2019-01-11 20:37:23 +01:00
<!DOCTYPE html>
2019-10-13 09:31:58 +02:00
<!-- 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" >
2019-01-11 20:37:23 +01:00
< 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 >
2019-10-13 09:31:58 +02:00
<!-- favicons --> < link rel = "icon" type = "image/png" sizes = "16x16" href = "../favicon-16x16.png" >
2019-01-11 20:37:23 +01:00
< link rel = "icon" type = "image/png" sizes = "32x32" href = "../favicon-32x32.png" >
2019-10-13 09:31:58 +02:00
< 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" >
2020-04-13 21:09:56 +02:00
<!-- jquery --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity = "sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin = "anonymous" > < / script > <!-- Bootstrap --> < link href = "https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel = "stylesheet" crossorigin = "anonymous" >
2020-04-17 19:16:30 +02:00
< script src = "https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity = "sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin = "anonymous" > < / script > <!-- bootstrap - toc --> < link rel = "stylesheet" href = "../bootstrap-toc.css" >
< script src = "../bootstrap-toc.js" > < / script > <!-- Font Awesome icons --> < link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity = "sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin = "anonymous" >
< link rel = "stylesheet" href = "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity = "sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin = "anonymous" >
<!-- clipboard.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity = "sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin = "anonymous" > < / script > <!-- headroom.js --> < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity = "sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin = "anonymous" > < / script > < script src = "https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity = "sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin = "anonymous" > < / script > <!-- pkgdown --> < link href = "../pkgdown.css" rel = "stylesheet" >
2020-02-23 20:56:11 +01:00
< script src = "../pkgdown.js" > < / script > < link href = "../extra.css" rel = "stylesheet" >
2019-10-13 09:31:58 +02:00
< script src = "../extra.js" > < / script > < meta property = "og:title" content = "Benchmarks" >
2020-04-13 21:09:56 +02:00
< meta property = "og:description" content = "AMR" >
2020-04-17 19:16:30 +02:00
< meta property = "og:image" content = "https://msberends.gitlab.io/AMR/logo.svg" >
2019-10-13 09:31:58 +02:00
<!-- 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]>
2019-01-11 20:37:23 +01:00
< 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]-->
2019-10-13 09:31:58 +02:00
< / head >
2020-04-17 19:16:30 +02:00
< body data-spy = "scroll" data-target = "#toc" >
2019-01-11 20:37:23 +01:00
< div class = "container template-article" >
2019-10-13 09:31:58 +02:00
< header > < div class = "navbar navbar-default navbar-fixed-top" role = "navigation" >
2019-01-11 20:37:23 +01:00
< 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 >
2020-04-17 19:16:30 +02:00
< span class = "version label label-default" data-toggle = "tooltip" data-placement = "bottom" title = "Latest development version" > 1.1.0< / span >
2019-01-11 20:37:23 +01:00
< / span >
< / div >
< div id = "navbar" class = "navbar-collapse collapse" >
< ul class = "nav navbar-nav" >
2019-10-13 09:31:58 +02:00
< li >
2019-01-11 20:37:23 +01:00
< 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" >
2019-10-13 09:31:58 +02:00
< li >
2019-01-11 20:37:23 +01:00
< 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 >
2020-03-07 21:48:21 +01:00
< li >
< a href = "../articles/PCA.html" >
< span class = "fa fa-compress" > < / span >
Conduct principal component analysis for AMR
< / a >
< / li >
2019-05-23 16:58:59 +02:00
< li >
< a href = "../articles/MDR.html" >
< span class = "fa fa-skull-crossbones" > < / span >
Determine multi-drug resistance (MDR)
< / 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 >
2019-05-10 16:44:59 +02:00
< a href = "../reference/ab_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/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 >
2019-10-13 09:31:58 +02:00
< ul class = "nav navbar-nav navbar-right" >
< li >
2019-01-11 20:37:23 +01:00
< 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 >
2019-10-13 09:31:58 +02:00
< / div >
<!-- /.nav - collapse -->
< / div >
<!-- /.container -->
< / div >
<!-- /.navbar -->
2019-01-11 20:37:23 +01:00
2019-09-23 13:53:50 +02:00
2019-10-13 09:31:58 +02:00
< / header > < div class = "row" >
2019-01-11 20:37:23 +01:00
< div class = "col-md-9 contents" >
< div class = "page-header toc-ignore" >
2020-04-17 19:16:30 +02:00
< h1 data-toc-skip > Benchmarks< / h1 >
2019-01-11 20:37:23 +01:00
< h4 class = "author" > Matthijs S. Berends< / h4 >
2020-04-17 19:16:30 +02:00
< h4 class = "date" > 15 April 2020< / h4 >
2019-01-11 20:37:23 +01:00
2020-04-17 19:16:30 +02:00
< small class = "dont-index" > Source: < a href = "https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" > < code > vignettes/benchmarks.Rmd< / code > < / a > < / small >
2019-01-11 20:37:23 +01:00
< div class = "hidden name" > < code > benchmarks.Rmd< / code > < / div >
< / div >
2019-10-13 09:31:58 +02:00
< 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 >
< p > Using the < code > microbenchmark< / code > package, we can review the calculation performance of this function. Its function < code > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark()< / a > < / code > runs different input expressions independently of each other and measures their time-to-result.< / p >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb1" > < html > < body > < pre class = "r" > < span class = "fu" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (< span class = "no" > microbenchmark< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (< span class = "no" > AMR< / span > )< / pre > < / body > < / html > < / div >
2019-12-20 15:05:58 +01:00
< p > In the next test, we try to ‘ ’ < em > Staphylococcus aureus< / em > . Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.< / p >
2019-12-20 21:06:39 +01:00
< p > The actual result is the same every time: it returns its microorganism code < code > B_STPHY_AURS< / 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 >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb2" > < html > < body > < pre class = "r" > < span class = "no" > S.aureus< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "sau"< / span > ), < span class = "co" > # WHONET code< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "stau"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "STAU"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "staaur"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "STAAUR"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S aureus"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ), < span class = "co" > # official taxonomic name< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Staphylococcus aureus (MRSA)"< / span > ), < span class = "co" > # additional text< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Sthafilokkockus aaureuz"< / span > ), < span class = "co" > # incorrect spelling< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "MRSA"< / span > ), < span class = "co" > # Methicillin Resistant S. aureus< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "VISA"< / span > ), < span class = "co" > # Vancomycin Intermediate S. aureus< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "VRSA"< / span > ), < span class = "co" > # Vancomycin Resistant S. aureus< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "fl" > 22242419< / span > ), < span class = "co" > # Catalogue of Life ID< / span >
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 10< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > S.aureus< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 2< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # as.mo("sau") 10.0 11.0 11 11.0 11.0 11 10< / span >
< span class = "co" > # as.mo("stau") 39.0 43.0 54 44.0 70.0 72 10< / span >
< span class = "co" > # as.mo("STAU") 43.0 44.0 52 47.0 68.0 71 10< / span >
< span class = "co" > # as.mo("staaur") 9.6 9.8 11 11.0 12.0 13 10< / span >
< span class = "co" > # as.mo("STAAUR") 9.6 11.0 17 11.0 11.0 45 10< / span >
< span class = "co" > # as.mo("S. aureus") 15.0 17.0 26 18.0 43.0 50 10< / span >
< span class = "co" > # as.mo("S aureus") 16.0 17.0 23 18.0 21.0 44 10< / span >
< span class = "co" > # as.mo("Staphylococcus aureus") 6.0 6.0 12 6.9 7.2 40 10< / span >
< span class = "co" > # as.mo("Staphylococcus aureus (MRSA)") 660.0 740.0 780 780.0 810.0 870 10< / span >
< span class = "co" > # as.mo("Sthafilokkockus aaureuz") 370.0 430.0 470 450.0 460.0 760 10< / span >
< span class = "co" > # as.mo("MRSA") 9.5 9.6 13 11.0 11.0 35 10< / span >
< span class = "co" > # as.mo("VISA") 25.0 26.0 38 30.0 50.0 58 10< / span >
< span class = "co" > # as.mo("VRSA") 25.0 29.0 55 55.0 56.0 150 10< / span >
< span class = "co" > # as.mo(22242419) 130.0 150.0 160 160.0 170.0 170 10< / span > < / pre > < / body > < / html > < / div >
2020-02-01 15:09:36 +01:00
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-4-1.png" width = "562.5" > < / p >
< 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.< / p >
< p > To achieve this speed, the < code > as.mo< / code > function also takes into account the prevalence of human pathogenic microorganisms. The downside of this is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of < em > Methanosarcina semesiae< / em > (< code > B_MTHNSR_SEMS< / code > ), a bug probably never found before in humans:< / p >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb3" > < html > < body > < pre class = "r" > < span class = "no" > M.semesiae< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "metsem"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "METSEM"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "M. semesiae"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "M. semesiae"< / span > ),
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Methanosarcina semesiae"< / span > ),
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 10< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > M.semesiae< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 4< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq< / span >
< span class = "co" > # as.mo("metsem") 1629.000 1648.000 1694.000 1681.000 1734.000< / span >
< span class = "co" > # as.mo("METSEM") 1577.000 1604.000 1675.000 1685.000 1700.000< / span >
< span class = "co" > # as.mo("M. semesiae") 17.390 17.470 26.150 18.020 43.560< / span >
< span class = "co" > # as.mo("M. semesiae") 17.390 17.880 27.570 18.310 45.910< / span >
< span class = "co" > # as.mo("Methanosarcina semesiae") 6.988 7.067 7.443 7.262 7.733< / span >
< span class = "co" > # max neval< / span >
< span class = "co" > # 1825.000 10< / span >
< span class = "co" > # 1793.000 10< / span >
< span class = "co" > # 48.390 10< / span >
< span class = "co" > # 50.960 10< / span >
< span class = "co" > # 8.381 10< / span > < / pre > < / body > < / html > < / div >
< p > That takes 5.6 times as much time on average. 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 > Methanosarcina semesiae< / em > ) are always very fast and only take some thousands of seconds to coerce - they are the most probable input from most data sets.< / p >
2019-09-20 14:18:29 +02:00
< 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 > Methanosarcina semesiae< / em > (which is uncommon):< / p >
2020-02-01 15:09:36 +01:00
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-6-1.png" width = "900" > < / p >
2019-04-09 10:34:40 +02:00
< p > Uncommon microorganisms take a lot more time than common microorganisms. 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" >
2019-10-13 09:31:58 +02:00
< h3 class = "hasAnchor" >
< a href = "#repetitive-results" class = "anchor" > < / a > Repetitive results< / h3 >
< 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_name()< / 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 >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb4" > < html > < body > < pre class = "r" > < span class = "fu" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (< span class = "no" > dplyr< / span > )
< span class = "co" > # take all MO codes from the example_isolates data set< / span >
< span class = "no" > x< / span > < span class = "kw" > < -< / span > < span class = "no" > example_isolates< / span > $< span class = "no" > mo< / span > < span class = "kw" > %> %< / span >
< span class = "co" > # keep only the unique ones< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/unique.html" > unique< / a > < / span > () < span class = "kw" > %> %< / span >
< span class = "co" > # pick 50 of them at random< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" > sample< / a > < / span > (< span class = "fl" > 50< / span > ) < span class = "kw" > %> %< / span >
< span class = "co" > # paste that 10,000 times< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/rep.html" > rep< / a > < / span > (< span class = "fl" > 10000< / span > ) < span class = "kw" > %> %< / span >
< span class = "co" > # scramble it< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" > sample< / a > < / span > ()
< span class = "co" > # got indeed 50 times 10,000 = half a million?< / span >
< span class = "fu" > < a href = "https://rdrr.io/r/base/length.html" > length< / a > < / span > (< span class = "no" > x< / span > )
< span class = "co" > # [1] 500000< / span >
< span class = "co" > # and how many unique values do we have?< / span >
< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" > n_distinct< / a > < / span > (< span class = "no" > x< / span > )
< span class = "co" > # [1] 50< / span >
< span class = "co" > # now let's see:< / span >
< span class = "no" > run_it< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "no" > x< / span > ),
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 100< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > run_it< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 3< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # mo_name(x) 1730 1790 1830 1810 1860 2030 100< / span > < / pre > < / body > < / html > < / div >
< p > So transforming 500,000 values (!!) of 50 unique values only takes 1.81 seconds (1814 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" >
2019-10-13 09:31:58 +02:00
< 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_name()< / a > < / code > , it almost doesn’ ‘ ’ < / p >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb5" > < html > < body > < pre class = "r" > < span class = "no" > run_it< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "kw" > A< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "B_STPHY_AURS"< / span > ),
< span class = "kw" > B< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),
< span class = "kw" > C< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 10< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > run_it< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 3< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # A 7.26 7.390 8.020 7.450 7.500 11.100 10< / span >
< span class = "co" > # B 15.30 15.700 20.500 15.800 17.000 56.300 10< / span >
< span class = "co" > # C 0.58 0.718 0.735 0.726 0.747 0.927 10< / span > < / pre > < / body > < / html > < / div >
< p > So going from < code > < a href = "../reference/mo_property.html" > mo_name("Staphylococcus aureus")< / a > < / code > to < code > "Staphylococcus aureus"< / code > takes 0.0007 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 = "cb6" > < html > < body > < pre class = "r" > < span class = "no" > run_it< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "kw" > A< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > (< span class = "st" > "aureus"< / span > ),
< span class = "kw" > B< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (< span class = "st" > "Staphylococcus"< / span > ),
< span class = "kw" > C< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),
< span class = "kw" > D< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_family< / a > < / span > (< span class = "st" > "Staphylococcaceae"< / span > ),
< span class = "kw" > E< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_order< / a > < / span > (< span class = "st" > "Bacillales"< / span > ),
< span class = "kw" > F< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_class< / a > < / span > (< span class = "st" > "Bacilli"< / span > ),
< span class = "kw" > G< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_phylum< / a > < / span > (< span class = "st" > "Firmicutes"< / span > ),
< span class = "kw" > H< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_kingdom< / a > < / span > (< span class = "st" > "Bacteria"< / span > ),
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 10< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > run_it< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 3< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # A 0.380 0.386 0.397 0.394 0.397 0.434 10< / span >
< span class = "co" > # B 0.413 0.417 0.444 0.424 0.430 0.627 10< / span >
< span class = "co" > # C 0.574 0.680 0.707 0.730 0.735 0.776 10< / span >
< span class = "co" > # D 0.407 0.419 0.430 0.430 0.435 0.470 10< / span >
< span class = "co" > # E 0.374 0.381 0.401 0.397 0.424 0.438 10< / span >
< span class = "co" > # F 0.366 0.380 0.389 0.387 0.395 0.422 10< / span >
< span class = "co" > # G 0.367 0.377 0.388 0.383 0.392 0.420 10< / span >
< span class = "co" > # H 0.368 0.374 0.386 0.382 0.390 0.430 10< / span > < / pre > < / body > < / html > < / div >
2020-02-01 15:09:36 +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 > anyway, 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" >
2019-10-13 09:31:58 +02:00
< 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 >
2020-04-17 19:16:30 +02:00
< div class = "sourceCode" id = "cb7" > < html > < body > < pre class = "r" > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "en"< / span > ) < span class = "co" > # or just mo_name("CoNS") on an English system< / span >
< span class = "co" > # [1] "Coagulase-negative Staphylococcus (CoNS)"< / span >
< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # or just mo_name("CoNS") on a Spanish system< / span >
< span class = "co" > # [1] "Staphylococcus coagulasa negativo (SCN)"< / span >
< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "nl"< / span > ) < span class = "co" > # or just mo_name("CoNS") on a Dutch system< / span >
< span class = "co" > # [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span >
< span class = "no" > run_it< / span > < span class = "kw" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "kw" > en< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "en"< / span > ),
< span class = "kw" > de< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "de"< / span > ),
< span class = "kw" > nl< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "nl"< / span > ),
< span class = "kw" > es< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "es"< / span > ),
< span class = "kw" > it< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "it"< / span > ),
< span class = "kw" > fr< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "fr"< / span > ),
< span class = "kw" > pt< / span > < span class = "kw" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "kw" > language< / span > < span class = "kw" > =< / span > < span class = "st" > "pt"< / span > ),
< span class = "kw" > times< / span > < span class = "kw" > =< / span > < span class = "fl" > 100< / span > )
< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (< span class = "no" > run_it< / span > , < span class = "kw" > unit< / span > < span class = "kw" > =< / span > < span class = "st" > "ms"< / span > , < span class = "kw" > signif< / span > < span class = "kw" > =< / span > < span class = "fl" > 4< / span > )
< span class = "co" > # Unit: milliseconds< / span >
< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # en 26.72 28.52 32.86 29.31 30.18 69.18 100< / span >
< span class = "co" > # de 27.86 30.67 40.23 31.44 46.42 170.40 100< / span >
< span class = "co" > # nl 34.45 36.94 44.89 37.95 40.54 76.41 100< / span >
< span class = "co" > # es 27.89 30.51 38.46 31.33 32.89 170.10 100< / span >
< span class = "co" > # it 29.15 30.37 35.85 31.04 32.39 65.33 100< / span >
< span class = "co" > # fr 28.18 30.37 35.80 31.11 32.25 78.14 100< / span >
< span class = "co" > # pt 28.23 30.55 36.89 31.32 32.77 67.79 100< / span > < / pre > < / body > < / html > < / div >
2019-01-11 20:37:23 +01:00
< p > Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.< / p >
< / div >
< / div >
2020-04-13 21:09:56 +02:00
< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / div >
< / div >
2019-10-13 09:31:58 +02:00
< footer > < div class = "copyright" >
2020-01-26 20:38:54 +01:00
< 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/a.w.friedrich/" > Alexander W. Friedrich< / a > , < a href = "https://www.rug.nl/staff/b.sinha/" > Bhanu N. M. Sinha< / a > , < a href = "https://www.rug.nl/staff/c.j.albers/" > Casper J. Albers< / a > , < a href = "https://www.rug.nl/staff/c.glasner/" > Corinna Glasner< / a > .< / p >
2019-01-11 20:37:23 +01:00
< / div >
< div class = "pkgdown" >
2020-04-17 19:16:30 +02:00
< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.5.0.< / p >
2019-01-11 20:37:23 +01:00
< / div >
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
< / footer >
2019-10-13 09:31:58 +02:00
< / div >
2019-01-11 20:37:23 +01:00
2020-02-23 20:56:11 +01:00
< / body >
2019-01-11 20:37:23 +01:00
< / html >
