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< h1 > Benchmarks< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
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< h4 class = "date" > 13 October 2019< / h4 >
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< div class = "hidden name" > < code > benchmarks.Rmd< / code > < / div >
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< p > < small > Source: < a href = "https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd" class = "uri" > https://gitlab.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd< / a > < / small > < / p >
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< 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 >
< div class = "sourceCode" id = "cb1" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb1-1" data-line-number = "1" > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (microbenchmark)< / a >
< a class = "sourceLine" id = "cb1-2" data-line-number = "2" > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (AMR)< / a > < / code > < / pre > < / div >
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< p > In the next test, we try to ‘ ’ < em > Staphylococcus aureus< / em > . 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 >
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< p > But the calculation time differs a lot:< / p >
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< div class = "sourceCode" id = "cb2" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb2-1" data-line-number = "1" > S.aureus < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< / a >
< a class = "sourceLine" id = "cb2-2" data-line-number = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "sau"< / span > ), < span class = "co" > # WHONET code< / span > < / a >
< a class = "sourceLine" id = "cb2-3" data-line-number = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "stau"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-4" data-line-number = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "STAU"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-5" data-line-number = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "staaur"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-6" data-line-number = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "STAAUR"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-7" data-line-number = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-8" data-line-number = "8" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-9" data-line-number = "9" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ), < span class = "co" > # official taxonomic name< / span > < / a >
< a class = "sourceLine" id = "cb2-10" data-line-number = "10" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Staphylococcus aureus (MRSA)"< / span > ), < span class = "co" > # additional text< / span > < / a >
< a class = "sourceLine" id = "cb2-11" data-line-number = "11" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Sthafilokkockus aaureuz"< / span > ), < span class = "co" > # incorrect spelling< / span > < / a >
< a class = "sourceLine" id = "cb2-12" data-line-number = "12" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "MRSA"< / span > ), < span class = "co" > # Methicillin Resistant S. aureus< / span > < / a >
< a class = "sourceLine" id = "cb2-13" data-line-number = "13" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "VISA"< / span > ), < span class = "co" > # Vancomycin Intermediate S. aureus< / span > < / a >
< a class = "sourceLine" id = "cb2-14" data-line-number = "14" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "VRSA"< / span > ), < span class = "co" > # Vancomycin Resistant S. aureus< / span > < / a >
< a class = "sourceLine" id = "cb2-15" data-line-number = "15" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "dv" > 22242419< / span > ), < span class = "co" > # Catalogue of Life ID< / span > < / a >
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< a class = "sourceLine" id = "cb2-16" data-line-number = "16" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb2-17" data-line-number = "17" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > 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 >
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< a class = "sourceLine" id = "cb2-18" data-line-number = "18" > < span class = "co" > # Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb2-19" data-line-number = "19" > < span class = "co" > # expr min lq mean median uq max< / span > < / a >
< a class = "sourceLine" id = "cb2-20" data-line-number = "20" > < span class = "co" > # as.mo("sau") 9.5 9.7 15 10 11 34< / span > < / a >
< a class = "sourceLine" id = "cb2-21" data-line-number = "21" > < span class = "co" > # as.mo("stau") 31.0 32.0 38 33 34 62< / span > < / a >
< a class = "sourceLine" id = "cb2-22" data-line-number = "22" > < span class = "co" > # as.mo("STAU") 31.0 32.0 39 35 39 56< / span > < / a >
< a class = "sourceLine" id = "cb2-23" data-line-number = "23" > < span class = "co" > # as.mo("staaur") 9.6 10.0 17 11 31 31< / span > < / a >
< a class = "sourceLine" id = "cb2-24" data-line-number = "24" > < span class = "co" > # as.mo("STAAUR") 9.6 9.8 13 10 10 34< / span > < / a >
< a class = "sourceLine" id = "cb2-25" data-line-number = "25" > < span class = "co" > # as.mo("S. aureus") 24.0 25.0 27 25 28 33< / span > < / a >
< a class = "sourceLine" id = "cb2-26" data-line-number = "26" > < span class = "co" > # as.mo("S aureus") 24.0 25.0 31 25 43 51< / span > < / a >
< a class = "sourceLine" id = "cb2-27" data-line-number = "27" > < span class = "co" > # as.mo("Staphylococcus aureus") 29.0 30.0 32 31 34 39< / span > < / a >
< a class = "sourceLine" id = "cb2-28" data-line-number = "28" > < span class = "co" > # as.mo("Staphylococcus aureus (MRSA)") 550.0 580.0 610 600 620 680< / span > < / a >
< a class = "sourceLine" id = "cb2-29" data-line-number = "29" > < span class = "co" > # as.mo("Sthafilokkockus aaureuz") 290.0 310.0 360 340 380 530< / span > < / a >
< a class = "sourceLine" id = "cb2-30" data-line-number = "30" > < span class = "co" > # as.mo("MRSA") 9.6 10.0 16 10 30 32< / span > < / a >
< a class = "sourceLine" id = "cb2-31" data-line-number = "31" > < span class = "co" > # as.mo("VISA") 19.0 20.0 21 20 21 22< / span > < / a >
< a class = "sourceLine" id = "cb2-32" data-line-number = "32" > < span class = "co" > # as.mo("VRSA") 20.0 20.0 26 21 24 46< / span > < / a >
< a class = "sourceLine" id = "cb2-33" data-line-number = "33" > < span class = "co" > # as.mo(22242419) 18.0 18.0 19 19 19 22< / span > < / a >
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< a class = "sourceLine" id = "cb2-34" data-line-number = "34" > < span class = "co" > # neval< / span > < / a >
< a class = "sourceLine" id = "cb2-35" data-line-number = "35" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-36" data-line-number = "36" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-37" data-line-number = "37" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-38" data-line-number = "38" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-39" data-line-number = "39" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-40" data-line-number = "40" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-41" data-line-number = "41" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-42" data-line-number = "42" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-43" data-line-number = "43" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-44" data-line-number = "44" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-45" data-line-number = "45" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-46" data-line-number = "46" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-47" data-line-number = "47" > < span class = "co" > # 10< / span > < / a >
< a class = "sourceLine" id = "cb2-48" data-line-number = "48" > < span class = "co" > # 10< / span > < / a > < / code > < / pre > < / div >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-5-1.png" width = "562.5" > < / p >
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< 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 >
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< 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 > Methanosarcina semesiae< / em > (< code > B_MTHNSR_SEMS< / code > ), a bug probably never found before in humans:< / p >
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< div class = "sourceCode" id = "cb3" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb3-1" data-line-number = "1" > M.semesiae < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "metsem"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-2" data-line-number = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "METSEM"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-3" data-line-number = "3" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "M. semesiae"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-4" data-line-number = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "M. semesiae"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-5" data-line-number = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Methanosarcina semesiae"< / span > ),< / a >
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< a class = "sourceLine" id = "cb3-6" data-line-number = "6" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb3-7" data-line-number = "7" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > print< / a > < / span > (M.semesiae, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 4< / span > )< / a >
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< a class = "sourceLine" id = "cb3-8" data-line-number = "8" > < span class = "co" > # Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb3-9" data-line-number = "9" > < span class = "co" > # expr min lq mean median uq< / span > < / a >
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< a class = "sourceLine" id = "cb3-10" data-line-number = "10" > < span class = "co" > # as.mo("metsem") 1293.00 1304.00 1394.00 1316.00 1395.00< / span > < / a >
< a class = "sourceLine" id = "cb3-11" data-line-number = "11" > < span class = "co" > # as.mo("METSEM") 1232.00 1278.00 1510.00 1309.00 1518.00< / span > < / a >
< a class = "sourceLine" id = "cb3-12" data-line-number = "12" > < span class = "co" > # as.mo("M. semesiae") 1874.00 1928.00 2063.00 1961.00 2167.00< / span > < / a >
< a class = "sourceLine" id = "cb3-13" data-line-number = "13" > < span class = "co" > # as.mo("M. semesiae") 1883.00 1926.00 2091.00 1978.00 2060.00< / span > < / a >
< a class = "sourceLine" id = "cb3-14" data-line-number = "14" > < span class = "co" > # as.mo("Methanosarcina semesiae") 30.23 31.64 35.26 31.82 38.29< / span > < / a >
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< a class = "sourceLine" id = "cb3-15" data-line-number = "15" > < span class = "co" > # max neval< / span > < / a >
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< a class = "sourceLine" id = "cb3-16" data-line-number = "16" > < span class = "co" > # 1929.00 10< / span > < / a >
< a class = "sourceLine" id = "cb3-17" data-line-number = "17" > < span class = "co" > # 2721.00 10< / span > < / a >
< a class = "sourceLine" id = "cb3-18" data-line-number = "18" > < span class = "co" > # 2676.00 10< / span > < / a >
< a class = "sourceLine" id = "cb3-19" data-line-number = "19" > < span class = "co" > # 2974.00 10< / span > < / a >
< a class = "sourceLine" id = "cb3-20" data-line-number = "20" > < span class = "co" > # 52.65 10< / span > < / a > < / code > < / pre > < / div >
< p > That takes 15.8 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 > Methanosarcina semesiae< / em > ) are almost fast - these are the most probable input from most data sets.< / p >
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< 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 >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-9-1.png" width = "562.5" > < / p >
< 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 >
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-11-1.png" width = "562.5" > < / p >
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< p > The highest outliers are the first times. All next determinations were done in only thousands of seconds.< / p >
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< 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 >
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< div id = "repetitive-results" class = "section level3" >
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< 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 >
< div class = "sourceCode" id = "cb4" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb4-1" data-line-number = "1" > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" > library< / a > < / span > (dplyr)< / a >
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< a class = "sourceLine" id = "cb4-2" data-line-number = "2" > < span class = "co" > # take all MO codes from the example_isolates data set< / span > < / a >
< a class = "sourceLine" id = "cb4-3" data-line-number = "3" > x < -< span class = "st" > < / span > example_isolates< span class = "op" > $< / span > mo < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb4-4" data-line-number = "4" > < span class = "st" > < / span > < span class = "co" > # keep only the unique ones< / span > < / a >
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< a class = "sourceLine" id = "cb4-5" data-line-number = "5" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/unique.html" > unique< / a > < / span > () < span class = "op" > %> %< / span > < / a >
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< a class = "sourceLine" id = "cb4-6" data-line-number = "6" > < span class = "st" > < / span > < span class = "co" > # pick 50 of them at random< / span > < / a >
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< a class = "sourceLine" id = "cb4-7" data-line-number = "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 >
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< a class = "sourceLine" id = "cb4-8" data-line-number = "8" > < span class = "st" > < / span > < span class = "co" > # paste that 10,000 times< / span > < / a >
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< a class = "sourceLine" id = "cb4-9" data-line-number = "9" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/rep.html" > rep< / a > < / span > (< span class = "dv" > 10000< / span > ) < span class = "op" > %> %< / span > < / a >
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< a class = "sourceLine" id = "cb4-10" data-line-number = "10" > < span class = "st" > < / span > < span class = "co" > # scramble it< / span > < / a >
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< a class = "sourceLine" id = "cb4-11" data-line-number = "11" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/sample.html" > sample< / a > < / span > ()< / a >
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< a class = "sourceLine" id = "cb4-12" data-line-number = "12" > < / a >
< a class = "sourceLine" id = "cb4-13" data-line-number = "13" > < span class = "co" > # got indeed 50 times 10,000 = half a million?< / span > < / a >
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< a class = "sourceLine" id = "cb4-14" data-line-number = "14" > < span class = "kw" > < a href = "https://rdrr.io/r/base/length.html" > length< / a > < / span > (x)< / a >
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< a class = "sourceLine" id = "cb4-15" data-line-number = "15" > < span class = "co" > # [1] 500000< / span > < / a >
< a class = "sourceLine" id = "cb4-16" data-line-number = "16" > < / a >
< a class = "sourceLine" id = "cb4-17" data-line-number = "17" > < span class = "co" > # and how many unique values do we have?< / span > < / a >
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< a class = "sourceLine" id = "cb4-18" data-line-number = "18" > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" > n_distinct< / a > < / span > (x)< / a >
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< a class = "sourceLine" id = "cb4-19" data-line-number = "19" > < span class = "co" > # [1] 50< / span > < / a >
< a class = "sourceLine" id = "cb4-20" data-line-number = "20" > < / a >
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< a class = "sourceLine" id = "cb4-21" data-line-number = "21" > < span class = "co" > # now let's see:< / span > < / a >
< a class = "sourceLine" id = "cb4-22" data-line-number = "22" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (x),< / a >
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< a class = "sourceLine" id = "cb4-23" data-line-number = "23" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb4-24" data-line-number = "24" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > 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 >
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< a class = "sourceLine" id = "cb4-25" data-line-number = "25" > < span class = "co" > # Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb4-26" data-line-number = "26" > < span class = "co" > # expr min lq mean median uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb4-27" data-line-number = "27" > < span class = "co" > # mo_name(x) 596 604 651 641 663 813 10< / span > < / a > < / code > < / pre > < / div >
< p > So transforming 500,000 values (!!) of 50 unique values only takes 0.64 seconds (641 ms). You only lose time on your unique input values.< / p >
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< / div >
< div id = "precalculated-results" class = "section level3" >
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< 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 >
< div class = "sourceCode" id = "cb5" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb5-1" data-line-number = "1" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "dt" > A =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "B_STPHY_AURS"< / span > ),< / a >
< a class = "sourceLine" id = "cb5-2" data-line-number = "2" > < span class = "dt" > B =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb5-3" data-line-number = "3" > < span class = "dt" > C =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
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< a class = "sourceLine" id = "cb5-4" data-line-number = "4" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb5-5" data-line-number = "5" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > 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 >
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< a class = "sourceLine" id = "cb5-6" data-line-number = "6" > < span class = "co" > # Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb5-7" data-line-number = "7" > < span class = "co" > # expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb5-8" data-line-number = "8" > < span class = "co" > # A 6.300 6.460 6.79 6.500 6.810 8.32 10< / span > < / a >
< a class = "sourceLine" id = "cb5-9" data-line-number = "9" > < span class = "co" > # B 24.600 24.700 28.70 25.600 26.600 51.30 10< / span > < / a >
< a class = "sourceLine" id = "cb5-10" data-line-number = "10" > < span class = "co" > # C 0.778 0.828 0.93 0.854 0.872 1.63 10< / span > < / a > < / code > < / pre > < / div >
< p > So going from < code > < a href = "../reference/mo_property.html" > mo_name("Staphylococcus aureus")< / a > < / code > to < code > "Staphylococcus aureus"< / code > takes 0.0009 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" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6-1" data-line-number = "1" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > 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 = "cb6-2" data-line-number = "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 = "cb6-3" data-line-number = "3" > < span class = "dt" > C =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb6-4" data-line-number = "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 = "cb6-5" data-line-number = "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 = "cb6-6" data-line-number = "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 = "cb6-7" data-line-number = "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 = "cb6-8" data-line-number = "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 >
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< a class = "sourceLine" id = "cb6-9" data-line-number = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb6-10" data-line-number = "10" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > 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 >
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< a class = "sourceLine" id = "cb6-11" data-line-number = "11" > < span class = "co" > # Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb6-12" data-line-number = "12" > < span class = "co" > # expr min lq mean median uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb6-13" data-line-number = "13" > < span class = "co" > # A 0.457 0.463 0.477 0.476 0.483 0.511 10< / span > < / a >
< a class = "sourceLine" id = "cb6-14" data-line-number = "14" > < span class = "co" > # B 0.486 0.496 0.508 0.499 0.512 0.569 10< / span > < / a >
< a class = "sourceLine" id = "cb6-15" data-line-number = "15" > < span class = "co" > # C 0.781 0.803 0.825 0.829 0.847 0.854 10< / span > < / a >
< a class = "sourceLine" id = "cb6-16" data-line-number = "16" > < span class = "co" > # D 0.479 0.495 0.528 0.510 0.517 0.749 10< / span > < / a >
< a class = "sourceLine" id = "cb6-17" data-line-number = "17" > < span class = "co" > # E 0.457 0.464 0.484 0.475 0.498 0.547 10< / span > < / a >
< a class = "sourceLine" id = "cb6-18" data-line-number = "18" > < span class = "co" > # F 0.458 0.464 0.472 0.468 0.477 0.496 10< / span > < / a >
< a class = "sourceLine" id = "cb6-19" data-line-number = "19" > < span class = "co" > # G 0.446 0.453 0.462 0.459 0.467 0.499 10< / span > < / a >
< a class = "sourceLine" id = "cb6-20" data-line-number = "20" > < span class = "co" > # H 0.426 0.458 0.467 0.467 0.472 0.507 10< / span > < / a > < / code > < / pre > < / div >
< 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 >
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< / div >
< div id = "results-in-other-languages" class = "section level3" >
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< h3 class = "hasAnchor" >
< a href = "#results-in-other-languages" class = "anchor" > < / a > Results in other languages< / h3 >
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< 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 >
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< div class = "sourceCode" id = "cb7" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb7-1" data-line-number = "1" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "en"< / span > ) < span class = "co" > # or just mo_name("CoNS") on an English system< / span > < / a >
< a class = "sourceLine" id = "cb7-2" data-line-number = "2" > < span class = "co" > # [1] "Coagulase-negative Staphylococcus (CoNS)"< / span > < / a >
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< a class = "sourceLine" id = "cb7-3" data-line-number = "3" > < / a >
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< a class = "sourceLine" id = "cb7-4" data-line-number = "4" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # or just mo_name("CoNS") on a Spanish system< / span > < / a >
< a class = "sourceLine" id = "cb7-5" data-line-number = "5" > < span class = "co" > # [1] "Staphylococcus coagulasa negativo (SCN)"< / span > < / a >
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< a class = "sourceLine" id = "cb7-6" data-line-number = "6" > < / a >
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< a class = "sourceLine" id = "cb7-7" data-line-number = "7" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ) < span class = "co" > # or just mo_name("CoNS") on a Dutch system< / span > < / a >
< a class = "sourceLine" id = "cb7-8" data-line-number = "8" > < span class = "co" > # [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span > < / a >
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< a class = "sourceLine" id = "cb7-9" data-line-number = "9" > < / a >
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< a class = "sourceLine" id = "cb7-10" data-line-number = "10" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" > microbenchmark< / a > < / span > (< span class = "dt" > en =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "en"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-11" data-line-number = "11" > < span class = "dt" > de =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "de"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-12" data-line-number = "12" > < span class = "dt" > nl =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-13" data-line-number = "13" > < span class = "dt" > es =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-14" data-line-number = "14" > < span class = "dt" > it =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "it"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-15" data-line-number = "15" > < span class = "dt" > fr =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "fr"< / span > ),< / a >
< a class = "sourceLine" id = "cb7-16" data-line-number = "16" > < span class = "dt" > pt =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "pt"< / span > ),< / a >
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< a class = "sourceLine" id = "cb7-17" data-line-number = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb7-18" data-line-number = "18" > < span class = "kw" > < a href = "https://rdrr.io/r/base/print.html" > 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 >
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< a class = "sourceLine" id = "cb7-19" data-line-number = "19" > < span class = "co" > # Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb7-20" data-line-number = "20" > < span class = "co" > # expr min lq mean median uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb7-21" data-line-number = "21" > < span class = "co" > # en 19.99 20.17 25.15 20.21 22.19 43.86 10< / span > < / a >
< a class = "sourceLine" id = "cb7-22" data-line-number = "22" > < span class = "co" > # de 21.17 21.47 26.00 21.51 21.85 44.12 10< / span > < / a >
< a class = "sourceLine" id = "cb7-23" data-line-number = "23" > < span class = "co" > # nl 26.69 26.71 27.24 27.10 27.80 28.04 10< / span > < / a >
< a class = "sourceLine" id = "cb7-24" data-line-number = "24" > < span class = "co" > # es 21.20 21.36 24.26 21.51 21.85 43.76 10< / span > < / a >
< a class = "sourceLine" id = "cb7-25" data-line-number = "25" > < span class = "co" > # it 21.09 21.24 26.27 21.59 22.46 46.14 10< / span > < / a >
< a class = "sourceLine" id = "cb7-26" data-line-number = "26" > < span class = "co" > # fr 21.16 21.35 23.98 21.51 22.11 44.93 10< / span > < / a >
< a class = "sourceLine" id = "cb7-27" data-line-number = "27" > < span class = "co" > # pt 21.10 21.13 21.35 21.28 21.37 22.24 10< / span > < / a > < / code > < / pre > < / div >
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< p > Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.< / p >
< / div >
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< div class = "col-md-3 hidden-xs hidden-sm" id = "sidebar" >
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< 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/a.w.friedrich/" > Alex 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 >
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< / div >
< div class = "pkgdown" >
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" > pkgdown< / a > 1.4.1.< / p >
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< / footer >
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< script src = "https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity = "sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin = "anonymous" > < / script > < script >
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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 >
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< / body >
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< / html >
