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< h1 > Benchmarks< / h1 >
< h4 class = "author" > Matthijs S. Berends< / h4 >
2019-02-23 16:02:31 +01:00
< h4 class = "date" > 23 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 < 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 AI (Artificial Intelligence) combined with the taxonomic tree of Catalogue of Life.< / p >
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< 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 >
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< a class = "sourceLine" id = "cb2-8" title = "8" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb2-9" title = "9" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (S.aureus, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb2-10" title = "10" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
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< a class = "sourceLine" id = "cb2-11" title = "11" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb2-12" title = "12" > < span class = "co" > #> as.mo("sau") 12.7 12.7 22.7 13.2 13.5 71.1 10< / span > < / a >
< a class = "sourceLine" id = "cb2-13" title = "13" > < span class = "co" > #> as.mo("stau") 87.6 87.8 90.2 87.9 90.6 104.0 10< / span > < / a >
< a class = "sourceLine" id = "cb2-14" title = "14" > < span class = "co" > #> as.mo("staaur") 12.6 12.6 12.8 12.7 12.8 13.6 10< / span > < / a >
< a class = "sourceLine" id = "cb2-15" title = "15" > < span class = "co" > #> as.mo("S. aureus") 24.0 24.2 32.0 24.5 25.4 63.2 10< / span > < / a >
< a class = "sourceLine" id = "cb2-16" title = "16" > < span class = "co" > #> as.mo("S. aureus") 24.1 24.1 29.3 24.2 24.6 74.0 10< / span > < / a >
< a class = "sourceLine" id = "cb2-17" title = "17" > < span class = "co" > #> as.mo("STAAUR") 12.6 12.7 16.6 12.7 12.8 51.5 10< / span > < / a >
< a class = "sourceLine" id = "cb2-18" title = "18" > < span class = "co" > #> as.mo("Staphylococcus aureus") 13.5 13.5 17.9 13.6 14.5 54.5 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 second input is the only one that has to be looked up thoroughly. All the others are known codes (the first is a WHONET code) or common laboratory codes, or common full organism names like the last one.< / p >
2019-02-20 10:38:24 +01:00
< p > To achieve this speed, the < code > as.mo< / code > function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of < em > 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 >
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< a class = "sourceLine" id = "cb3-7" title = "7" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb3-8" title = "8" > < 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" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb3-9" title = "9" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb3-10" title = "10" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb3-11" title = "11" > < span class = "co" > #> as.mo("myle") 134 135 144 135 138 184 10< / span > < / a >
< a class = "sourceLine" id = "cb3-12" title = "12" > < span class = "co" > #> as.mo("mycleo") 445 458 479 487 493 500 10< / span > < / a >
< a class = "sourceLine" id = "cb3-13" title = "13" > < span class = "co" > #> as.mo("M. leonicaptivi") 204 207 224 214 245 248 10< / span > < / a >
< a class = "sourceLine" id = "cb3-14" title = "14" > < span class = "co" > #> as.mo("M. leonicaptivi") 205 206 223 208 246 250 10< / span > < / a >
< a class = "sourceLine" id = "cb3-15" title = "15" > < span class = "co" > #> as.mo("MYCLEO") 446 448 480 486 492 529 10< / span > < / a >
< a class = "sourceLine" id = "cb3-16" title = "16" > < span class = "co" > #> as.mo("Mycoplasma leonicaptivi") 146 149 170 169 191 193 10< / span > < / a > < / code > < / pre > < / div >
< p > That takes 9.1 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 >
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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 > Mycoplasma leonicaptivi< / em > (which is very uncommon):< / p >
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< 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 >
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< a class = "sourceLine" id = "cb4-3" title = "3" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/graphics/topics/boxplot" > boxplot< / a > < / span > (< span class = "kw" > < a href = "https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark" > microbenchmark< / a > < / span > (< span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "M. leonicaptivi"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-4" title = "4" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Mycoplasma leonicaptivi"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-5" title = "5" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "P. brevis"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-6" title = "6" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Prevotella brevis"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-7" title = "7" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "E. coli"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-8" title = "8" > < span class = "kw" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > (< span class = "st" > "Escherichia coli"< / span > ),< / a >
< a class = "sourceLine" id = "cb4-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 50< / span > ),< / a >
< a class = "sourceLine" id = "cb4-10" title = "10" > < span class = "dt" > horizontal =< / span > < span class = "ot" > TRUE< / span > , < span class = "dt" > las =< / span > < span class = "dv" > 1< / span > , < span class = "dt" > unit =< / span > < span class = "st" > "s"< / span > , < span class = "dt" > log =< / span > < span class = "ot" > FALSE< / span > ,< / a >
< a class = "sourceLine" id = "cb4-11" title = "11" > < span class = "dt" > xlab =< / span > < span class = "st" > ""< / span > , < span class = "dt" > ylab =< / span > < span class = "st" > "Time in seconds"< / span > ,< / a >
< a class = "sourceLine" id = "cb4-12" title = "12" > < span class = "dt" > main =< / span > < span class = "st" > "Benchmarks per prevalence"< / span > )< / a > < / code > < / pre > < / div >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-5-1.png" width = "720" > < / 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" >
< 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 >
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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/base/topics/library" > library< / a > < / span > (dplyr)< / a >
< a class = "sourceLine" id = "cb5-2" title = "2" > < span class = "co" > # take 500,000 random MO codes from the septic_patients data set< / span > < / a >
< a class = "sourceLine" id = "cb5-3" title = "3" > x =< span class = "st" > < / span > septic_patients < span class = "op" > %> %< / span > < / a >
< a class = "sourceLine" id = "cb5-4" 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 = "cb5-5" 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 = "cb5-6" title = "6" > < / a >
< a class = "sourceLine" id = "cb5-7" title = "7" > < span class = "co" > # got the right length?< / span > < / a >
< a class = "sourceLine" id = "cb5-8" title = "8" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/length" > length< / a > < / span > (x)< / a >
< a class = "sourceLine" id = "cb5-9" title = "9" > < span class = "co" > #> [1] 500000< / span > < / a >
< a class = "sourceLine" id = "cb5-10" title = "10" > < / a >
< a class = "sourceLine" id = "cb5-11" title = "11" > < span class = "co" > # and how many unique values do we have?< / span > < / a >
< a class = "sourceLine" id = "cb5-12" 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 = "cb5-13" title = "13" > < span class = "co" > #> [1] 95< / span > < / a >
< a class = "sourceLine" id = "cb5-14" title = "14" > < / a >
< a class = "sourceLine" id = "cb5-15" title = "15" > < span class = "co" > # now let's see:< / span > < / a >
< a class = "sourceLine" id = "cb5-16" 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 >
< a class = "sourceLine" id = "cb5-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb5-18" title = "18" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-19" title = "19" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-20" title = "20" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-21" title = "21" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-22" title = "22" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-23" title = "23" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-24" title = "24" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-25" title = "25" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-26" title = "26" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-27" title = "27" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb5-28" title = "28" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb5-29" title = "29" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb5-30" title = "30" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb5-31" title = "31" > < span class = "co" > #> mo_fullname(x) 623 641 708 648 822 864 10< / span > < / a > < / code > < / pre > < / div >
< p > So transforming 500,000 values (!) of 95 unique values only takes 0.65 seconds (647 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 >
2019-02-22 22:12:10 +01:00
< div class = "sourceCode" id = "cb6" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb6-1" 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 = "cb6-2" 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 = "cb6-3" 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 = "cb6-4" title = "4" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
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< a class = "sourceLine" id = "cb6-5" title = "5" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-6" title = "6" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-7" title = "7" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-8" title = "8" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-9" title = "9" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-10" title = "10" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-11" title = "11" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-12" title = "12" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-13" title = "13" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-14" title = "14" > < span class = "co" > #> [1] "is any"< / span > < / a >
< a class = "sourceLine" id = "cb6-15" title = "15" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb6-16" title = "16" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb6-17" title = "17" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
< a class = "sourceLine" id = "cb6-18" title = "18" > < span class = "co" > #> A 6.500 6.590 6.710 6.680 6.870 6.900 10< / span > < / a >
< a class = "sourceLine" id = "cb6-19" title = "19" > < span class = "co" > #> B 24.900 25.000 25.300 25.300 25.500 25.800 10< / span > < / a >
< a class = "sourceLine" id = "cb6-20" title = "20" > < span class = "co" > #> C 0.259 0.383 0.387 0.395 0.411 0.564 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 = "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_species< / a > < / span > (< span class = "st" > "aureus"< / 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_genus< / a > < / span > (< span class = "st" > "Staphylococcus"< / span > ),< / a >
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< 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 >
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< a class = "sourceLine" id = "cb7-4" 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 = "cb7-5" 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 = "cb7-6" 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 = "cb7-7" 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 = "cb7-8" 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 = "cb7-9" title = "9" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb7-10" title = "10" > < span class = "kw" > < a href = "https://www.rdocumentation.org/packages/base/topics/print" > print< / a > < / span > (run_it, < span class = "dt" > unit =< / span > < span class = "st" > "ms"< / span > , < span class = "dt" > signif =< / span > < span class = "dv" > 3< / span > )< / a >
< a class = "sourceLine" id = "cb7-11" title = "11" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb7-12" title = "12" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
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< a class = "sourceLine" id = "cb7-13" title = "13" > < span class = "co" > #> A 0.304 0.337 0.393 0.396 0.440 0.513 10< / span > < / a >
< a class = "sourceLine" id = "cb7-14" title = "14" > < span class = "co" > #> B 0.297 0.304 0.348 0.349 0.380 0.409 10< / span > < / a >
< a class = "sourceLine" id = "cb7-15" title = "15" > < span class = "co" > #> C 0.312 0.361 0.428 0.427 0.513 0.527 10< / span > < / a >
< a class = "sourceLine" id = "cb7-16" title = "16" > < span class = "co" > #> D 0.242 0.254 0.302 0.298 0.328 0.414 10< / span > < / a >
< a class = "sourceLine" id = "cb7-17" title = "17" > < span class = "co" > #> E 0.243 0.296 0.325 0.328 0.348 0.431 10< / span > < / a >
< a class = "sourceLine" id = "cb7-18" title = "18" > < span class = "co" > #> F 0.237 0.257 0.302 0.322 0.329 0.343 10< / span > < / a >
< a class = "sourceLine" id = "cb7-19" title = "19" > < span class = "co" > #> G 0.242 0.260 0.306 0.325 0.341 0.345 10< / span > < / a >
< a class = "sourceLine" id = "cb7-20" title = "20" > < span class = "co" > #> H 0.244 0.283 0.322 0.335 0.360 0.375 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 = "cb8" > < pre class = "sourceCode r" > < code class = "sourceCode r" > < a class = "sourceLine" id = "cb8-1" 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 = "cb8-2" title = "2" > < span class = "co" > #> [1] "Coagulase Negative Staphylococcus (CoNS)"< / span > < / a >
< a class = "sourceLine" id = "cb8-3" title = "3" > < / a >
< a class = "sourceLine" id = "cb8-4" 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 = "cb8-5" title = "5" > < span class = "co" > #> [1] "Staphylococcus coagulasa negativo (CoNS)"< / span > < / a >
< a class = "sourceLine" id = "cb8-6" title = "6" > < / a >
< a class = "sourceLine" id = "cb8-7" 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 = "cb8-8" title = "8" > < span class = "co" > #> [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span > < / a >
< a class = "sourceLine" id = "cb8-9" title = "9" > < / a >
< a class = "sourceLine" id = "cb8-10" 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 = "cb8-11" 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 = "cb8-12" 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 = "cb8-13" 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 = "cb8-14" 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 = "cb8-15" 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 = "cb8-16" 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 = "cb8-17" title = "17" > < span class = "dt" > times =< / span > < span class = "dv" > 10< / span > )< / a >
< a class = "sourceLine" id = "cb8-18" 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 = "cb8-19" title = "19" > < span class = "co" > #> Unit: milliseconds< / span > < / a >
< a class = "sourceLine" id = "cb8-20" title = "20" > < span class = "co" > #> expr min lq mean median uq max neval< / span > < / a >
2019-02-23 18:08:28 +01:00
< a class = "sourceLine" id = "cb8-21" title = "21" > < span class = "co" > #> en 14.72 14.90 15.64 15.22 15.27 20.60 10< / span > < / a >
< a class = "sourceLine" id = "cb8-22" title = "22" > < span class = "co" > #> de 23.41 23.59 27.01 23.69 23.77 57.27 10< / span > < / a >
< a class = "sourceLine" id = "cb8-23" title = "23" > < span class = "co" > #> nl 23.40 23.58 23.80 23.72 23.83 24.46 10< / span > < / a >
< a class = "sourceLine" id = "cb8-24" title = "24" > < span class = "co" > #> es 23.18 24.35 37.51 24.80 57.35 58.29 10< / span > < / a >
< a class = "sourceLine" id = "cb8-25" title = "25" > < span class = "co" > #> it 23.26 23.47 27.11 23.68 24.14 57.07 10< / span > < / a >
< a class = "sourceLine" id = "cb8-26" title = "26" > < span class = "co" > #> fr 23.37 23.65 27.05 23.76 23.80 57.26 10< / span > < / a >
< a class = "sourceLine" id = "cb8-27" title = "27" > < span class = "co" > #> pt 23.34 23.47 24.02 23.70 23.86 26.79 10< / span > < / a > < / code > < / pre > < / div >
2019-01-11 20:37:23 +01:00
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