<p><div><div><div><div data-show-faces="false" data-height="21" data-width="100" data-layout="button_count" data-send="true" data-href="https://www.r-bloggers.com/taxize-seven-years-of-taxonomy-in-r/"></div></div><div></div></div><div></div></div>
<div>
(This article was first published on <strong><a href="https://ropensci.org/technotes/2018/05/23/taxize-seven-years/"> rOpenSci - open tools for open science</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p><a rel="nofollow" href="https://github.com/ropensci/taxize" target="_blank">taxize</a> was seven years old this last Saturday!</p>

<h2>What is taxize?</h2>
<p><code>taxize</code> is designed around making working with taxonomic names easier – abstracting away the details of what each of 20 or so taxonomic data sources require for a given use case.</p>
<p>A samping of use cases covered in <code>taxize</code> (all of these across many different data sources):</p>
<ul>
<li>Taxonomic identifier from a taxonomic name and vice versa</li>
<li>Taxonomic name from a vernacular (common) name and vice versa</li>
<li>Taxonomic hierarchy/classification from identifier or name</li>
<li>Taxonomic children of an identifier or name</li>
<li>All taxa downstream to a certain rank from identifier or name</li>
<li>Taxonomic name synonyms from identifier or name</li>
<li>Lowest common taxon and rank for an identifier or name</li>
<li>Resolve taxonomic names, i.e., fix spelling errors</li>
</ul>
<p></p>
<h2>History</h2>
<p><code>taxize</code> was one of our first packages. Our first commit was on <a rel="nofollow" href="https://ropensci.org/technotes/2018/05/23/taxize-seven-years/#link-to-first-commit" target="_blank">2011-05-19</a>, uneventfully adding an empty README:</p>
<p><a rel="nofollow" href="https://github.com/ropensci/taxize/commit/667004eac329869099fdccb481138f572576cb69" target="_blank"><img alt="first_commit" src="https://i1.wp.com/ropensci.org/img/blog-images/2018-05-23-taxize-seven-years/taxize-first-commit.png?w=456&ssl=1" data-recalc-dims="1"></a></p>
<p>We’ve come a long way since May 2011. We’ve added a lot of new functionality and many new contributors.</p>
<p></p>
<h3>Commit history</h3>
<p>Get git commits for <code>taxize</code> using a few tidyverse packages as well as <a rel="nofollow" href="https://github.com/ropensci/git2r" target="_blank">git2r</a>, our R package for working with git repositories:</p>
<pre><code>library(git2r)
library(ggplot2)
library(dplyr)

repo &lt;- git2r::repository(&quot;~/github/ropensci/taxize&quot;)
res &lt;- commits(repo)
</code></pre>
<p>A graph of commit history</p>
<pre><code>dates &lt;- vapply(res, function(z) {
    as.character(as.POSIXct(z@author@when@time, origin = &quot;1970-01-01&quot;))
}, character(1))
df &lt;- tbl_df(data.frame(date = dates, stringsAsFactors = FALSE)) %>% 
    group_by(date) %>%
    summarise(count = n()) %>%
    mutate(cumsum = cumsum(count)) %>%
    ungroup()
ggplot(df, aes(x = as.Date(date), y = cumsum)) +
    geom_line(size = 2) +
    theme_grey(base_size = 16) +
    scale_x_date(labels = scales::date_format(&quot;%Y/%m&quot;)) +
    labs(x = 'May 2011 to May 2018', y = 'Cumulative Git Commits')
</code></pre>
<p><img alt="plot of chunk unnamed-chunk-3" src="https://i0.wp.com/ropensci.org/img/blog-images/2018-05-23-taxize-seven-years/unnamed-chunk-3-1.png?w=456&ssl=1" data-recalc-dims="1"></p>
<h3>Contributors</h3>
<p>A graph of new contributors through time</p>
<pre><code>date_name &lt;- lapply(res, function(z) {
    data_frame(
        date = as.character(as.POSIXct(z@author@when@time, origin = &quot;1970-01-01&quot;)),
        name = z@author@name
    )
})
date_name &lt;- bind_rows(date_name)

firstdates &lt;- date_name %>%
    group_by(name) %>%
    arrange(date) %>%
    filter(rank(date, ties.method = &quot;first&quot;) == 1) %>%
    ungroup() %>%
    mutate(count = 1) %>%
    arrange(date) %>%
    mutate(cumsum = cumsum(count))

## plot
ggplot(firstdates, aes(as.Date(date), cumsum)) +
  geom_line(size = 2) +
  theme_grey(base_size = 18) +
  scale_x_date(labels = scales::date_format(&quot;%Y/%m&quot;)) +
  labs(x = 'May 2011 to May 2018', y = 'Cumulative New Contributors')
</code></pre>
<p><img alt="plot of chunk unnamed-chunk-4" src="https://i2.wp.com/ropensci.org/img/blog-images/2018-05-23-taxize-seven-years/unnamed-chunk-4-1.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>taxize</code> contributors, including those that have opened issues (click to go to their GitHub profile):</p>
<p><a rel="nofollow" href="https://github.com/afkoeppel" target="_blank">afkoeppel</a> – <a rel="nofollow" href="https://github.com/ahhurlbert" target="_blank">ahhurlbert</a> – <a rel="nofollow" href="https://github.com/albnd" target="_blank">albnd</a> – <a rel="nofollow" href="https://github.com/Alectoria" target="_blank">Alectoria</a> – <a rel="nofollow" href="https://github.com/andzandz11" target="_blank">andzandz11</a> – <a rel="nofollow" href="https://github.com/antagomir" target="_blank">antagomir</a> – <a rel="nofollow" href="https://github.com/arendsee" target="_blank">arendsee</a> – <a rel="nofollow" href="https://github.com/ashenkin" target="_blank">ashenkin</a> – <a rel="nofollow" href="https://github.com/ashiklom" target="_blank">ashiklom</a> – <a rel="nofollow" href="https://github.com/bomeara" target="_blank">bomeara</a> – <a rel="nofollow" href="https://github.com/bw4sz" target="_blank">bw4sz</a> – <a rel="nofollow" href="https://github.com/cboettig" target="_blank">cboettig</a> – <a rel="nofollow" href="https://github.com/cdeterman" target="_blank">cdeterman</a> – <a rel="nofollow" href="https://github.com/ChrKoenig" target="_blank">ChrKoenig</a> – <a rel="nofollow" href="https://github.com/chuckrp" target="_blank">chuckrp</a> – <a rel="nofollow" href="https://github.com/clarson2191" target="_blank">clarson2191</a> – <a rel="nofollow" href="https://github.com/claudenozeres" target="_blank">claudenozeres</a> – <a rel="nofollow" href="https://github.com/cmzambranat" target="_blank">cmzambranat</a> – <a rel="nofollow" href="https://github.com/daattali" target="_blank">daattali</a> – <a rel="nofollow" href="https://github.com/DanielGMead" target="_blank">DanielGMead</a> – <a rel="nofollow" href="https://github.com/davharris" target="_blank">davharris</a> – <a rel="nofollow" href="https://github.com/davidvilanova" target="_blank">davidvilanova</a> – <a rel="nofollow" href="https://github.com/diogoprov" target="_blank">diogoprov</a> – <a rel="nofollow" href="https://github.com/dlebauer" target="_blank">dlebauer</a> – <a rel="nofollow" href="https://github.com/dlenz1" target="_blank">dlenz1</a> – <a rel="nofollow" href="https://github.com/dschlaep" target="_blank">dschlaep</a> – <a rel="nofollow" href="https://github.com/EDiLD" target="_blank">EDiLD</a> – <a rel="nofollow" href="https://github.com/emhart" target="_blank">emhart</a> – <a rel="nofollow" href="https://github.com/fdschneider" target="_blank">fdschneider</a> – <a rel="nofollow" href="https://github.com/fgabriel1891" target="_blank">fgabriel1891</a> – <a rel="nofollow" href="https://github.com/fmichonneau" target="_blank">fmichonneau</a> – <a rel="nofollow" href="https://github.com/gedankenstuecke" target="_blank">gedankenstuecke</a> – <a rel="nofollow" href="https://github.com/gimoya" target="_blank">gimoya</a> – <a rel="nofollow" href="https://github.com/GISKid" target="_blank">GISKid</a> – <a rel="nofollow" href="https://github.com/git-og" target="_blank">git-og</a> – <a rel="nofollow" href="https://github.com/glaroc" target="_blank">glaroc</a> – <a rel="nofollow" href="https://github.com/gustavobio" target="_blank">gustavobio</a> – <a rel="nofollow" href="https://github.com/ibartomeus" target="_blank">ibartomeus</a> – <a rel="nofollow" href="https://github.com/jangorecki" target="_blank">jangorecki</a> – <a rel="nofollow" href="https://github.com/jarioksa" target="_blank">jarioksa</a> – <a rel="nofollow" href="https://github.com/jebyrnes" target="_blank">jebyrnes</a> – <a rel="nofollow" href="https://github.com/johnbaums" target="_blank">johnbaums</a> – <a rel="nofollow" href="https://github.com/jonmcalder" target="_blank">jonmcalder</a> – <a rel="nofollow" href="https://github.com/JoStaerk" target="_blank">JoStaerk</a> – <a rel="nofollow" href="https://github.com/jsgosnell" target="_blank">jsgosnell</a> – <a rel="nofollow" href="https://github.com/kamapu" target="_blank">kamapu</a> – <a rel="nofollow" href="https://github.com/karthik" target="_blank">karthik</a> – <a rel="nofollow" href="https://github.com/KevCaz" target="_blank">KevCaz</a> – <a rel="nofollow" href="https://github.com/kgturner" target="_blank">kgturner</a> – <a rel="nofollow" href="https://github.com/kmeverson" target="_blank">kmeverson</a> – <a rel="nofollow" href="https://github.com/Koalha" target="_blank">Koalha</a> – <a rel="nofollow" href="https://github.com/ljvillanueva" target="_blank">ljvillanueva</a> – <a rel="nofollow" href="https://github.com/Markus2015" target="_blank">Markus2015</a> – <a rel="nofollow" href="https://github.com/mcsiple" target="_blank">mcsiple</a> – <a rel="nofollow" href="https://github.com/MikkoVihtakari" target="_blank">MikkoVihtakari</a> – <a rel="nofollow" href="https://github.com/millerjef" target="_blank">millerjef</a> – <a rel="nofollow" href="https://github.com/miriamgrace" target="_blank">miriamgrace</a> – <a rel="nofollow" href="https://github.com/mpnelsen" target="_blank">mpnelsen</a> – <a rel="nofollow" href="https://github.com/MUSEZOOLVERT" target="_blank">MUSEZOOLVERT</a> – <a rel="nofollow" href="https://github.com/nate-d-olson" target="_blank">nate-d-olson</a> – <a rel="nofollow" href="https://github.com/nmatzke" target="_blank">nmatzke</a> – <a rel="nofollow" href="https://github.com/npch" target="_blank">npch</a> – <a rel="nofollow" href="https://github.com/paternogbc" target="_blank">paternogbc</a> – <a rel="nofollow" href="https://github.com/philippi" target="_blank">philippi</a> – <a rel="nofollow" href="https://github.com/pmarchand1" target="_blank">pmarchand1</a> – <a rel="nofollow" href="https://github.com/pssguy" target="_blank">pssguy</a> – <a rel="nofollow" href="https://github.com/RodgerG" target="_blank">RodgerG</a> – <a rel="nofollow" href="https://github.com/rossmounce" target="_blank">rossmounce</a> – <a rel="nofollow" href="https://github.com/sariya" target="_blank">sariya</a> – <a rel="nofollow" href="https://github.com/scelmendorf" target="_blank">scelmendorf</a> – <a rel="nofollow" href="https://github.com/sckott" target="_blank">sckott</a> – <a rel="nofollow" href="https://github.com/SimonGoring" target="_blank">SimonGoring</a> – <a rel="nofollow" href="https://github.com/snsheth" target="_blank">snsheth</a> – <a rel="nofollow" href="https://github.com/snubian" target="_blank">snubian</a> – <a rel="nofollow" href="https://github.com/Squiercg" target="_blank">Squiercg</a> – <a rel="nofollow" href="https://github.com/tdjames1" target="_blank">tdjames1</a> – <a rel="nofollow" href="https://github.com/tmkurobe" target="_blank">tmkurobe</a> – <a rel="nofollow" href="https://github.com/tpaulson1" target="_blank">tpaulson1</a> – <a rel="nofollow" href="https://github.com/tpoisot" target="_blank">tpoisot</a> – <a rel="nofollow" href="https://github.com/vijaybarve" target="_blank">vijaybarve</a> – <a rel="nofollow" href="https://github.com/wcornwell" target="_blank">wcornwell</a> – <a rel="nofollow" href="https://github.com/willpearse" target="_blank">willpearse</a> – <a rel="nofollow" href="https://github.com/wpetry" target="_blank">wpetry</a> – <a rel="nofollow" href="https://github.com/zachary-foster" target="_blank">zachary-foster</a></p>
<p></p>
<h2>taxize usage</h2>
<p>Eduard Szöcs and I wrote a paper describing <code>taxize</code> back in 2013, published in F1000Research.</p>
<blockquote>
<p>Scott Chamberlain and Eduard Szöcs (2013). taxize – taxonomic search and retrieval in R. F1000Research 2:191. <a rel="nofollow" href="https://doi.org/10.12688/f1000research.2-191.v1" target="_blank">https://doi.org/10.12688/f1000research.2-191.v1</a></p>
</blockquote>
<p>The paper has probably made <code>taxize</code> users more likely to cite the package, though we have no direct proof of that.</p>
<p>The paper above and/or the package have been cited <strong>69</strong> times over the past 7 years.</p>
<p>The way <code>taxize</code> is used in research is often in “cleaning” taxonomic names in one way or another. In addition, many users use <code>taxize</code> to get taxonomic names for certain groups of interest.</p>
<p>One example comes from the paper</p>
<blockquote>
<p>Weber, M. G., Porturas, L. D., &amp; Taylor, S. A. (2016). Foliar nectar enhances plant–mite mutualisms: the effect of leaf sugar on the control of powdery mildew by domatia-inhabiting mites. Annals of Botany, 118(3), 459–466. doi:10.1093/aob/mcw118</p>
</blockquote>
<div>
<a rel="nofollow" href="https://doi.org/10.1093/aob/mcw118" target="_blank"><img title="taxize methods example" src="https://i2.wp.com/ropensci.org/img/blog-images/2018-05-23-taxize-seven-years/taxize-methods.png?w=456&ssl=1" data-recalc-dims="1"></a>
</div>
<p></p>
<h2>Features coming down the road</h2>
<ul>
<li>Integration with <a rel="nofollow" href="https://github.com/ropensci/taxa" target="_blank">taxa</a> package (maintained by one of our rOpenSci fellows <a rel="nofollow" href="https://github.com/zachary-foster" target="_blank">Zachary Foster</a>) in all <code>get_*()</code> functions. This will make the outputs of all <code>get_*()</code> more consistent and easier to integrate into your downstream workflows.</li>
<li>not taxize per se, but <a rel="nofollow" href="https://github.com/ropensci/taxizedb" target="_blank">taxizedb</a> is starting to really take shape due to help from <a rel="nofollow" href="https://github.com/arendsee" target="_blank">Zebulun Arendsee</a>. <code>taxizedb</code> will make taxonomic name work much faster for large datasets. It’s worth checking out.</li>
</ul>
<p></p>
<h2>Thanks!</h2>
<p>A hug thanks goes to all <code>taxize</code> users and contributors. It’s awesome to see how useful <code>taxize</code> has been through the years, and we look forward to making it even better moving forward.</p>
	<p>
<div>
<div>To <strong>leave a comment</strong> for the author, please follow the link and comment on their blog: <strong><a href="https://ropensci.org/technotes/2018/05/23/taxize-seven-years/"> rOpenSci - open tools for open science</a></strong>.</div>
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