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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 >
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< 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 > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
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< 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 uq max< / span > < / a >
< a class = "sourceLine" id = "cb2-13" title = "13" > < span class = "co" > #> as.mo("sau") 42.500 42.800 44.200 43.100 43.900 53.700< / span > < / a >
< a class = "sourceLine" id = "cb2-14" title = "14" > < span class = "co" > #> as.mo("stau") 76.300 76.800 82.800 77.000 78.800 116.000< / span > < / a >
< a class = "sourceLine" id = "cb2-15" title = "15" > < span class = "co" > #> as.mo("staaur") 42.700 43.000 47.100 43.600 43.900 80.700< / span > < / a >
< a class = "sourceLine" id = "cb2-16" title = "16" > < span class = "co" > #> as.mo("S. aureus") 18.400 18.500 18.800 18.800 19.200 19.300< / span > < / a >
< a class = "sourceLine" id = "cb2-17" title = "17" > < span class = "co" > #> as.mo("S. aureus") 18.400 18.400 23.600 18.600 19.300 67.100< / span > < / a >
< a class = "sourceLine" id = "cb2-18" title = "18" > < span class = "co" > #> as.mo("STAAUR") 42.700 42.800 43.200 43.000 43.600 44.100< / span > < / a >
< a class = "sourceLine" id = "cb2-19" title = "19" > < span class = "co" > #> as.mo("Staphylococcus aureus") 11.400 11.500 11.700 11.600 11.800 12.500< / span > < / a >
< a class = "sourceLine" id = "cb2-20" title = "20" > < span class = "co" > #> as.mo("B_STPHY_AUR") 0.267 0.297 0.403 0.431 0.478 0.509< / span > < / a >
< a class = "sourceLine" id = "cb2-21" title = "21" > < span class = "co" > #> neval< / span > < / a >
< a class = "sourceLine" id = "cb2-22" title = "22" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-23" title = "23" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-24" title = "24" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-25" title = "25" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-26" title = "26" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-27" title = "27" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-28" title = "28" > < span class = "co" > #> 10< / span > < / a >
< a class = "sourceLine" id = "cb2-29" title = "29" > < span class = "co" > #> 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 (267 millionths of seconds).< / 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 > 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 >
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< 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 > , < span class = "dt" > signif =< / span > < span class = "dv" > 4< / span > )< / a >
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< 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 median< / span > < / a >
< a class = "sourceLine" id = "cb3-12" title = "12" > < span class = "co" > #> as.mo("myle") 111.9000 112.0000 112.4000 112.2000< / span > < / a >
< a class = "sourceLine" id = "cb3-13" title = "13" > < span class = "co" > #> as.mo("mycleo") 381.4000 381.8000 388.5000 382.1000< / span > < / a >
< a class = "sourceLine" id = "cb3-14" title = "14" > < span class = "co" > #> as.mo("M. leonicaptivi") 203.0000 203.2000 212.5000 203.6000< / span > < / a >
< a class = "sourceLine" id = "cb3-15" title = "15" > < span class = "co" > #> as.mo("M. leonicaptivi") 203.0000 203.1000 212.7000 203.6000< / span > < / a >
< a class = "sourceLine" id = "cb3-16" title = "16" > < span class = "co" > #> as.mo("MYCLEO") 381.8000 382.4000 394.5000 382.9000< / span > < / a >
< a class = "sourceLine" id = "cb3-17" title = "17" > < span class = "co" > #> as.mo("Mycoplasma leonicaptivi") 102.8000 103.0000 103.4000 103.2000< / span > < / a >
< a class = "sourceLine" id = "cb3-18" title = "18" > < span class = "co" > #> as.mo("B_MYCPL_LEO") 0.3183 0.5657 0.5693 0.5727< / span > < / a >
< a class = "sourceLine" id = "cb3-19" title = "19" > < span class = "co" > #> uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb3-20" title = "20" > < span class = "co" > #> 112.4000 113.5000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-21" title = "21" > < span class = "co" > #> 385.4000 439.9000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-22" title = "22" > < span class = "co" > #> 205.8000 253.9000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-23" title = "23" > < span class = "co" > #> 207.2000 252.3000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-24" title = "24" > < span class = "co" > #> 421.1000 422.1000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-25" title = "25" > < span class = "co" > #> 103.4000 105.7000 10< / span > < / a >
< a class = "sourceLine" id = "cb3-26" title = "26" > < span class = "co" > #> 0.5994 0.7446 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 >
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< 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 = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (x),< / a >
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< a class = "sourceLine" id = "cb6-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< 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 > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
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< a class = "sourceLine" id = "cb6-19" title = "19" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< 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" > #> mo_fullname(x) 438 453 468 468 482 499 10< / span > < / a > < / code > < / pre > < / div >
< p > So transforming 500,000 values (!) of 95 unique values only takes 0.47 seconds (468 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 >
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< a class = "sourceLine" id = "cb7-5" title = "5" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
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< 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 38.600 38.700 39.40 39.100 39.400 42.900 10< / span > < / a >
< a class = "sourceLine" id = "cb7-9" title = "9" > < span class = "co" > #> B 19.600 19.800 20.00 19.900 20.000 20.700 10< / span > < / a >
< a class = "sourceLine" id = "cb7-10" title = "10" > < span class = "co" > #> C 0.255 0.261 0.37 0.386 0.499 0.505 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 >
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< div class = "sourceCode" id = "cb8" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb8-1" title = "1" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "dt" > A =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > (< span class = "st" > "aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-2" title = "2" > < span class = "dt" > B =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > (< span class = "st" > "Staphylococcus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-3" title = "3" > < span class = "dt" > C =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "Staphylococcus aureus"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-4" title = "4" > < span class = "dt" > D =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_family< / a > < / span > (< span class = "st" > "Staphylococcaceae"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-5" title = "5" > < span class = "dt" > E =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_order< / a > < / span > (< span class = "st" > "Bacillales"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-6" title = "6" > < span class = "dt" > F =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_class< / a > < / span > (< span class = "st" > "Bacilli"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-7" title = "7" > < span class = "dt" > G =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_phylum< / a > < / span > (< span class = "st" > "Firmicutes"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-8" title = "8" > < span class = "dt" > H =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_kingdom< / a > < / span > (< span class = "st" > "Bacteria"< / span > ),< / a >
< a class = "sourceLine" id = "cb8-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb8-10" title = "10" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
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< a class = "sourceLine" id = "cb8-11" title = "11" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb8-12" title = "12" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb8-13" title = "13" > < span class = "co" > #> A 0.282 0.311 0.372 0.359 0.437 0.513 10< / span > < / a >
< a class = "sourceLine" id = "cb8-14" title = "14" > < span class = "co" > #> B 0.285 0.316 0.355 0.363 0.382 0.443 10< / span > < / a >
< a class = "sourceLine" id = "cb8-15" title = "15" > < span class = "co" > #> C 0.258 0.408 0.439 0.430 0.504 0.565 10< / span > < / a >
< a class = "sourceLine" id = "cb8-16" title = "16" > < span class = "co" > #> D 0.268 0.304 0.322 0.321 0.360 0.366 10< / span > < / a >
< a class = "sourceLine" id = "cb8-17" title = "17" > < span class = "co" > #> E 0.259 0.273 0.312 0.295 0.357 0.391 10< / span > < / a >
< a class = "sourceLine" id = "cb8-18" title = "18" > < span class = "co" > #> F 0.250 0.275 0.327 0.294 0.343 0.614 10< / span > < / a >
< a class = "sourceLine" id = "cb8-19" title = "19" > < span class = "co" > #> G 0.254 0.281 0.312 0.320 0.338 0.369 10< / span > < / a >
< a class = "sourceLine" id = "cb8-20" title = "20" > < span class = "co" > #> H 0.257 0.265 0.311 0.316 0.329 0.397 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 >
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< a class = "sourceLine" id = "cb9-4" title = "4" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on a Spanish system< / span > < / a >
< a class = "sourceLine" id = "cb9-5" title = "5" > < span class = "co" > #> [1] "Staphylococcus coagulasa negativo (CoNS)"< / span > < / a >
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< a class = "sourceLine" id = "cb9-6" title = "6" > < / a >
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< a class = "sourceLine" id = "cb9-7" title = "7" > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ) < span class = "co" > # or just mo_fullname("CoNS") on a Dutch system< / span > < / a >
< a class = "sourceLine" id = "cb9-8" title = "8" > < span class = "co" > #> [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span > < / a >
< a class = "sourceLine" id = "cb9-9" title = "9" > < / a >
< a class = "sourceLine" id = "cb9-10" title = "10" > run_it < -< span class = "st" > < / span > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "dt" > en =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "en"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-11" title = "11" > < span class = "dt" > de =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "de"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-12" title = "12" > < span class = "dt" > nl =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "nl"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-13" title = "13" > < span class = "dt" > es =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "es"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-14" title = "14" > < span class = "dt" > it =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "it"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-15" title = "15" > < span class = "dt" > fr =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "fr"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-16" title = "16" > < span class = "dt" > pt =< / span > < span class = "kw" > < a href = "../reference/mo_property.html" > mo_fullname< / a > < / span > (< span class = "st" > "CoNS"< / span > , < span class = "dt" > language =< / span > < span class = "st" > "pt"< / span > ),< / a >
< a class = "sourceLine" id = "cb9-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb9-18" title = "18" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 4< / span > )< / a >
< a class = "sourceLine" id = "cb9-19" title = "19" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb9-20" title = "20" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb9-21" title = "21" > < span class = "co" > #> en 10.69 11.02 11.06 11.08 11.21 11.29 10< / span > < / a >
< a class = "sourceLine" id = "cb9-22" title = "22" > < span class = "co" > #> de 19.09 19.48 19.49 19.55 19.62 19.66 10< / span > < / a >
< a class = "sourceLine" id = "cb9-23" title = "23" > < span class = "co" > #> nl 19.25 19.58 19.66 19.60 19.72 20.61 10< / span > < / a >
< a class = "sourceLine" id = "cb9-24" title = "24" > < span class = "co" > #> es 19.17 19.54 26.16 19.61 20.23 52.49 10< / span > < / a >
< a class = "sourceLine" id = "cb9-25" title = "25" > < span class = "co" > #> it 19.10 19.46 26.14 19.69 19.92 52.56 10< / span > < / a >
< a class = "sourceLine" id = "cb9-26" title = "26" > < span class = "co" > #> fr 19.10 19.36 19.50 19.50 19.59 20.13 10< / span > < / a >
< a class = "sourceLine" id = "cb9-27" title = "27" > < span class = "co" > #> pt 19.26 19.50 23.19 19.71 20.48 53.09 10< / span > < / a > < / code > < / pre > < / div >
2019-01-11 20:37:23 +01:00
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