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< h1 data-toc-skip > Benchmarks< / h1 >
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< small class = "dont-index" > Source: < a href = "https://github.com/msberends/AMR/blob/HEAD/vignettes/benchmarks.Rmd" class = "external-link" > < code > vignettes/benchmarks.Rmd< / code > < / a > < / small >
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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://www.catalogueoflife.org" class = "external-link" > Catalogue of Life< / a > (CoL) and
the < a href = "https://lpsn.dsmz.de" class = "external-link" > List of Prokaryotic names with
Standing in Nomenclature< / a > (LPSN). We created a function
< code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > that transforms any user input value to a valid
microbial ID by using intelligent rules combined with the microbial
taxonomy.< / p >
< p > Using the < code > microbenchmark< / code > package, we can review the
calculation performance of this function. Its function
< code > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > 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 = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://github.com/joshuaulrich/microbenchmark/" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > )< / span >
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< span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://msberends.github.io/AMR/" > AMR< / a > < / span > < span class = "op" > )< / span >
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< span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > library< / a > < / span > < span class = "op" > (< / span > < span class = "va" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > dplyr< / a > < / span > < span class = "op" > )< / span > < / code > < / pre > < / div >
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< p > In the next test, we try to ‘ ’
microbial code of < em > Staphylococcus aureus< / em > . Coercion is a
computational process of forcing output based on an input. For
microorganism names, coercing user input to taxonomically valid
microorganism names is crucial to ensure correct interpretation and to
enable grouping based on taxonomic properties.< / p >
< p > The actual result is the same every time: it returns its
microorganism code < code > B_STPHY_AURS< / code > (< em > B< / em > stands for
< em > Bacteria< / em > , its taxonomic kingdom).< / p >
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< p > But the calculation time differs a lot:< / p >
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< div class = "sourceCode" id = "cb2" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span class = "va" > S.aureus< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > (< / span >
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< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "sau"< / span > < span class = "op" > )< / span > , < span class = "co" > # WHONET code< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "stau"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "STAU"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "staaur"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "STAAUR"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S. aureus"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S aureus"< / span > < span class = "op" > )< / span > ,
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcus aureus"< / span > < span class = "op" > )< / span > , < span class = "co" > # official taxonomic name< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcus aureus (MRSA)"< / span > < span class = "op" > )< / span > , < span class = "co" > # additional text< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Sthafilokkockus aaureuz"< / span > < span class = "op" > )< / span > , < span class = "co" > # incorrect spelling< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "MRSA"< / span > < span class = "op" > )< / span > , < span class = "co" > # Methicillin Resistant S. aureus< / span >
< span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "VISA"< / span > < span class = "op" > )< / span > , < span class = "co" > # Vancomycin Intermediate S. aureus< / span >
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times < span class = "op" > =< / span > < span class = "fl" > 25< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" class = "external-link" > print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > S.aureus< / span > , unit < span class = "op" > =< / span > < span class = "st" > "ms"< / span > , signif < span class = "op" > =< / span > < span class = "fl" > 2< / span > < span class = "op" > )< / span >
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< span class = "co" > # Unit: milliseconds< / span >
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< < < < < < < HEAD
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # as.mo("sau") 12.0 13 18.0 14.0 15.0 48 25< / span >
< span class = "co" > # as.mo("stau") 54.0 59 80.0 91.0 96.0 99 25< / span >
< span class = "co" > # as.mo("STAU") 53.0 61 77.0 66.0 94.0 100 25< / span >
< span class = "co" > # as.mo("staaur") 12.0 13 19.0 14.0 16.0 62 25< / span >
< span class = "co" > # as.mo("STAAUR") 12.0 13 16.0 14.0 15.0 48 25< / span >
< span class = "co" > # as.mo("S. aureus") 28.0 30 38.0 33.0 35.0 69 25< / span >
< span class = "co" > # as.mo("S aureus") 27.0 31 46.0 34.0 65.0 73 25< / span >
< span class = "co" > # as.mo("Staphylococcus aureus") 3.7 4 6.7 4.3 4.5 36 25< / span >
< span class = "co" > # as.mo("Staphylococcus aureus (MRSA)") 260.0 270 290.0 280.0 290.0 360 25< / span >
< span class = "co" > # as.mo("Sthafilokkockus aaureuz") 190.0 210 220.0 210.0 220.0 330 25< / span >
< span class = "co" > # as.mo("MRSA") 12.0 13 20.0 14.0 16.0 68 25< / span >
< span class = "co" > # as.mo("VISA") 22.0 23 32.0 25.0 27.0 63 25< / span > < / code > < / pre > < / div >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-4-1.png" width = "750" > < / p >
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< p > In the table above, all measurements are shown in milliseconds
(thousands of seconds). A value of 5 milliseconds means it can determine
200 input values per second. It case of 200 milliseconds, this is only 5
input values per second. It is clear that accepted taxonomic names are
extremely fast, but some variations are up to 67 times slower to
determine.< / p >
< p > To improve performance, we implemented two important algorithms to
save unnecessary calculations: < strong > repetitive results< / strong > and
< strong > already precalculated results< / strong > .< / p >
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=======
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # as.mo("sau") 20.0 20.0 25.0 20.0 21 57 25< / span >
< span class = "co" > # as.mo("stau") 94.0 94.0 110.0 95.0 130 130 25< / span >
< span class = "co" > # as.mo("STAU") 94.0 95.0 110.0 130.0 130 130 25< / span >
< span class = "co" > # as.mo("staaur") 20.0 20.0 28.0 20.0 21 58 25< / span >
< span class = "co" > # as.mo("STAAUR") 20.0 20.0 25.0 20.0 21 57 25< / span >
< span class = "co" > # as.mo("S. aureus") 56.0 56.0 72.0 57.0 92 97 25< / span >
< span class = "co" > # as.mo("S aureus") 55.0 56.0 66.0 56.0 75 93 25< / span >
< span class = "co" > # as.mo("Staphylococcus aureus") 5.7 5.8 7.3 5.9 6 41 25< / span >
< span class = "co" > # as.mo("Staphylococcus aureus (MRSA)") 370.0 370.0 390.0 380.0 410 410 25< / span >
< span class = "co" > # as.mo("Sthafilokkockus aaureuz") 260.0 290.0 300.0 290.0 300 330 25< / span >
< span class = "co" > # as.mo("MRSA") 20.0 20.0 23.0 20.0 20 56 25< / span >
< span class = "co" > # as.mo("VISA") 34.0 35.0 48.0 35.0 35 220 25< / span > < / code > < / pre > < / div >
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< p > < img src = "benchmarks_files/figure-html/unnamed-chunk-4-1.png" width = "750" > < / p >
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< p > In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 65 times slower to determine.< / p >
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< p > To improve performance, we implemented two important algorithms to save unnecessary calculations: < strong > repetitive results< / strong > and < strong > already precalculated results< / strong > .< / p >
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< div class = "section level3" >
< h3 id = "repetitive-results" > Repetitive results< a class = "anchor" aria-label = "anchor" href = "#repetitive-results" > < / a >
< / h3 >
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< p > Repetitive results are values that are present more than once in a
vector. Unique values will only be calculated once by
< code > < a href = "../reference/as.mo.html" > as.mo()< / a > < / code > . So running
< code > as.mo(c("E. coli", "E. coli"))< / code > will check the value
< code > "E. coli"< / code > only once.< / p >
< p > To prove this, we will use < code > < a href = "../reference/mo_property.html" > mo_name()< / a > < / code > for testing - 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 = "cb3" > < pre class = "downlit sourceCode r" >
< code class = "sourceCode R" > < span class = "co" > # start with the example_isolates data set< / span >
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< span class = "va" > x< / span > < span class = "op" > < -< / span > < span class = "va" > example_isolates< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span >
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< span class = "co" > # take all MO codes from the 'mo' column< / span >
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< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/pull.html" class = "external-link" > pull< / a > < / span > < span class = "op" > (< / span > < span class = "va" > mo< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span >
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< span class = "co" > # and copy them a thousand times< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/rep.html" class = "external-link" > rep< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 1000< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span >
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< span class = "co" > # then scramble them< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/sample.html" class = "external-link" > sample< / a > < / span > < span class = "op" > (< / span > < span class = "op" > )< / span >
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< span class = "co" > # what do these values look like? They are of class < mo> :< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/utils/head.html" class = "external-link" > head< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span >
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< span class = "co" > # Class < mo> < / span >
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< < < < < < < HEAD
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< span class = "co" > # [1] B_ESCHR_COLI B_STRPT_MITS B_STRPT_ANGN B_STPHY_CONS B_ESCHR_COLI< / span >
< span class = "co" > # [6] B_ESCHR_COLI< / span >
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=======
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< span class = "co" > # [1] B_PROTS_MRBL B_STPHY_CONS B_ESCHR_COLI B_PSDMN_AERG B_ENTRC_FCLS< / span >
< span class = "co" > # [6] B_STPHY_AURS< / span >
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< span class = "co" > # as the example_isolates data set has 2,000 rows, we should have 2 million items< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/length.html" class = "external-link" > length< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span >
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< span class = "co" > # [1] 2000000< / span >
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< span class = "co" > # and how many unique values do we have?< / span >
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< span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/n_distinct.html" class = "external-link" > n_distinct< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span >
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< span class = "co" > # [1] 90< / span >
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< span class = "co" > # now let's see:< / span >
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< span class = "va" > run_it< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > ,
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times < span class = "op" > =< / span > < span class = "fl" > 10< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" class = "external-link" > print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > run_it< / span > , unit < span class = "op" > =< / span > < span class = "st" > "ms"< / span > , signif < span class = "op" > =< / span > < span class = "fl" > 3< / span > < span class = "op" > )< / span >
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< span class = "co" > # Unit: milliseconds< / span >
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< span class = "co" > # expr min lq mean median uq max neval< / span >
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< < < < < < < HEAD
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< span class = "co" > # mo_name(x) 207 225 288 233 370 414 10< / span > < / code > < / pre > < / div >
< p > So getting official taxonomic names of 2,000,000 (!!) items
consisting of 90 unique values only takes 0.233 seconds. That is 117
nanoseconds on average. You only lose time on your unique input
values.< / p >
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=======
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< span class = "co" > # mo_name(x) 265 269 357 298 471 516 10< / span > < / code > < / pre > < / div >
< p > So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.298 seconds. That is 149 nanoseconds on average. You only lose time on your unique input values.< / p >
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< / div >
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< div class = "section level3" >
< h3 id = "precalculated-results" > Precalculated results< a class = "anchor" aria-label = "anchor" href = "#precalculated-results" > < / a >
< / h3 >
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< p > What about precalculated results? If the input is an already
precalculated result of a helper function such as
< code > < a href = "../reference/mo_property.html" > mo_name()< / a > < / code > , it almost doesn’
words, if you run < code > < a href = "../reference/mo_property.html" > mo_name()< / a > < / code > on a valid taxonomic name, it
will return the results immediately (see ‘ ’ < / p >
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< div class = "sourceCode" id = "cb4" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span class = "va" > run_it< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > (< / span > A < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "STAAUR"< / span > < span class = "op" > )< / span > ,
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B < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S. aureus"< / span > < span class = "op" > )< / span > ,
C < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcus aureus"< / span > < span class = "op" > )< / span > ,
times < span class = "op" > =< / span > < span class = "fl" > 10< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" class = "external-link" > print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > run_it< / span > , unit < span class = "op" > =< / span > < span class = "st" > "ms"< / span > , signif < span class = "op" > =< / span > < span class = "fl" > 3< / span > < span class = "op" > )< / span >
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< span class = "co" > # Unit: milliseconds< / span >
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< < < < < < < HEAD
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # A 10.3 10.90 11.20 11.10 11.20 12.40 10< / span >
< span class = "co" > # B 31.3 32.70 38.20 33.90 35.20 79.80 10< / span >
< span class = "co" > # C 2.5 2.64 2.79 2.78 2.85 3.13 10< / span > < / code > < / pre > < / div >
< p > So going from < code > mo_name("Staphylococcus aureus")< / code > to
< code > "Staphylococcus aureus"< / code > takes 0.0028 seconds - it doesn’
even start calculating < 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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=======
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # A 12.30 12.30 12.60 12.50 12.60 14.2 10< / span >
< span class = "co" > # B 61.70 61.90 62.70 62.40 62.50 66.2 10< / span >
< span class = "co" > # C 3.04 3.05 6.92 3.12 3.21 40.9 10< / span > < / code > < / pre > < / div >
< p > So going from < code > mo_name("Staphylococcus aureus")< / code > to < code > "Staphylococcus aureus"< / code > takes 0.0031 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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>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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< div class = "sourceCode" id = "cb5" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span class = "va" > run_it< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > (< / span > A < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_species< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "aureus"< / span > < span class = "op" > )< / span > ,
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B < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_genus< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcus"< / span > < span class = "op" > )< / span > ,
C < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcus aureus"< / span > < span class = "op" > )< / span > ,
D < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_family< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Staphylococcaceae"< / span > < span class = "op" > )< / span > ,
E < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_order< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Bacillales"< / span > < span class = "op" > )< / span > ,
F < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_class< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Bacilli"< / span > < span class = "op" > )< / span > ,
G < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_phylum< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Firmicutes"< / span > < span class = "op" > )< / span > ,
H < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_kingdom< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Bacteria"< / span > < span class = "op" > )< / span > ,
times < span class = "op" > =< / span > < span class = "fl" > 10< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" class = "external-link" > print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > run_it< / span > , unit < span class = "op" > =< / span > < span class = "st" > "ms"< / span > , signif < span class = "op" > =< / span > < span class = "fl" > 3< / span > < span class = "op" > )< / span >
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< span class = "co" > # Unit: milliseconds< / span >
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< span class = "co" > # expr min lq mean median uq max neval< / span >
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< < < < < < < HEAD
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< span class = "co" > # A 2.30 2.55 2.68 2.66 2.85 2.94 10< / span >
< span class = "co" > # B 2.27 2.38 2.59 2.56 2.83 2.88 10< / span >
< span class = "co" > # C 2.22 2.25 2.51 2.47 2.74 2.87 10< / span >
< span class = "co" > # D 2.21 2.40 2.68 2.73 2.94 3.08 10< / span >
< span class = "co" > # E 2.22 2.28 2.46 2.45 2.56 2.81 10< / span >
< span class = "co" > # F 2.19 2.34 2.52 2.48 2.71 3.04 10< / span >
< span class = "co" > # G 2.23 2.40 2.52 2.46 2.62 2.88 10< / span >
< span class = "co" > # H 2.13 2.25 2.42 2.47 2.50 2.77 10< / span > < / code > < / pre > < / div >
< p > Of course, when running < code > mo_phylum("Firmicutes")< / code > the
function has zero knowledge about the actual microorganism, namely
< em > S. aureus< / em > . But since the result would be
< code > "Firmicutes"< / code > anyway, there is no point in calculating the
result. And because this package contains all phyla of all known
bacteria, it can just return the initial value immediately.< / p >
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=======
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< span class = "co" > # A 3.02 3.09 3.22 3.10 3.46 3.55 10< / span >
< span class = "co" > # B 3.03 3.04 3.21 3.12 3.42 3.48 10< / span >
< span class = "co" > # C 3.03 3.05 3.08 3.06 3.12 3.16 10< / span >
< span class = "co" > # D 2.98 3.01 3.17 3.09 3.40 3.47 10< / span >
< span class = "co" > # E 3.01 3.06 3.19 3.12 3.43 3.43 10< / span >
< span class = "co" > # F 2.95 2.99 3.11 3.05 3.16 3.46 10< / span >
< span class = "co" > # G 2.94 3.06 3.19 3.13 3.41 3.54 10< / span >
< span class = "co" > # H 2.93 3.01 3.12 3.08 3.19 3.42 10< / span > < / code > < / pre > < / div >
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< p > Of course, when running < code > mo_phylum("Firmicutes")< / code > the function has zero knowledge about the actual microorganism, namely < em > S. aureus< / em > . But since the result would be < code > "Firmicutes"< / code > anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.< / p >
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>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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< / div >
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< div class = "section level3" >
< h3 id = "results-in-other-languages" > Results in other languages< a class = "anchor" aria-label = "anchor" href = "#results-in-other-languages" > < / a >
< / 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’
with the other languages):< / p >
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< div class = "sourceCode" id = "cb6" > < pre class = "downlit sourceCode r" >
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< code class = "sourceCode R" > < span class = "va" > CoNS< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "../reference/as.mo.html" > as.mo< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "CoNS"< / span > < span class = "op" > )< / span >
< span class = "va" > CoNS< / span >
< span class = "co" > # Class < mo> < / span >
< span class = "co" > # [1] B_STPHY_CONS< / span >
< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "en"< / span > < span class = "op" > )< / span > < span class = "co" > # or just mo_name(CoNS) on an English system< / span >
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< span class = "co" > # [1] "Coagulase-negative Staphylococcus (CoNS)"< / span >
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< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "es"< / span > < span class = "op" > )< / span > < span class = "co" > # or just mo_name(CoNS) on a Spanish system< / span >
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< span class = "co" > # [1] "Staphylococcus coagulasa negativo (SCN)"< / span >
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< span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "nl"< / span > < span class = "op" > )< / span > < span class = "co" > # or just mo_name(CoNS) on a Dutch system< / span >
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< span class = "co" > # [1] "Coagulase-negatieve Staphylococcus (CNS)"< / span >
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< span class = "va" > run_it< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html" class = "external-link" > microbenchmark< / a > < / span > < span class = "op" > (< / span > da < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "da"< / span > < span class = "op" > )< / span > ,
de < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "de"< / span > < span class = "op" > )< / span > ,
en < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "en"< / span > < span class = "op" > )< / span > ,
es < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "es"< / span > < span class = "op" > )< / span > ,
fr < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "fr"< / span > < span class = "op" > )< / span > ,
it < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "it"< / span > < span class = "op" > )< / span > ,
nl < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "nl"< / span > < span class = "op" > )< / span > ,
pt < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "pt"< / span > < span class = "op" > )< / span > ,
ru < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "ru"< / span > < span class = "op" > )< / span > ,
sv < span class = "op" > =< / span > < span class = "fu" > < a href = "../reference/mo_property.html" > mo_name< / a > < / span > < span class = "op" > (< / span > < span class = "va" > CoNS< / span > , language < span class = "op" > =< / span > < span class = "st" > "sv"< / span > < span class = "op" > )< / span > ,
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times < span class = "op" > =< / span > < span class = "fl" > 100< / span > < span class = "op" > )< / span >
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< span class = "fu" > < a href = "https://rdrr.io/r/base/print.html" class = "external-link" > print< / a > < / span > < span class = "op" > (< / span > < span class = "va" > run_it< / span > , unit < span class = "op" > =< / span > < span class = "st" > "ms"< / span > , signif < span class = "op" > =< / span > < span class = "fl" > 4< / span > < span class = "op" > )< / span >
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< span class = "co" > # Unit: milliseconds< / span >
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< < < < < < < HEAD
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # da 2.1730 2.476 3.956 2.609 2.873 45.180 100< / span >
< span class = "co" > # de 2.2170 2.497 3.161 2.646 2.855 48.260 100< / span >
< span class = "co" > # en 0.9509 1.122 1.640 1.183 1.321 38.430 100< / span >
< span class = "co" > # es 2.1870 2.546 2.763 2.659 2.872 5.676 100< / span >
< span class = "co" > # fr 1.9880 2.339 2.609 2.456 2.636 5.197 100< / span >
< span class = "co" > # it 2.2580 2.475 4.081 2.619 2.867 47.080 100< / span >
< span class = "co" > # nl 2.3120 2.535 2.792 2.664 2.822 8.113 100< / span >
< span class = "co" > # pt 2.1930 2.417 3.329 2.528 2.783 48.600 100< / span >
< span class = "co" > # ru 2.0470 2.360 2.596 2.481 2.683 6.030 100< / span >
< span class = "co" > # sv 2.2030 2.443 3.077 2.545 2.703 43.350 100< / span > < / code > < / pre > < / div >
< p > Currently supported languages are Danish, Dutch, English, French,
German, Italian, Portuguese, Russian, Spanish and Swedish.< / p >
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=======
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< span class = "co" > # expr min lq mean median uq max neval< / span >
< span class = "co" > # da 3.579 3.689 3.811 3.737 3.894 4.626 100< / span >
< span class = "co" > # de 3.600 3.694 4.205 3.750 3.869 43.820 100< / span >
< span class = "co" > # en 1.686 1.720 1.828 1.766 1.822 2.244 100< / span >
< span class = "co" > # es 3.618 3.688 4.633 3.772 4.083 43.890 100< / span >
< span class = "co" > # fr 3.493 3.602 4.104 3.658 3.785 41.860 100< / span >
< span class = "co" > # it 3.543 3.628 4.152 3.702 3.810 44.040 100< / span >
< span class = "co" > # nl 3.625 3.716 5.024 3.763 3.924 44.220 100< / span >
< span class = "co" > # pt 3.510 3.610 3.742 3.684 3.861 4.096 100< / span >
< span class = "co" > # ru 3.568 3.680 4.534 3.742 3.871 41.170 100< / span >
< span class = "co" > # sv 3.585 3.664 3.833 3.748 4.046 4.987 100< / span > < / code > < / pre > < / div >
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< p > Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.< / p >
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>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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< / div >
< / div >
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< div class = "col-md-3 hidden-xs hidden-sm" id = "pkgdown-sidebar" >
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< / div >
< / div >
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< footer > < div class = "copyright" >
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< p > < / p >
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< p > Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.< / p >
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< / div >
< div class = "pkgdown" >
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< p > < / p >
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< < < < < < < HEAD
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a >
2.0.2.< / p >
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=======
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< p > Site built with < a href = "https://pkgdown.r-lib.org/" class = "external-link" > pkgdown< / a > 2.0.2.< / p >
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>>>>>>> 8c9feea087f568fd4abbdb325140d1d628e6856f
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< / div >
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< / footer >
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< / div >
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< / body >
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< / html >
