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< h1 > Benchmarks< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
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< h4 class = "date" > 20 February 2019< / h4 >
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< div class = "hidden name" > < code > benchmarks.Rmd< / code > < / div >
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< p > One of the most important features of this package is the complete microbial taxonomic database, supplied by the Catalogue of Life (< a href = "http://catalogueoflife.org" class = "uri" > http://catalogueoflife.org< / 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 AI (Artificial Intelligence) 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://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 >
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< 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 >
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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 MO code < code > B_STPHY_AUR< / code > (< em > B< / em > stands for < em > Bacteria< / em > , the taxonomic kingdom).< / p >
< p > But the calculation time differs a lot. Here, the AI effect can be reviewed best:< / p >
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< 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 >
< a class = "sourceLine" id = "cb2-4" title = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "S. aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-5" 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" > "STAAUR"< / span > ),< / a >
< 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 >
< a class = "sourceLine" id = "cb2-8" title = "8" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "B_STPHY_AUR"< / span > ),< / a >
< a class = "sourceLine" id = "cb2-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb2-10" title = "10" > < 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 > )< / a >
< a class = "sourceLine" id = "cb2-11" title = "11" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb2-12" title = "12" > < span class = "co" > #> expr min lq mean median< / span > < / a >
< a class = "sourceLine" id = "cb2-13" title = "13" > < span class = "co" > #> as.mo("sau") 42.680497 42.766053 43.5046242 43.2246305< / span > < / a >
< a class = "sourceLine" id = "cb2-14" title = "14" > < span class = "co" > #> as.mo("stau") 76.627901 76.760320 82.2084011 77.2020310< / span > < / a >
< a class = "sourceLine" id = "cb2-15" title = "15" > < span class = "co" > #> as.mo("staaur") 42.751945 42.828281 46.8816599 43.0017665< / span > < / a >
< a class = "sourceLine" id = "cb2-16" title = "16" > < span class = "co" > #> as.mo("S. aureus") 18.328588 18.370632 22.3298018 18.4252830< / span > < / a >
< a class = "sourceLine" id = "cb2-17" title = "17" > < span class = "co" > #> as.mo("S. aureus") 18.258048 18.385997 18.7710600 18.5449555< / span > < / a >
< a class = "sourceLine" id = "cb2-18" title = "18" > < span class = "co" > #> as.mo("STAAUR") 42.734554 42.854751 43.6593017 43.6353320< / span > < / a >
< a class = "sourceLine" id = "cb2-19" title = "19" > < span class = "co" > #> as.mo("Staphylococcus aureus") 11.466961 11.572841 16.5287637 11.6172940< / span > < / a >
< a class = "sourceLine" id = "cb2-20" title = "20" > < span class = "co" > #> as.mo("B_STPHY_AUR") 0.284603 0.302692 0.4095492 0.4190475< / span > < / a >
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< a class = "sourceLine" id = "cb2-21" title = "21" > < span class = "co" > #> uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb2-22" title = "22" > < span class = "co" > #> 44.091919 45.191431 10< / span > < / a >
< a class = "sourceLine" id = "cb2-23" title = "23" > < span class = "co" > #> 78.670409 123.715942 10< / span > < / a >
< a class = "sourceLine" id = "cb2-24" title = "24" > < span class = "co" > #> 43.089558 81.640969 10< / span > < / a >
< a class = "sourceLine" id = "cb2-25" title = "25" > < span class = "co" > #> 18.546004 57.384741 10< / span > < / a >
< a class = "sourceLine" id = "cb2-26" title = "26" > < span class = "co" > #> 19.235128 19.693775 10< / span > < / a >
< a class = "sourceLine" id = "cb2-27" title = "27" > < span class = "co" > #> 44.189907 45.381609 10< / span > < / a >
< a class = "sourceLine" id = "cb2-28" title = "28" > < span class = "co" > #> 12.175081 59.815567 10< / span > < / a >
< a class = "sourceLine" id = "cb2-29" title = "29" > < span class = "co" > #> 0.482254 0.500343 10< / span > < / a > < / code > < / pre > < / div >
< p > In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of < code > < a href = "../reference/as.mo.html" > as.mo("B_STPHY_AUR")< / a > < / code > , the input is already a valid MO code, so it only almost takes no time at all (284 millionths of seconds).< / p >
< 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 > Mycoplasma leonicaptivi< / em > (< code > B_MYCPL_LEO< / 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" title = "1" > M.leonicaptivi < -< 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" > "myle"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-2" title = "2" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "mycleo"< / 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" > "M. leonicaptivi"< / 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" > "M. leonicaptivi"< / 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" > "MYCLEO"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Mycoplasma leonicaptivi"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "B_MYCPL_LEO"< / span > ),< / a >
< a class = "sourceLine" id = "cb3-8" title = "8" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb3-9" title = "9" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (M.leonicaptivi, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > )< / a >
< a class = "sourceLine" id = "cb3-10" title = "10" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb3-11" title = "11" > < span class = "co" > #> expr min lq mean< / span > < / a >
< a class = "sourceLine" id = "cb3-12" title = "12" > < span class = "co" > #> as.mo("myle") 112.493914 112.698409 113.5834588< / span > < / a >
< a class = "sourceLine" id = "cb3-13" title = "13" > < span class = "co" > #> as.mo("mycleo") 382.813554 382.992838 389.0918181< / span > < / a >
< a class = "sourceLine" id = "cb3-14" title = "14" > < span class = "co" > #> as.mo("M. leonicaptivi") 202.903596 203.855253 211.7932317< / span > < / a >
< a class = "sourceLine" id = "cb3-15" title = "15" > < span class = "co" > #> as.mo("M. leonicaptivi") 203.761037 204.178479 212.5451427< / span > < / a >
< a class = "sourceLine" id = "cb3-16" title = "16" > < span class = "co" > #> as.mo("MYCLEO") 382.602355 383.481517 393.2696052< / span > < / a >
< a class = "sourceLine" id = "cb3-17" title = "17" > < span class = "co" > #> as.mo("Mycoplasma leonicaptivi") 103.701176 103.991018 109.5707840< / span > < / a >
< a class = "sourceLine" id = "cb3-18" title = "18" > < span class = "co" > #> as.mo("B_MYCPL_LEO") 0.312051 0.564876 0.5870787< / span > < / a >
< a class = "sourceLine" id = "cb3-19" title = "19" > < span class = "co" > #> median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb3-20" title = "20" > < span class = "co" > #> 113.363438 114.20691 115.907686 10< / span > < / a >
< a class = "sourceLine" id = "cb3-21" title = "21" > < span class = "co" > #> 384.139806 388.34114 421.458483 10< / span > < / a >
< a class = "sourceLine" id = "cb3-22" title = "22" > < span class = "co" > #> 204.186195 205.16631 243.204461 10< / span > < / a >
< a class = "sourceLine" id = "cb3-23" title = "23" > < span class = "co" > #> 204.715173 207.97372 244.462163 10< / span > < / a >
< a class = "sourceLine" id = "cb3-24" title = "24" > < span class = "co" > #> 383.918409 386.97938 434.456156 10< / span > < / a >
< a class = "sourceLine" id = "cb3-25" title = "25" > < span class = "co" > #> 104.428888 104.87207 153.125617 10< / span > < / a >
< a class = "sourceLine" id = "cb3-26" title = "26" > < span class = "co" > #> 0.567914 0.63779 0.859048 10< / span > < / a > < / code > < / pre > < / div >
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< p > That takes 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:< / p >
< 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 >
< a class = "sourceLine" id = "cb4-3" title = "3" > < span class = "co" > # highest value on y axis< / span > < / a >
< a class = "sourceLine" id = "cb4-4" title = "4" > max_y_axis < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/Extremes" > max< / a > < / span > (S.aureus< span class = "op" > $< / span > time, M.leonicaptivi< span class = "op" > $< / span > time, < span class = "dt" > na.rm =< / span > < span class = "ot" > TRUE< / span > ) < span class = "op" > /< / span > < span class = "st" > < / span > < span class = "fl" > 1e6< / span > < / a >
< a class = "sourceLine" id = "cb4-5" title = "5" > < / a >
< a class = "sourceLine" id = "cb4-6" title = "6" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > (S.aureus, < 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" > "ms"< / span > , < span class = "dt" > log =< / span > < span class = "ot" > FALSE< / span > , < span class = "dt" > xlab =< / span > < span class = "st" > ""< / 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 > , max_y_axis),< / a >
< a class = "sourceLine" id = "cb4-7" title = "7" > < span class = "dt" > main =< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/expression" > expression< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/paste" > paste< / a > < / span > (< span class = "st" > "Benchmark of "< / span > , < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/grDevices/topics/plotmath" > italic< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ))))< / a > < / code > < / pre > < / div >
< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-4-1.png" width = "720" > < / p >
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< div class = "sourceCode" id = "cb5" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb5-1" title = "1" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > (M.leonicaptivi, < 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" > "ms"< / span > , < span class = "dt" > log =< / span > < span class = "ot" > FALSE< / span > , < span class = "dt" > xlab =< / span > < span class = "st" > ""< / 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 > , max_y_axis),< / a >
< a class = "sourceLine" id = "cb5-2" title = "2" > < span class = "dt" > main =< / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/expression" > expression< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/paste" > paste< / a > < / span > (< span class = "st" > "Benchmark of "< / span > , < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/grDevices/topics/plotmath" > italic< / a > < / span > (< span class = "st" > "Mycoplasma leonicaptivi"< / span > ))))< / a > < / code > < / pre > < / div >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-4-2.png" width = "720" > < / p >
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< p > 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 >
< div id = "repetitive-results" class = "section level3" >
< h3 class = "hasAnchor" >
< a href = "#repetitive-results" class = "anchor" > < / a > Repetitive results< / h3 >
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< p > Repetitive results mean that unique values 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 >
< 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 >
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< a class = "sourceLine" id = "cb6-2" title = "2" > < span class = "co" > # take 500,000 random 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 > < / a >
< a class = "sourceLine" id = "cb6-4" title = "4" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/sample.html" > sample_n< / a > < / span > (< span class = "dv" > 500000< / span > , < span class = "dt" > replace =< / span > < span class = "ot" > TRUE< / span > ) < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb6-5" title = "5" > < span class = "st" > < / span > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/pull.html" > pull< / a > < / span > (mo)< / a >
< a class = "sourceLine" id = "cb6-6" title = "6" > < / a >
< a class = "sourceLine" id = "cb6-7" title = "7" > < span class = "co" > # got the right length?< / span > < / a >
< a class = "sourceLine" id = "cb6-8" title = "8" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/length" > length< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb6-9" title = "9" > < span class = "co" > #> [1] 500000< / span > < / a >
< a class = "sourceLine" id = "cb6-10" title = "10" > < / a >
< a class = "sourceLine" id = "cb6-11" title = "11" > < span class = "co" > # and how many unique values do we have?< / span > < / a >
< a class = "sourceLine" id = "cb6-12" title = "12" > < span class = "kw" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" > n_distinct< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb6-13" title = "13" > < span class = "co" > #> [1] 95< / span > < / a >
< a class = "sourceLine" id = "cb6-14" title = "14" > < / a >
< a class = "sourceLine" id = "cb6-15" title = "15" > < span class = "co" > # now let's see:< / span > < / a >
< a class = "sourceLine" id = "cb6-16" title = "16" > 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" > X =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (x),< / a >
< a class = "sourceLine" id = "cb6-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb6-18" 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 > )< / a >
< a class = "sourceLine" id = "cb6-19" title = "19" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb6-20" title = "20" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb6-21" title = "21" > < span class = "co" > #> X 413.2556 431.8327 448.3355 445.8654 465.2447 480.5499 10< / span > < / a > < / code > < / pre > < / div >
< p > So transforming 500,000 values (!) of 95 unique values only takes 0.45 seconds (445 ms). You only lose time on your unique input values.< / p >
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< / 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 >
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< 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 >
< 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 >
< 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 > )< / a >
< a class = "sourceLine" id = "cb7-6" title = "6" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< 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 39.603291 39.713640 39.950479 39.8150500 40.172707 40.664181 10< / span > < / a >
< a class = "sourceLine" id = "cb7-9" title = "9" > < span class = "co" > #> B 19.570436 19.623515 19.964292 19.9376620 20.228830 20.609744 10< / span > < / a >
< a class = "sourceLine" id = "cb7-10" title = "10" > < span class = "co" > #> C 0.251429 0.333144 0.389883 0.3866775 0.499087 0.510401 10< / span > < / a > < / code > < / pre > < / div >
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< p > So going from < code > < a href = "../reference/mo_property.html" > mo_fullname("Staphylococcus aureus")< / a > < / code > to < code > "Staphylococcus aureus"< / code > takes 0.0004 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" > < 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 = "dt" > unit =< / span > < span class = "st" > "ms"< / 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 >
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< a class = "sourceLine" id = "cb8-13" title = "13" > < span class = "co" > #> A 0.298084 0.370509 0.4040816 0.4065820 0.449569 0.475480 10< / span > < / a >
< a class = "sourceLine" id = "cb8-14" title = "14" > < span class = "co" > #> B 0.293753 0.306115 0.3352809 0.3212705 0.370160 0.386154 10< / span > < / a >
< a class = "sourceLine" id = "cb8-15" title = "15" > < span class = "co" > #> C 0.307652 0.353328 0.4106327 0.3943595 0.467239 0.548255 10< / span > < / a >
< a class = "sourceLine" id = "cb8-16" title = "16" > < span class = "co" > #> D 0.244376 0.262954 0.2987189 0.3027975 0.338102 0.353747 10< / span > < / a >
< a class = "sourceLine" id = "cb8-17" title = "17" > < span class = "co" > #> E 0.249614 0.255550 0.2985027 0.2772710 0.351931 0.397049 10< / span > < / a >
< a class = "sourceLine" id = "cb8-18" title = "18" > < span class = "co" > #> F 0.259531 0.282439 0.3248814 0.3193850 0.345575 0.415906 10< / span > < / a >
< a class = "sourceLine" id = "cb8-19" title = "19" > < span class = "co" > #> G 0.249055 0.266516 0.3293723 0.3020295 0.344528 0.616350 10< / span > < / a >
< a class = "sourceLine" id = "cb8-20" title = "20" > < span class = "co" > #> H 0.242141 0.288515 0.3122614 0.3152295 0.339779 0.355773 10< / span > < / a > < / code > < / pre > < / div >
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< 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" >
< 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 = "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" > "fr"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on a French system< / span > < / a >
< a class = "sourceLine" id = "cb9-5" title = "5" > < span class = "co" > #> [1] "Staphylococcus à coagulase négative (CoNS)"< / span > < / a >
< a class = "sourceLine" id = "cb9-6" title = "6" > < / a >
< a class = "sourceLine" id = "cb9-7" title = "7" > < 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 = "cb9-8" title = "8" > < 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 = "cb9-9" title = "9" > < 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 = "cb9-10" title = "10" > < 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 = "cb9-11" title = "11" > < 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 = "cb9-12" title = "12" > < 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 = "cb9-13" title = "13" > < 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 = "cb9-14" title = "14" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > ,< / a >
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2019-02-20 10:38:24 +01:00
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2019-01-11 20:37:23 +01:00
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