10" > < span class = "dt" > horizontal =< / span > < span class = "ot" > TRUE< / span > , < span class = "dt" > las =< / span > < span class = "dv" > 1< / span > , < span class = "dt" > unit =< / span > < span class = "st" > "s"< / span > , < span class = "dt" > log =< / span > < span class = "ot" > FALSE< / span > ,< / a >
2019-03-15 13:57:25 +01:00
< a class = "sourceLine" id = "cb4-11" title = "11" > < span class = "dt" > xlab =< / span > < span class = "st" > ""< / span > , < span class = "dt" > ylab =< / span > < span class = "st" > "Time in seconds"< / span > , < span class = "dt" > ylim =< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/c" > c< / a > < / span > (< span class = "dv" > 0< / span > , < span class = "fl" > 0.5< / span > ),< / a >
2019-02-22 22:12:10 +01:00
< a class = "sourceLine" id = "cb4-12" title = "12" > < span class = "dt" > main =< / span > < span class = "st" > "Benchmarks per prevalence"< / span > )< / a > < / code > < / pre > < / div >
2019-02-21 18:55:52 +01:00
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-5-1.png" width = "720" > < / p >
2019-03-15 13:57:25 +01:00
< p > In reality, the < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > functions < strong > learns from its own output to speed up determinations for next times< / strong > . In above figure, this effect was disabled to show the difference with the boxplot below - when you would use < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > yourself:< / p >
2019-03-27 11:22:36 +01:00
< pre > < code > #> File /home/uscloud/.Rhistory_mo removed.< / code > < / pre >
2019-03-15 13:57:25 +01:00
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-6-1.png" width = "720" > < / p >
< p > The highest outliers are the first times. All next determinations were done in only thousands of seconds.< / p >
< p > Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: < strong > repetitive results< / strong > and < strong > already precalculated results< / strong > .< / p >
2019-01-11 20:37:23 +01:00
< div id = "repetitive-results" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#repetitive-results" class = "anchor" > < / a > Repetitive results< / h3 >
2019-02-28 13:56:28 +01:00
< p > Repetitive results are unique values that are present more than once. Unique values will only be calculated once by < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > . We will use < code > < a href = "../reference/mo_property.html" > mo_fullname()< / a > < / code > for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses < code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > internally.< / p >
2019-03-27 11:22:36 +01:00
< div class = "sourceCode" id = "cb6" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6-1" title = "1" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/library" > library< / a > < / span > (dplyr)< / a >
< a class = "sourceLine" id = "cb6-2" title = "2" > < span class = "co" > # take all MO codes from the septic_patients data set< / span > < / a >
< a class = "sourceLine" id = "cb6-3" title = "3" > x < -< span class = "st" > < / span > septic_patients< span class = "op" > $< / span > mo < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb6-4" title = "4" > < span class = "st" > < / span > < span class = "co" > # keep only the unique ones< / span > < / a >
< a class = "sourceLine" id = "cb6-5" title = "5" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/unique" > unique< / a > < / span > () < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb6-6" title = "6" > < span class = "st" > < / span > < span class = "co" > # pick 50 of them at random< / span > < / a >
< a class = "sourceLine" id = "cb6-7" title = "7" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/sample.html" > sample< / a > < / span > (< span class = "dv" > 50< / span > ) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb6-8" title = "8" > < span class = "st" > < / span > < span class = "co" > # paste that 10,000 times< / span > < / a >
< a class = "sourceLine" id = "cb6-9" title = "9" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/rep" > rep< / a > < / span > (< span class = "dv" > 10000< / span > ) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb6-10" title = "10" > < span class = "st" > < / span > < span class = "co" > # scramble it< / span > < / a >
< a class = "sourceLine" id = "cb6-11" title = "11" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/sample.html" > sample< / a > < / span > ()< / a >
< a class = "sourceLine" id = "cb6-12" title = "12" > < / a >
< a class = "sourceLine" id = "cb6-13" title = "13" > < span class = "co" > # got indeed 50 times 10,000 = half a million?< / span > < / a >
< a class = "sourceLine" id = "cb6-14" title = "14" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/length" > length< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb6-15" title = "15" > < span class = "co" > #> [1] 500000< / span > < / a >
< a class = "sourceLine" id = "cb6-16" title = "16" > < / a >
< a class = "sourceLine" id = "cb6-17" title = "17" > < span class = "co" > # and how many unique values do we have?< / span > < / a >
< a class = "sourceLine" id = "cb6-18" title = "18" > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" > n_distinct< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb6-19" title = "19" > < span class = "co" > #> [1] 50< / span > < / a >
< a class = "sourceLine" id = "cb6-20" title = "20" > < / a >
< a class = "sourceLine" id = "cb6-21" title = "21" > < span class = "co" > # now let's see:< / span > < / a >
< a class = "sourceLine" id = "cb6-22" title = "22" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (x),< / a >
< a class = "sourceLine" id = "cb6-23" title = "23" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb6-24" title = "24" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb6-25" title = "25" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb6-26" title = "26" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb6-27" title = "27" > < span class = "co" > #> mo_fullname(x) 825 845 887 867 903 1080 10< / span > < / a > < / code > < / pre > < / div >
< p > So transforming 500,000 values (!!) of 50 unique values only takes 0.87 seconds (867 ms). You only lose time on your unique input values.< / p >
2019-01-11 20:37:23 +01:00
< / div >
< div id = "precalculated-results" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#precalculated-results" class = "anchor" > < / a > Precalculated results< / h3 >
< p > What about precalculated results? If the input is an already precalculated result of a helper function like < code > < a href = "../reference/mo_property.html" > mo_fullname()< / a > < / code > , it almost doesn’ ‘ ’ < / p >
2019-03-27 11:22:36 +01:00
< div class = "sourceCode" id = "cb7" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb7-1" title = "1" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "dt" > A =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "B_STPHY_AUR"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-2" title = "2" > < span class = "dt" > B =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
2019-02-20 00:04:48 +01:00
< a class = "sourceLine" id = "cb7-3" title = "3" > < span class = "dt" > C =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
2019-03-27 11:22:36 +01:00
< a class = "sourceLine" id = "cb7-4" title = "4" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb7-5" title = "5" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb7-6" title = "6" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb7-7" title = "7" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb7-8" title = "8" > < span class = "co" > #> A 12.400 12.700 13.100 13.000 13.400 13.700 10< / span > < / a >
< a class = "sourceLine" id = "cb7-9" title = "9" > < span class = "co" > #> B 26.300 26.600 27.900 28.400 28.700 29.000 10< / span > < / a >
< a class = "sourceLine" id = "cb7-10" title = "10" > < span class = "co" > #> C 0.486 0.502 0.727 0.821 0.849 0.982 10< / span > < / a > < / code > < / pre > < / div >
< p > So going from < code > < a href = "../reference/mo_property.html" > mo_fullname("Staphylococcus aureus")< / a > < / code > to < code > "Staphylococcus aureus"< / code > takes 0.0008 seconds - it doesn’ < em > if the result would be the same as the expected resulting value< / em > . That goes for all helper functions:< / p >
< div class = "sourceCode" id = "cb8" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb8-1" title = "1" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "dt" > A =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > (< span class = "st" > "aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-2" title = "2" > < span class = "dt" > B =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (< span class = "st" > "Staphylococcus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-3" title = "3" > < span class = "dt" > C =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-4" title = "4" > < span class = "dt" > D =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_family< / a > < / span > (< span class = "st" > "Staphylococcaceae"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-5" title = "5" > < span class = "dt" > E =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_order< / a > < / span > (< span class = "st" > "Bacillales"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-6" title = "6" > < span class = "dt" > F =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_class< / a > < / span > (< span class = "st" > "Bacilli"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-7" title = "7" > < span class = "dt" > G =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_phylum< / a > < / span > (< span class = "st" > "Firmicutes"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-8" title = "8" > < span class = "dt" > H =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_kingdom< / a > < / span > (< span class = "st" > "Bacteria"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb8-10" title = "10" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb8-11" title = "11" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb8-12" title = "12" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb8-13" title = "13" > < span class = "co" > #> A 0.371 0.432 0.463 0.471 0.500 0.525 10< / span > < / a >
< a class = "sourceLine" id = "cb8-14" title = "14" > < span class = "co" > #> B 0.479 0.531 0.557 0.553 0.566 0.631 10< / span > < / a >
< a class = "sourceLine" id = "cb8-15" title = "15" > < span class = "co" > #> C 0.511 0.676 0.834 0.904 0.959 1.090 10< / span > < / a >
< a class = "sourceLine" id = "cb8-16" title = "16" > < span class = "co" > #> D 0.422 0.444 0.483 0.494 0.501 0.559 10< / span > < / a >
< a class = "sourceLine" id = "cb8-17" title = "17" > < span class = "co" > #> E 0.383 0.458 0.502 0.477 0.507 0.778 10< / span > < / a >
< a class = "sourceLine" id = "cb8-18" title = "18" > < span class = "co" > #> F 0.362 0.376 0.476 0.426 0.473 0.947 10< / span > < / a >
< a class = "sourceLine" id = "cb8-19" title = "19" > < span class = "co" > #> G 0.361 0.368 0.451 0.452 0.500 0.610 10< / span > < / a >
< a class = "sourceLine" id = "cb8-20" title = "20" > < span class = "co" > #> H 0.359 0.383 0.431 0.437 0.458 0.505 10< / span > < / a > < / code > < / pre > < / div >
2019-02-20 00:04:48 +01:00
< p > Of course, when running < code > < a href = "../reference/mo_property.html" > mo_phylum("Firmicutes")< / a > < / code > the function has zero knowledge about the actual microorganism, namely < em > S. aureus< / em > . But since the result would be < code > "Firmicutes"< / code > too, there is no point in calculating the result. And because this package ‘ ’ < / p >
2019-01-11 20:37:23 +01:00
< / div >
< div id = "results-in-other-languages" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#results-in-other-languages" class = "anchor" > < / a > Results in other languages< / h3 >
2019-02-20 10:38:24 +01:00
< p > When the system language is non-English and supported by this < code > AMR< / code > package, some functions will have a translated result. This almost does’ < / p >
2019-03-27 11:22:36 +01:00
< div class = "sourceCode" id = "cb9" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb9-1" title = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "en"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on an English system< / span > < / a >
< a class = "sourceLine" id = "cb9-2" title = "2" > < span class = "co" > #> [1] "Coagulase-negative Staphylococcus (CoNS)"< / span > < / a >
< a class = "sourceLine" id = "cb9-3" title = "3" > < / a >
< a class = "sourceLine" id = "cb9-4" title = "4" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on a Spanish system< / span > < / a >
< a class = "sourceLine" id = "cb9-5" title = "5" > < span class = "co" > #> [1] "Staphylococcus coagulasa negativo (SCN)"< / span > < / a >
< a class = "sourceLine" id = "cb9-6" title = "6" > < / a >
< a class = "sourceLine" id = "cb9-7" title = "7" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on a Dutch system< / span > < / a >
< a class = "sourceLine" id = "cb9-8" title = "8" > < span class = "co" > #> [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span > < / a >
< a class = "sourceLine" id = "cb9-9" title = "9" > < / a >
< a class = "sourceLine" id = "cb9-10" title = "10" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "dt" > en =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "en"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-11" title = "11" > < span class = "dt" > de =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "de"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-12" title = "12" > < span class = "dt" > nl =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-13" title = "13" > < span class = "dt" > es =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-14" title = "14" > < span class = "dt" > it =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "it"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-15" title = "15" > < span class = "dt" > fr =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "fr"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-16" title = "16" > < span class = "dt" > pt =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "pt"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb9-18" title = "18" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 4< / span > )< / a >
< a class = "sourceLine" id = "cb9-19" title = "19" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb9-20" title = "20" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb9-21" title = "21" > < span class = "co" > #> en 18.83 19.19 24.20 19.53 20.67 63.66 10< / span > < / a >
< a class = "sourceLine" id = "cb9-22" title = "22" > < span class = "co" > #> de 31.53 32.10 36.79 32.22 33.81 75.80 10< / span > < / a >
< a class = "sourceLine" id = "cb9-23" title = "23" > < span class = "co" > #> nl 31.24 31.78 32.22 32.10 32.24 33.43 10< / span > < / a >
< a class = "sourceLine" id = "cb9-24" title = "24" > < span class = "co" > #> es 31.40 32.07 45.82 33.08 75.31 76.95 10< / span > < / a >
< a class = "sourceLine" id = "cb9-25" title = "25" > < span class = "co" > #> it 31.17 31.95 36.82 32.09 32.19 79.48 10< / span > < / a >
< a class = "sourceLine" id = "cb9-26" title = "26" > < span class = "co" > #> fr 31.48 31.64 31.89 31.96 32.07 32.33 10< / span > < / a >
< a class = "sourceLine" id = "cb9-27" title = "27" > < span class = "co" > #> pt 31.27 31.66 36.80 32.06 32.34 80.53 10< / span > < / a > < / code > < / pre > < / div >
2019-01-11 20:37:23 +01:00
< p > Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.< / p >
< / div >
< / div >
< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
< / div >
< / div >
< footer > < div class = "copyright" >
< p > Developed by < a href = "https://www.rug.nl/staff/m.s.berends/" > Matthijs S. Berends< / a > , < a href = "https://www.rug.nl/staff/c.f.luz/" > Christian F. Luz< / a > , < a href = "https://www.rug.nl/staff/c.glasner/" > Corinna Glasner< / a > , < a href = "https://www.rug.nl/staff/a.w.friedrich/" > Alex W. Friedrich< / a > , < a href = "https://www.rug.nl/staff/b.sinha/" > Bhanu N. M. Sinha< / a > .< / p >
< / div >
< div class = "pkgdown" >
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.3.0.< / p >
< / div >
< / footer >
< / div >
< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script > < script >
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
return hit;
});
}
});
< / script >
< / body >
< / html >
