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(v1.5.0.9023) mo properties speed improvement

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dr. M.S. (Matthijs) Berends 2021-02-21 23:19:40 +01:00
parent 062c49fca1
commit 0fdabff1ba
18 changed files with 62 additions and 86 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.5.0.9022 Version: 1.5.0.9023
Date: 2021-02-21 Date: 2021-02-21
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9022 # AMR 1.5.0.9023
## <small>Last updated: 21 February 2021</small> ## <small>Last updated: 21 February 2021</small>
### New ### New

1
R/globals.R
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@ -26,6 +26,7 @@
globalVariables(c(".rowid", globalVariables(c(".rowid",
"ab", "ab",
"ab_txt", "ab_txt",
"affect_mo_name",
"angle", "angle",
"antibiotic", "antibiotic",
"antibiotics", "antibiotics",

15
R/mo.R
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@ -766,21 +766,24 @@ exec_as.mo <- function(x,
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB) # Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
x[i] <- lookup(mo == toupper(gsub("g([abcdfghk])s", x[i] <- lookup(mo == toupper(gsub("g([abcdfghk])s",
"B_STRPT_GRP\\1", "B_STRPT_GRP\\1",
x_backup_without_spp[i])), uncertainty = -1) x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next next
} }
if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") { if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") {
# Streptococci in different languages, like "estreptococos grupo B" # Streptococci in different languages, like "estreptococos grupo B"
x[i] <- lookup(mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$", x[i] <- lookup(mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$",
"B_STRPT_GRP\\2", "B_STRPT_GRP\\2",
x_backup_without_spp[i])), uncertainty = -1) x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next next
} }
if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") { if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") {
# Streptococci in different languages, like "Group A Streptococci" # Streptococci in different languages, like "Group A Streptococci"
x[i] <- lookup(mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*", x[i] <- lookup(mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*",
"B_STRPT_GRP\\1", "B_STRPT_GRP\\1",
x_backup_without_spp[i])), uncertainty = -1) x_backup_without_spp[i],
perl = TRUE)), uncertainty = -1)
next next
} }
if (x_backup_without_spp[i] %like_case% "haemoly.*strep") { if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
@ -843,7 +846,7 @@ exec_as.mo <- function(x,
# Salmonella Group A to Z, just return S. species for now # Salmonella Group A to Z, just return S. species for now
x[i] <- lookup(genus == "Salmonella", uncertainty = -1) x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
next next
} else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) & } else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
!x_backup[i] %like% "t[iy](ph|f)[iy]") { !x_backup[i] %like% "t[iy](ph|f)[iy]") {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica # Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
# except for S. typhi, S. paratyphi, S. typhimurium # except for S. typhi, S. paratyphi, S. typhimurium
@ -1108,7 +1111,7 @@ exec_as.mo <- function(x,
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n")) cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
} }
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") { if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) { if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
if (isTRUE(debug)) { if (isTRUE(debug)) {
message("Running '", paste(b.x_trimmed, "species"), "'") message("Running '", paste(b.x_trimmed, "species"), "'")
} }
@ -1852,7 +1855,7 @@ print.mo_uncertainties <- function(x, ...) {
width = 0.98 * getOption("width")), width = 0.98 * getOption("width")),
collapse = "") collapse = "")
# after strwrap, make taxonomic names italic # after strwrap, make taxonomic names italic
candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates) candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "), candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
"Also matched", "Also matched",
candidates, fixed = TRUE) candidates, fixed = TRUE)

6
R/mo_property.R
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@ -723,12 +723,6 @@ mo_validate <- function(x, property, language, ...) {
x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...) x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
} else if (!all(x %in% MO_lookup[, property, drop = TRUE]) } else if (!all(x %in% MO_lookup[, property, drop = TRUE])
| has_Becker_or_Lancefield) { | has_Becker_or_Lancefield) {
accepted_args <- names(as.list(args("as.mo")))
accepted_args <- accepted_args[!accepted_args %in% c("", "...", "x", "property")]
stop_if(!all(names(dots) %in% names(as.list(args("as.mo")))),
"invalid argument(s): ", vector_and(names(dots)[!names(dots) %in% names(as.list(args("as.mo")))], quotes = "'"),
".\nAccepted arguments are ", vector_and(accepted_args, quotes = "'"), ".",
call = FALSE)
x <- exec_as.mo(x, property = property, language = language, ...) x <- exec_as.mo(x, property = property, language = language, ...)
} }

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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

91
docs/articles/benchmarks.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>
@ -192,7 +192,6 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Benchmarks</h1> <h1 data-toc-skip>Benchmarks</h1>
<h4 class="date">21 February 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/benchmarks.Rmd"><code>vignettes/benchmarks.Rmd</code></a></small>
<div class="hidden name"><code>benchmarks.Rmd</code></div> <div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -226,42 +225,22 @@
<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> <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>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>, <span class="co"># Vancomycin Resistant S. aureus</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"VRSA"</span><span class="op">)</span>, <span class="co"># Vancomycin Resistant S. aureus</span>
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="co"># [1] "^st.* au"</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html">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> <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>
<span class="co"># Unit: milliseconds</span> <span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># as.mo("sau") 12.0 12.0 13.0 14.0 14.0 16 10</span> <span class="co"># as.mo("sau") 11.0 12.0 27.0 13.0 49.0 51 10</span>
<span class="co"># as.mo("stau") 55.0 67.0 88.0 95.0 98.0 120 10</span> <span class="co"># as.mo("stau") 53.0 57.0 76.0 74.0 93.0 100 10</span>
<span class="co"># as.mo("STAU") 57.0 66.0 110.0 100.0 130.0 250 10</span> <span class="co"># as.mo("STAU") 53.0 54.0 69.0 56.0 58.0 190 10</span>
<span class="co"># as.mo("staaur") 12.0 12.0 17.0 13.0 14.0 54 10</span> <span class="co"># as.mo("staaur") 11.0 12.0 21.0 13.0 42.0 44 10</span>
<span class="co"># as.mo("STAAUR") 11.0 12.0 17.0 13.0 14.0 61 10</span> <span class="co"># as.mo("STAAUR") 11.0 12.0 16.0 13.0 14.0 48 10</span>
<span class="co"># as.mo("S. aureus") 30.0 32.0 62.0 69.0 93.0 95 10</span> <span class="co"># as.mo("S. aureus") 27.0 27.0 38.0 32.0 35.0 75 10</span>
<span class="co"># as.mo("S aureus") 29.0 33.0 43.0 37.0 53.0 71 10</span> <span class="co"># as.mo("S aureus") 27.0 29.0 38.0 30.0 36.0 73 10</span>
<span class="co"># as.mo("Staphylococcus aureus") 2.2 2.4 2.6 2.6 2.8 3 10</span> <span class="co"># as.mo("Staphylococcus aureus") 3.1 3.2 6.9 3.5 3.7 38 10</span>
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 270.0 290.0 330.0 310.0 380.0 430 10</span> <span class="co"># as.mo("Staphylococcus aureus (MRSA)") 250.0 260.0 270.0 260.0 280.0 290 10</span>
<span class="co"># as.mo("Sthafilokkockus aaureuz") 190.0 210.0 240.0 250.0 270.0 290 10</span> <span class="co"># as.mo("Sthafilokkockus aaureuz") 160.0 200.0 200.0 200.0 210.0 230 10</span>
<span class="co"># as.mo("MRSA") 12.0 12.0 14.0 13.0 15.0 16 10</span> <span class="co"># as.mo("MRSA") 10.0 11.0 12.0 11.0 13.0 14 10</span>
<span class="co"># as.mo("VISA") 21.0 22.0 29.0 24.0 25.0 79 10</span> <span class="co"># as.mo("VISA") 19.0 20.0 26.0 22.0 24.0 61 10</span>
<span class="co"># as.mo("VRSA") 21.0 24.0 35.0 28.0 56.0 58 10</span></code></pre></div> <span class="co"># as.mo("VRSA") 19.0 20.0 24.0 21.0 22.0 56 10</span></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p> <p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p> <p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p> <p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
@ -291,8 +270,8 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">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> <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>
<span class="co"># Unit: milliseconds</span> <span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># mo_name(x) 125 144 182 171 186 298 10</span></code></pre></div> <span class="co"># mo_name(x) 137 146 178 172 193 282 10</span></code></pre></div>
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.171 seconds. You only lose time on your unique input values.</p> <p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.172 seconds. You only lose time on your unique input values.</p>
</div> </div>
<div id="precalculated-results" class="section level3"> <div id="precalculated-results" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -306,10 +285,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">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> <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>
<span class="co"># Unit: milliseconds</span> <span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 7.08 7.37 15.90 7.94 9.02 48.9 10</span> <span class="co"># A 7.12 7.56 7.89 7.7 8.39 8.69 10</span>
<span class="co"># B 23.50 24.00 25.20 24.10 26.20 30.1 10</span> <span class="co"># B 23.90 24.50 35.10 24.8 27.40 77.50 10</span>
<span class="co"># C 1.54 1.62 1.76 1.71 1.81 2.3 10</span></code></pre></div> <span class="co"># C 1.73 1.84 1.95 1.9 2.09 2.36 10</span></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0017 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p> <p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0019 seconds - it doesn’t even start calculating <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="cb5"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</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>, <code class="sourceCode R"><span class="va">run_it</span> <span class="op">&lt;-</span> <span class="fu">microbenchmark</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>,
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>, 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>,
@ -323,14 +302,14 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">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> <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>
<span class="co"># Unit: milliseconds</span> <span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># A 1.63 1.92 1.99 2.01 2.11 2.29 10</span> <span class="co"># A 1.54 1.57 1.73 1.69 1.88 2.00 10</span>
<span class="co"># B 1.67 1.89 2.01 1.96 2.12 2.62 10</span> <span class="co"># B 1.51 1.52 1.75 1.70 1.86 2.41 10</span>
<span class="co"># C 1.86 1.87 1.96 1.97 2.04 2.13 10</span> <span class="co"># C 1.55 1.60 1.70 1.70 1.81 1.86 10</span>
<span class="co"># D 1.63 1.82 1.90 1.94 2.00 2.06 10</span> <span class="co"># D 1.55 1.59 1.71 1.66 1.83 1.94 10</span>
<span class="co"># E 1.60 1.94 3.05 1.97 2.24 12.60 10</span> <span class="co"># E 1.50 1.55 1.68 1.61 1.78 2.10 10</span>
<span class="co"># F 1.66 1.90 2.18 1.95 2.01 4.33 10</span> <span class="co"># F 1.51 1.62 1.75 1.79 1.82 2.02 10</span>
<span class="co"># G 1.84 1.89 1.99 1.98 2.02 2.24 10</span> <span class="co"># G 1.52 1.53 1.68 1.60 1.80 2.02 10</span>
<span class="co"># H 1.79 1.95 2.08 2.06 2.25 2.36 10</span></code></pre></div> <span class="co"># H 1.53 1.54 1.63 1.60 1.67 1.84 10</span></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p> <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> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div> </div>
<div id="results-in-other-languages" class="section level3"> <div id="results-in-other-languages" class="section level3">
@ -358,13 +337,13 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">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> <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>
<span class="co"># Unit: milliseconds</span> <span class="co"># Unit: milliseconds</span>
<span class="co"># expr min lq mean median uq max neval</span> <span class="co"># expr min lq mean median uq max neval</span>
<span class="co"># en 17.21 17.88 21.68 18.14 19.20 71.64 100</span> <span class="co"># en 17.38 17.71 25.63 18.11 19.75 81.61 100</span>
<span class="co"># de 20.08 20.74 26.58 21.26 22.41 159.80 100</span> <span class="co"># de 20.14 20.61 24.87 20.91 21.57 85.23 100</span>
<span class="co"># nl 24.88 25.81 31.01 26.32 27.03 74.57 100</span> <span class="co"># nl 25.02 25.46 28.40 25.83 26.58 78.47 100</span>
<span class="co"># es 19.91 20.80 26.33 21.28 22.60 80.34 100</span> <span class="co"># es 19.90 20.41 24.86 20.77 21.78 81.38 100</span>
<span class="co"># it 19.96 20.63 25.21 21.20 22.25 76.35 100</span> <span class="co"># it 20.01 20.44 24.40 20.80 21.57 76.08 100</span>
<span class="co"># fr 19.61 20.38 26.62 21.15 22.59 80.90 100</span> <span class="co"># fr 19.85 20.23 29.97 20.89 23.56 192.40 100</span>
<span class="co"># pt 19.87 20.58 27.65 20.92 23.22 80.73 100</span></code></pre></div> <span class="co"># pt 19.90 20.26 26.53 20.75 22.56 85.69 100</span></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p> <p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div> </div>
</div> </div>

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1509022" class="section level1"> <div id="amr-1509023" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9022"> <h1 class="page-header" data-toc-text="1.5.0.9023">
<a href="#amr-1509022" class="anchor"></a>AMR 1.5.0.9022<small> Unreleased </small> <a href="#amr-1509023" class="anchor"></a>AMR 1.5.0.9023<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-21-february-2021" class="section level2"> <div id="last-updated-21-february-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-02-21T21:55Z last_built: 2021-02-21T22:18Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9023</span>
</span> </span>
</div> </div>

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@ -1,6 +1,5 @@
--- ---
title: "Benchmarks" title: "Benchmarks"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output: output:
rmarkdown::html_vignette: rmarkdown::html_vignette:
toc: true toc: true