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  1. 4
      DESCRIPTION
  2. 4
      R/catalogue_of_life.R
  3. 3
      README.md
  4. 952
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      docs/reference/as.mo.html
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      docs/reference/catalogue_of_life.html
  15. 4
      docs/reference/catalogue_of_life_version.html
  16. 4
      docs/reference/microorganisms.codes.html
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      docs/reference/microorganisms.html
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      docs/reference/microorganisms.old.html
  19. 4
      docs/reference/mo_property.html
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      index.md
  21. 4
      man/as.mo.Rd
  22. 4
      man/catalogue_of_life.Rd
  23. 4
      man/catalogue_of_life_version.Rd
  24. 4
      man/microorganisms.Rd
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  27. 4
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      vignettes/benchmarks.Rmd

4
DESCRIPTION

@ -48,15 +48,15 @@ Imports: @@ -48,15 +48,15 @@ Imports:
crayon (>= 1.3.0),
data.table (>= 1.9.0),
dplyr (>= 0.7.0),
ggplot2,
hms,
knitr (>= 1.0.0),
microbenchmark,
rlang (>= 0.2.0),
tidyr (>= 0.7.0)
Suggests:
covr (>= 3.0.1),
curl,
ggplot2,
microbenchmark,
readxl,
rmarkdown,
rstudioapi,

4
R/catalogue_of_life.R

@ -29,8 +29,8 @@ @@ -29,8 +29,8 @@
#' Included are:
#' \itemize{
#' \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
#' \item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
#' \item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
#' \item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
#' \item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
#' \item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
#' \item{The responsible author(s) and year of scientific publication}
#' }

3
README.md

@ -1,4 +1,5 @@ @@ -1,4 +1,5 @@
# AMR (for R)
% AMR (for R)
<img src="man/figures/logo.png" align="right" height="120px" />
### Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.

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docs/articles/benchmarks.html

@ -216,27 +216,27 @@ @@ -216,27 +216,27 @@
<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_STPHY_AUR"</span>),</a>
<a class="sourceLine" id="cb2-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; expr min lq mean median</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("sau") 42.680497 42.766053 43.5046242 43.2246305</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("stau") 76.627901 76.760320 82.2084011 77.2020310</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("staaur") 42.751945 42.828281 46.8816599 43.0017665</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 18.328588 18.370632 22.3298018 18.4252830</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 18.258048 18.385997 18.7710600 18.5449555</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("STAAUR") 42.734554 42.854751 43.6593017 43.6353320</span></a>
<a class="sourceLine" id="cb2-19" title="19"><span class="co">#&gt; as.mo("Staphylococcus aureus") 11.466961 11.572841 16.5287637 11.6172940</span></a>
<a class="sourceLine" id="cb2-20" title="20"><span class="co">#&gt; as.mo("B_STPHY_AUR") 0.284603 0.302692 0.4095492 0.4190475</span></a>
<a class="sourceLine" id="cb2-21" title="21"><span class="co">#&gt; uq max neval</span></a>
<a class="sourceLine" id="cb2-22" title="22"><span class="co">#&gt; 44.091919 45.191431 10</span></a>
<a class="sourceLine" id="cb2-23" title="23"><span class="co">#&gt; 78.670409 123.715942 10</span></a>
<a class="sourceLine" id="cb2-24" title="24"><span class="co">#&gt; 43.089558 81.640969 10</span></a>
<a class="sourceLine" id="cb2-25" title="25"><span class="co">#&gt; 18.546004 57.384741 10</span></a>
<a class="sourceLine" id="cb2-26" title="26"><span class="co">#&gt; 19.235128 19.693775 10</span></a>
<a class="sourceLine" id="cb2-27" title="27"><span class="co">#&gt; 44.189907 45.381609 10</span></a>
<a class="sourceLine" id="cb2-28" title="28"><span class="co">#&gt; 12.175081 59.815567 10</span></a>
<a class="sourceLine" id="cb2-29" title="29"><span class="co">#&gt; 0.482254 0.500343 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (284 millionths of seconds).</p>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("sau") 42.500 42.800 44.200 43.100 43.900 53.700</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("stau") 76.300 76.800 82.800 77.000 78.800 116.000</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("staaur") 42.700 43.000 47.100 43.600 43.900 80.700</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 18.400 18.500 18.800 18.800 19.200 19.300</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 18.400 18.400 23.600 18.600 19.300 67.100</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("STAAUR") 42.700 42.800 43.200 43.000 43.600 44.100</span></a>
<a class="sourceLine" id="cb2-19" title="19"><span class="co">#&gt; as.mo("Staphylococcus aureus") 11.400 11.500 11.700 11.600 11.800 12.500</span></a>
<a class="sourceLine" id="cb2-20" title="20"><span class="co">#&gt; as.mo("B_STPHY_AUR") 0.267 0.297 0.403 0.431 0.478 0.509</span></a>
<a class="sourceLine" id="cb2-21" title="21"><span class="co">#&gt; neval</span></a>
<a class="sourceLine" id="cb2-22" title="22"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-23" title="23"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-24" title="24"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-25" title="25"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-26" title="26"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-27" title="27"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-28" title="28"><span class="co">#&gt; 10</span></a>
<a class="sourceLine" id="cb2-29" title="29"><span class="co">#&gt; 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of <code><a href="../reference/as.mo.html">as.mo("B_STPHY_AUR")</a></code>, the input is already a valid MO code, so it only almost takes no time at all (267 millionths of seconds).</p>
<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>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">M.leonicaptivi &lt;-<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>
@ -246,24 +246,24 @@ @@ -246,24 +246,24 @@
<a class="sourceLine" id="cb3-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Mycoplasma leonicaptivi"</span>),</a>
<a class="sourceLine" id="cb3-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"B_MYCPL_LEO"</span>),</a>
<a class="sourceLine" id="cb3-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(M.leonicaptivi, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; expr min lq mean</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("myle") 112.493914 112.698409 113.5834588</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("mycleo") 382.813554 382.992838 389.0918181</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 202.903596 203.855253 211.7932317</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("M. leonicaptivi") 203.761037 204.178479 212.5451427</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("MYCLEO") 382.602355 383.481517 393.2696052</span></a>
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 103.701176 103.991018 109.5707840</span></a>
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#&gt; as.mo("B_MYCPL_LEO") 0.312051 0.564876 0.5870787</span></a>
<a class="sourceLine" id="cb3-19" title="19"><span class="co">#&gt; median uq max neval</span></a>
<a class="sourceLine" id="cb3-20" title="20"><span class="co">#&gt; 113.363438 114.20691 115.907686 10</span></a>
<a class="sourceLine" id="cb3-21" title="21"><span class="co">#&gt; 384.139806 388.34114 421.458483 10</span></a>
<a class="sourceLine" id="cb3-22" title="22"><span class="co">#&gt; 204.186195 205.16631 243.204461 10</span></a>
<a class="sourceLine" id="cb3-23" title="23"><span class="co">#&gt; 204.715173 207.97372 244.462163 10</span></a>
<a class="sourceLine" id="cb3-24" title="24"><span class="co">#&gt; 383.918409 386.97938 434.456156 10</span></a>
<a class="sourceLine" id="cb3-25" title="25"><span class="co">#&gt; 104.428888 104.87207 153.125617 10</span></a>
<a class="sourceLine" id="cb3-26" title="26"><span class="co">#&gt; 0.567914 0.63779 0.859048 10</span></a></code></pre></div>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; expr min lq mean median</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("myle") 111.9000 112.0000 112.4000 112.2000</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("mycleo") 381.4000 381.8000 388.5000 382.1000</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("M. leonicaptivi") 203.0000 203.2000 212.5000 203.6000</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co">#&gt; as.mo("M. leonicaptivi") 203.0000 203.1000 212.7000 203.6000</span></a>
<a class="sourceLine" id="cb3-16" title="16"><span class="co">#&gt; as.mo("MYCLEO") 381.8000 382.4000 394.5000 382.9000</span></a>
<a class="sourceLine" id="cb3-17" title="17"><span class="co">#&gt; as.mo("Mycoplasma leonicaptivi") 102.8000 103.0000 103.4000 103.2000</span></a>
<a class="sourceLine" id="cb3-18" title="18"><span class="co">#&gt; as.mo("B_MYCPL_LEO") 0.3183 0.5657 0.5693 0.5727</span></a>
<a class="sourceLine" id="cb3-19" title="19"><span class="co">#&gt; uq max neval</span></a>
<a class="sourceLine" id="cb3-20" title="20"><span class="co">#&gt; 112.4000 113.5000 10</span></a>
<a class="sourceLine" id="cb3-21" title="21"><span class="co">#&gt; 385.4000 439.9000 10</span></a>
<a class="sourceLine" id="cb3-22" title="22"><span class="co">#&gt; 205.8000 253.9000 10</span></a>
<a class="sourceLine" id="cb3-23" title="23"><span class="co">#&gt; 207.2000 252.3000 10</span></a>
<a class="sourceLine" id="cb3-24" title="24"><span class="co">#&gt; 421.1000 422.1000 10</span></a>
<a class="sourceLine" id="cb3-25" title="25"><span class="co">#&gt; 103.4000 105.7000 10</span></a>
<a class="sourceLine" id="cb3-26" title="26"><span class="co">#&gt; 0.5994 0.7446 10</span></a></code></pre></div>
<p>That takes 6 times as much time on average! A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -296,13 +296,13 @@ @@ -296,13 +296,13 @@
<a class="sourceLine" id="cb6-13" title="13"><span class="co">#&gt; [1] 95</span></a>
<a class="sourceLine" id="cb6-14" title="14"></a>
<a class="sourceLine" id="cb6-15" title="15"><span class="co"># now let's see:</span></a>
<a class="sourceLine" id="cb6-16" title="16">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">X =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(x),</a>
<a class="sourceLine" id="cb6-16" title="16">run_it &lt;-<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="cb6-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<a class="sourceLine" id="cb6-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#&gt; X 413.2556 431.8327 448.3355 445.8654 465.2447 480.5499 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.45 seconds (445 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb6-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-21" title="21"><span class="co">#&gt; mo_fullname(x) 438 453 468 468 482 499 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!) of 95 unique values only takes 0.47 seconds (468 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -312,33 +312,33 @@ @@ -312,33 +312,33 @@
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb7-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb7-4" title="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb7-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<a class="sourceLine" id="cb7-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#&gt; A 39.603291 39.713640 39.950479 39.8150500 40.172707 40.664181 10</span></a>
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#&gt; B 19.570436 19.623515 19.964292 19.9376620 20.228830 20.609744 10</span></a>
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#&gt; C 0.251429 0.333144 0.389883 0.3866775 0.499087 0.510401 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-8" title="8"><span class="co">#&gt; A 38.600 38.700 39.40 39.100 39.400 42.900 10</span></a>
<a class="sourceLine" id="cb7-9" title="9"><span class="co">#&gt; B 19.600 19.800 20.00 19.900 20.000 20.700 10</span></a>
<a class="sourceLine" id="cb7-10" title="10"><span class="co">#&gt; C 0.255 0.261 0.37 0.386 0.499 0.505 10</span></a></code></pre></div>
<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’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="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb8-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb8-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb8-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb8-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
<a class="sourceLine" id="cb8-10" title="10"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">C =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">D =</span> <span class="kw"><a href="../reference/mo_property.html">mo_family</a></span>(<span class="st">"Staphylococcaceae"</span>),</a>
<a class="sourceLine" id="cb8-5" title="5"> <span class="dt">E =</span> <span class="kw"><a href="../reference/mo_property.html">mo_order</a></span>(<span class="st">"Bacillales"</span>),</a>
<a class="sourceLine" id="cb8-6" title="6"> <span class="dt">F =</span> <span class="kw"><a href="../reference/mo_property.html">mo_class</a></span>(<span class="st">"Bacilli"</span>),</a>
<a class="sourceLine" id="cb8-7" title="7"> <span class="dt">G =</span> <span class="kw"><a href="../reference/mo_property.html">mo_phylum</a></span>(<span class="st">"Firmicutes"</span>),</a>
<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">H =</span> <span class="kw"><a href="../reference/mo_property.html">mo_kingdom</a></span>(<span class="st">"Bacteria"</span>),</a>
<a class="sourceLine" id="cb8-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb8-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb8-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#&gt; A 0.298084 0.370509 0.4040816 0.4065820 0.449569 0.475480 10</span></a>
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#&gt; B 0.293753 0.306115 0.3352809 0.3212705 0.370160 0.386154 10</span></a>
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#&gt; C 0.307652 0.353328 0.4106327 0.3943595 0.467239 0.548255 10</span></a>
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#&gt; D 0.244376 0.262954 0.2987189 0.3027975 0.338102 0.353747 10</span></a>
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#&gt; E 0.249614 0.255550 0.2985027 0.2772710 0.351931 0.397049 10</span></a>
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#&gt; F 0.259531 0.282439 0.3248814 0.3193850 0.345575 0.415906 10</span></a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; G 0.249055 0.266516 0.3293723 0.3020295 0.344528 0.616350 10</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; H 0.242141 0.288515 0.3122614 0.3152295 0.339779 0.355773 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-13" title="13"><span class="co">#&gt; A 0.282 0.311 0.372 0.359 0.437 0.513 10</span></a>
<a class="sourceLine" id="cb8-14" title="14"><span class="co">#&gt; B 0.285 0.316 0.355 0.363 0.382 0.443 10</span></a>
<a class="sourceLine" id="cb8-15" title="15"><span class="co">#&gt; C 0.258 0.408 0.439 0.430 0.504 0.565 10</span></a>
<a class="sourceLine" id="cb8-16" title="16"><span class="co">#&gt; D 0.268 0.304 0.322 0.321 0.360 0.366 10</span></a>
<a class="sourceLine" id="cb8-17" title="17"><span class="co">#&gt; E 0.259 0.273 0.312 0.295 0.357 0.391 10</span></a>
<a class="sourceLine" id="cb8-18" title="18"><span class="co">#&gt; F 0.250 0.275 0.327 0.294 0.343 0.614 10</span></a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; G 0.254 0.281 0.312 0.320 0.338 0.369 10</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; H 0.257 0.265 0.311 0.316 0.329 0.397 10</span></a></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> too, 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 id="results-in-other-languages" class="section level3">
@ -348,27 +348,30 @@ @@ -348,27 +348,30 @@
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>) <span class="co"># or just mo_fullname("CoNS") on an English system</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="co">#&gt; [1] "Coagulase Negative Staphylococcus (CoNS)"</span></a>
<a class="sourceLine" id="cb9-3" title="3"></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>) <span class="co"># or just mo_fullname("CoNS") on a French system</span></a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co">#&gt; [1] "Staphylococcus à coagulase négative (CoNS)"</span></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># or just mo_fullname("CoNS") on a Spanish system</span></a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co">#&gt; [1] "Staphylococcus coagulasa negativo (CoNS)"</span></a>
<a class="sourceLine" id="cb9-6" title="6"></a>
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb9-8" title="8"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb9-9" title="9"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb9-10" title="10"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb9-11" title="11"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb9-12" title="12"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb9-13" title="13"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb9-14" title="14"> <span class="dt">times =</span> <span class="dv">10</span>,</a>
<a class="sourceLine" id="cb9-15" title="15"> <span class="dt">unit =</span> <span class="st">"ms"</span>)</a>
<a class="sourceLine" id="cb9-16" title="16"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb9-17" title="17"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb9-18" title="18"><span class="co">#&gt; en 10.74026 11.10686 11.09997 11.11563 11.20366 11.34076 10</span></a>
<a class="sourceLine" id="cb9-19" title="19"><span class="co">#&gt; de 19.15977 19.59293 19.76980 19.71204 19.78338 20.54633 10</span></a>
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#&gt; nl 19.42929 19.54013 19.75978 19.67233 19.77263 20.58935 10</span></a>
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#&gt; es 19.31042 19.66821 19.65120 19.69552 19.73421 19.75538 10</span></a>
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#&gt; it 19.26362 19.34003 22.93301 19.62998 19.67213 52.79729 10</span></a>
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#&gt; fr 19.33011 19.54739 26.16391 19.64726 19.87145 52.40164 10</span></a>
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#&gt; pt 19.22800 19.50164 26.41786 19.66766 20.96244 53.16479 10</span></a></code></pre></div>
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>) <span class="co"># or just mo_fullname("CoNS") on a Dutch system</span></a>
<a class="sourceLine" id="cb9-8" title="8"><span class="co">#&gt; [1] "Coagulase-negatieve Staphylococcus (CNS)"</span></a>
<a class="sourceLine" id="cb9-9" title="9"></a>
<a class="sourceLine" id="cb9-10" title="10">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">en =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"en"</span>),</a>
<a class="sourceLine" id="cb9-11" title="11"> <span class="dt">de =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"de"</span>),</a>
<a class="sourceLine" id="cb9-12" title="12"> <span class="dt">nl =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"nl"</span>),</a>
<a class="sourceLine" id="cb9-13" title="13"> <span class="dt">es =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"es"</span>),</a>
<a class="sourceLine" id="cb9-14" title="14"> <span class="dt">it =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"it"</span>),</a>
<a class="sourceLine" id="cb9-15" title="15"> <span class="dt">fr =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"fr"</span>),</a>
<a class="sourceLine" id="cb9-16" title="16"> <span class="dt">pt =</span> <span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"CoNS"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>),</a>
<a class="sourceLine" id="cb9-17" title="17"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb9-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb9-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb9-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb9-21" title="21"><span class="co">#&gt; en 10.69 11.02 11.06 11.08 11.21 11.29 10</span></a>
<a class="sourceLine" id="cb9-22" title="22"><span class="co">#&gt; de 19.09 19.48 19.49 19.55 19.62 19.66 10</span></a>
<a class="sourceLine" id="cb9-23" title="23"><span class="co">#&gt; nl 19.25 19.58 19.66 19.60 19.72 20.61 10</span></a>
<a class="sourceLine" id="cb9-24" title="24"><span class="co">#&gt; es 19.17 19.54 26.16 19.61 20.23 52.49 10</span></a>
<a class="sourceLine" id="cb9-25" title="25"><span class="co">#&gt; it 19.10 19.46 26.14 19.69 19.92 52.56 10</span></a>
<a class="sourceLine" id="cb9-26" title="26"><span class="co">#&gt; fr 19.10 19.36 19.50 19.50 19.59 20.13 10</span></a>
<a class="sourceLine" id="cb9-27" title="27"><span class="co">#&gt; pt 19.26 19.50 23.19 19.71 20.48 53.09 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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docs/index.html

@ -202,7 +202,8 @@ @@ -202,7 +202,8 @@
<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen, the Netherlands, and the Medical Microbiology &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and is free software; you can freely use and distribute it for both personal and commercial (but <strong>not</strong> patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation. Read the full license <a href="./LICENSE-text.html">here</a>.</p>
<p>This package can be used for:</p>
<ul>
<li>Reference for microorganisms, since it contains allmost all 60,000 microbial species of the Catalogue of Life</li>
<li>Reference for microorganisms, since it contains almost all 60,000 microbial (sub)species from the <a href="http://www.catalogueoflife.org">Catalogue of Life</a>
</li>
<li>Calculating antimicrobial resistance</li>
<li>Calculating empirical susceptibility of both mono therapy and combination therapy</li>
<li>Predicting future antimicrobial resistance using regression models</li>
@ -249,6 +250,7 @@ @@ -249,6 +250,7 @@
<p>This package is available <a href="https://cran.r-project.org/package=AMR">on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R with:</p>
<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/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><em>Note:</em> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
@ -273,14 +275,17 @@ @@ -273,14 +275,17 @@
<p>This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>).</p>
<p>Included are:</p>
<ul>
<li>All ~55,000 species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</li>
<li>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</li>
<li>All ~15,000 previously accepted names of included species that have been taxonomically renamed</li>
<li>The responsible author(s) and year of scientific publication</li>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li>
<p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales.</p>
<p>The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p>
</li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>This data is updated annually - check the included version with <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
<p><strong>About</strong></p>
<p>The Catalogue of Life (<a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p><strong>About the Catalogue of Life</strong></p>
<p>The <a href="http://www.catalogueoflife.org">Catalogue of Life</a> is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>Read more about the data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div>
<div id="antimicrobial-reference-data" class="section level4">

4
docs/reference/as.mo.html

@ -344,8 +344,8 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i @@ -344,8 +344,8 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/catalogue_of_life.html

@ -249,8 +249,8 @@ @@ -249,8 +249,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/catalogue_of_life_version.html

@ -250,8 +250,8 @@ @@ -250,8 +250,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code>catalogue_of_life_version</code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/microorganisms.codes.html

@ -257,8 +257,8 @@ @@ -257,8 +257,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/microorganisms.html

@ -281,8 +281,8 @@ @@ -281,8 +281,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/microorganisms.old.html

@ -263,8 +263,8 @@ @@ -263,8 +263,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

4
docs/reference/mo_property.html

@ -330,8 +330,8 @@ @@ -330,8 +330,8 @@
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
<p>Included are:</p><ul>
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
<li><p>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</p></li>
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>

18
index.md

@ -15,7 +15,7 @@ This R package is actively maintained and is free software; you can freely use a @@ -15,7 +15,7 @@ This R package is actively maintained and is free software; you can freely use a
This package can be used for:
* Reference for microorganisms, since it contains allmost all 60,000 microbial species of the Catalogue of Life
* Reference for microorganisms, since it contains almost all 60,000 microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org)
* Calculating antimicrobial resistance
* Calculating empirical susceptibility of both mono therapy and combination therapy
* Predicting future antimicrobial resistance using regression models
@ -66,6 +66,8 @@ install.packages("AMR") @@ -66,6 +66,8 @@ install.packages("AMR")
It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
*Note:* Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.
#### Latest development version
The latest and unpublished development version can be installed with (**precaution: may be unstable**):
@ -88,17 +90,21 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -88,17 +90,21 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
* All ~55,000 species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses
* All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses
* All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales.
The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera *Aspergillus*, *Candida*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
* All ~15,000 previously accepted names of included species that have been taxonomically renamed
The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of *Aspergillus*, *Candida*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
* All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed
* The responsible author(s) and year of scientific publication
This data is updated annually - check the included version with `catalogue_of_life_version()`.
**About**
**About the Catalogue of Life**
The Catalogue of Life ([www.catalogueoflife.org](http://www.catalogueoflife.org)) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The [Catalogue of Life](http://www.catalogueoflife.org) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
Read more about the data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).

4
man/as.mo.Rd

@ -118,8 +118,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -118,8 +118,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/catalogue_of_life.Rd

@ -14,8 +14,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -14,8 +14,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/catalogue_of_life_version.Rd

@ -17,8 +17,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -17,8 +17,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/microorganisms.Rd

@ -46,8 +46,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -46,8 +46,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/microorganisms.codes.Rd

@ -23,8 +23,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -23,8 +23,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/microorganisms.old.Rd

@ -28,8 +28,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -28,8 +28,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

4
man/mo_property.Rd

@ -101,8 +101,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f @@ -101,8 +101,8 @@ This package contains the complete taxonomic tree of almost all microorganisms f
Included are:
\itemize{
\item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed}
\item{All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant (sub)species are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
\item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
\item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
\item{The responsible author(s) and year of scientific publication}
}

54
vignettes/benchmarks.Rmd vendored

@ -46,7 +46,7 @@ S.aureus <- microbenchmark(as.mo("sau"), @@ -46,7 +46,7 @@ S.aureus <- microbenchmark(as.mo("sau"),
as.mo("Staphylococcus aureus"),
as.mo("B_STPHY_AUR"),
times = 10)
print(S.aureus, unit = "ms")
print(S.aureus, unit = "ms", signif = 3)
```
In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 10 milliseconds means it can determine 100 input values per second. It case of 50 milliseconds, this is only 20 input values per second. The more an input value resembles a full name, the faster the result will be found. In case of `as.mo("B_STPHY_AUR")`, the input is already a valid MO code, so it only almost takes no time at all (`r as.integer(min(S.aureus$time, na.rm = TRUE) / 1000)` millionths of seconds).
@ -62,7 +62,7 @@ M.leonicaptivi <- microbenchmark(as.mo("myle"), @@ -62,7 +62,7 @@ M.leonicaptivi <- microbenchmark(as.mo("myle"),
as.mo("Mycoplasma leonicaptivi"),
as.mo("B_MYCPL_LEO"),
times = 10)
print(M.leonicaptivi, unit = "ms")
print(M.leonicaptivi, unit = "ms", signif = 4)
```
That takes `r round(mean(M.leonicaptivi$time, na.rm = TRUE) / mean(S.aureus$time, na.rm = TRUE), 1)` times as much time on average! A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance:
@ -99,9 +99,9 @@ length(x) @@ -99,9 +99,9 @@ length(x)
n_distinct(x)
# now let's see:
run_it <- microbenchmark(X = mo_fullname(x),
run_it <- microbenchmark(mo_fullname(x),
times = 10)
print(run_it, unit = "ms")
print(run_it, unit = "ms", signif = 3)
```
So transforming 500,000 values (!) of `r n_distinct(x)` unique values only takes `r round(median(run_it$time, na.rm = TRUE) / 1e9, 2)` seconds (`r as.integer(median(run_it$time, na.rm = TRUE) / 1e6)` ms). You only lose time on your unique input values.
@ -115,22 +115,22 @@ run_it <- microbenchmark(A = mo_fullname("B_STPHY_AUR"), @@ -115,22 +115,22 @@ run_it <- microbenchmark(A = mo_fullname("B_STPHY_AUR"),
B = mo_fullname("S. aureus"),
C = mo_fullname("Staphylococcus aureus"),
times = 10)
print(run_it, unit = "ms")
print(run_it, unit = "ms", signif = 3)
```
So going from `mo_fullname("Staphylococcus aureus")` to `"Staphylococcus aureus"` takes `r format(round(run_it %>% filter(expr == "C") %>% pull(time) %>% median() / 1e9, 4), scientific = FALSE)` seconds - it doesn't even start calculating *if the result would be the same as the expected resulting value*. That goes for all helper functions:
```{r}
microbenchmark(A = mo_species("aureus"),
B = mo_genus("Staphylococcus"),
C = mo_fullname("Staphylococcus aureus"),
D = mo_family("Staphylococcaceae"),
E = mo_order("Bacillales"),
F = mo_class("Bacilli"),
G = mo_phylum("Firmicutes"),
H = mo_kingdom("Bacteria"),
times = 10,
unit = "ms")
run_it <- microbenchmark(A = mo_species("aureus"),
B = mo_genus("Staphylococcus"),
C = mo_fullname("Staphylococcus aureus"),
D = mo_family("Staphylococcaceae"),
E = mo_order("Bacillales"),
F = mo_class("Bacilli"),
G = mo_phylum("Firmicutes"),
H = mo_kingdom("Bacteria"),
times = 10)
print(run_it, unit = "ms", signif = 3)
```
Of course, when running `mo_phylum("Firmicutes")` the function has zero knowledge about the actual microorganism, namely *S. aureus*. But since the result would be `"Firmicutes"` too, 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.
@ -142,17 +142,19 @@ When the system language is non-English and supported by this `AMR` package, som @@ -142,17 +142,19 @@ When the system language is non-English and supported by this `AMR` package, som
```{r}
mo_fullname("CoNS", language = "en") # or just mo_fullname("CoNS") on an English system
mo_fullname("CoNS", language = "fr") # or just mo_fullname("CoNS") on a French system
microbenchmark(en = mo_fullname("CoNS", language = "en"),
de = mo_fullname("CoNS", language = "de"),
nl = mo_fullname("CoNS", language = "nl"),
es = mo_fullname("CoNS", language = "es"),
it = mo_fullname("CoNS", language = "it"),
fr = mo_fullname("CoNS", language = "fr"),
pt = mo_fullname("CoNS", language = "pt"),
times = 10,
unit = "ms")
mo_fullname("CoNS", language = "es") # or just mo_fullname("CoNS") on a Spanish system
mo_fullname("CoNS", language = "nl") # or just mo_fullname("CoNS") on a Dutch system
run_it <- microbenchmark(en = mo_fullname("CoNS", language = "en"),
de = mo_fullname("CoNS", language = "de"),
nl = mo_fullname("CoNS", language = "nl"),
es = mo_fullname("CoNS", language = "es"),
it = mo_fullname("CoNS", language = "it"),
fr = mo_fullname("CoNS", language = "fr"),
pt = mo_fullname("CoNS", language = "pt"),
times = 10)
print(run_it, unit = "ms", signif = 4)
```
Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.

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