Scott Chamberlain

[taxize](https://github.com/ropensci/taxize) was seven years old this
last Saturday!

## What is taxize?

`taxize` 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.

A samping of use cases covered in `taxize` (all of these across many
different data sources):

- Taxonomic identifier from a taxonomic name and vice versa
- Taxonomic name from a vernacular (common) name and vice versa
- Taxonomic hierarchy/classification from identifier or name
- Taxonomic children of an identifier or name
- All taxa downstream to a certain rank from identifier or name
- Taxonomic name synonyms from identifier or name
- Lowest common taxon and rank for an identifier or name
- Resolve taxonomic names, i.e., fix spelling errors

## History

`taxize` was one of our first packages. Our first commit was on
[2011-05-19](https://github.com/ropensci/taxize/commit/667004eac),
uneventfully adding an empty README:

<figure class="center">
<a href="https://github.com/ropensci/taxize/commit/667004eac"><img
src="/img/blog-images/2018-05-23-taxize-seven-years/taxize-first-commit.png"
width="200" alt="screenshot of the first commit" /></a>
</figure>

We've come a long way since May 2011. We've added a lot of new
functionality and many new contributors.

### Commit history

Get git commits for `taxize` using a few tidyverse packages as well as
[git2r](https://github.com/ropensci/git2r), our R package for working
with git repositories:

::: {.highlight}
``` {.chroma tabindex="0"}
library(git2r)library(ggplot2)library(dplyr)repo <- git2r::repository("~/github/ropensci/taxize")res <- commits(repo)
```
:::

A graph of commit history

::: {.highlight}
``` {.chroma tabindex="0"}
dates <- vapply(res, function(z) {    as.character(as.POSIXct(z@author@when@time, origin = "1970-01-01"))}, character(1))df <- 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("%Y/%m")) +    labs(x = 'May 2011 to May 2018', y = 'Cumulative Git Commits')
```
:::

![plot of chunk
unnamed-chunk-3](/img/blog-images/2018-05-23-taxize-seven-years/unnamed-chunk-3-1.png)

### Contributors

A graph of new contributors through time

::: {.highlight}
``` {.chroma tabindex="0"}
date_name <- lapply(res, function(z) {    data_frame(        date = as.character(as.POSIXct(z@author@when@time, origin = "1970-01-01")),        name = z@author@name    )})date_name <- bind_rows(date_name)firstdates <- date_name %>%    group_by(name) %>%    arrange(date) %>%    filter(rank(date, ties.method = "first") == 1) %>%    ungroup() %>%    mutate(count = 1) %>%    arrange(date) %>%    mutate(cumsum = cumsum(count))## plotggplot(firstdates, aes(as.Date(date), cumsum)) +  geom_line(size = 2) +  theme_grey(base_size = 18) +  scale_x_date(labels = scales::date_format("%Y/%m")) +  labs(x = 'May 2011 to May 2018', y = 'Cumulative New Contributors')
```
:::

![plot of chunk
unnamed-chunk-4](/img/blog-images/2018-05-23-taxize-seven-years/unnamed-chunk-4-1.png)

`taxize` contributors, including those that have opened issues (click to
go to their GitHub profile):

[afkoeppel](https://github.com/afkoeppel) -
[ahhurlbert](https://github.com/ahhurlbert) -
[albnd](https://github.com/albnd) -
[Alectoria](https://github.com/Alectoria) -
[andzandz11](https://github.com/andzandz11) -
[antagomir](https://github.com/antagomir) -
[arendsee](https://github.com/arendsee) -
[ashenkin](https://github.com/ashenkin) -
[ashiklom](https://github.com/ashiklom) -
[bomeara](https://github.com/bomeara) -
[bw4sz](https://github.com/bw4sz) -
[cboettig](https://github.com/cboettig) -
[cdeterman](https://github.com/cdeterman) -
[ChrKoenig](https://github.com/ChrKoenig) -
[chuckrp](https://github.com/chuckrp) -
[clarson2191](https://github.com/clarson2191) -
[claudenozeres](https://github.com/claudenozeres) -
[cmzambranat](https://github.com/cmzambranat) -
[daattali](https://github.com/daattali) -
[DanielGMead](https://github.com/DanielGMead) -
[davharris](https://github.com/davharris) -
[davidvilanova](https://github.com/davidvilanova) -
[diogoprov](https://github.com/diogoprov) -
[dlebauer](https://github.com/dlebauer) -
[dlenz1](https://github.com/dlenz1) -
[dschlaep](https://github.com/dschlaep) -
[EDiLD](https://github.com/EDiLD) -
[emhart](https://github.com/emhart) -
[fdschneider](https://github.com/fdschneider) -
[fgabriel1891](https://github.com/fgabriel1891) -
[fmichonneau](https://github.com/fmichonneau) -
[gedankenstuecke](https://github.com/gedankenstuecke) -
[gimoya](https://github.com/gimoya) -
[GISKid](https://github.com/GISKid) -
[git-og](https://github.com/git-og) -
[glaroc](https://github.com/glaroc) -
[gustavobio](https://github.com/gustavobio) -
[ibartomeus](https://github.com/ibartomeus) -
[jangorecki](https://github.com/jangorecki) -
[jarioksa](https://github.com/jarioksa) -
[jebyrnes](https://github.com/jebyrnes) -
[johnbaums](https://github.com/johnbaums) -
[jonmcalder](https://github.com/jonmcalder) -
[JoStaerk](https://github.com/PrincessPi314) -
[jsgosnell](https://github.com/jsgosnell) -
[kamapu](https://github.com/kamapu) -
[karthik](https://github.com/karthik) -
[KevCaz](https://github.com/KevCaz) -
[kgturner](https://github.com/kgturner) -
[kmeverson](https://github.com/kmeverson) -
[Koalha](https://github.com/Koalha) -
[ljvillanueva](https://github.com/ljvillanueva) -
[Markus2015](https://github.com/Markus2015) -
[mcsiple](https://github.com/mcsiple) -
[MikkoVihtakari](https://github.com/MikkoVihtakari) -
[millerjef](https://github.com/millerjef) -
[miriamgrace](https://github.com/miriamgrace) -
[mpnelsen](https://github.com/mpnelsen) -
[MUSEZOOLVERT](https://github.com/MUSEZOOLVERT) -
[nate-d-olson](https://github.com/nate-d-olson) -
[nmatzke](https://github.com/nmatzke) -
[npch](https://github.com/npch) -
[paternogbc](https://github.com/paternogbc) -
[philippi](https://github.com/philippi) -
[pmarchand1](https://github.com/pmarchand1) -
[pssguy](https://github.com/pssguy) -
[RodgerG](https://github.com/RodgerG) -
[rossmounce](https://github.com/rossmounce) -
[sariya](https://github.com/sariya) -
[scelmendorf](https://github.com/scelmendorf) -
[sckott](https://github.com/sckott) -
[SimonGoring](https://github.com/SimonGoring) -
[snsheth](https://github.com/snsheth) -
[snubian](https://github.com/snubian) -
[Squiercg](https://github.com/Squiercg) -
[tdjames1](https://github.com/tdjames1) -
[tmkurobe](https://github.com/tmkurobe) -
[tpaulson1](https://github.com/tpaulson1) -
[tpoisot](https://github.com/tpoisot) -
[vijaybarve](https://github.com/vijaybarve) -
[wcornwell](https://github.com/wcornwell) -
[willpearse](https://github.com/willpearse) -
[wpetry](https://github.com/wpetry) -
[zachary-foster](https://github.com/zachary-foster)

## taxize usage

Eduard Szöcs and I wrote a paper describing `taxize` back in 2013,
published in F1000Research.

> Scott Chamberlain and Eduard Szöcs (2013). taxize - taxonomic search
> and retrieval in R. F1000Research 2:191.
> <https://doi.org/10.12688/f1000research.2-191.v1>

The paper has probably made `taxize` users more likely to cite the
package, though we have no direct proof of that.

The paper above and/or the package have been cited **69** times over the
past 7 years.

The way `taxize` is used in research is often in "cleaning" taxonomic
names in one way or another. In addition, many users use `taxize` to get
taxonomic names for certain groups of interest.

One example comes from the paper

> Weber, M. G., Porturas, L. D., & 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

<figure class="center">
<a href="https://doi.org/10.1093/aob/mcw118"><img
src="/img/blog-images/2018-05-23-taxize-seven-years/taxize-methods.png"
alt="taxize methods example" /></a>
<figcaption><p>taxize methods example</p></figcaption>
</figure>

## Features coming down the road

- Integration with [taxa](https://github.com/ropensci/taxa) package
  (maintained by one of our rOpenSci fellows [Zachary
  Foster](https://github.com/zachary-foster)) in all `get_*()`
  functions. This will make the outputs of all `get_*()` more consistent
  and easier to integrate into your downstream workflows.
- not taxize per se, but
  [taxizedb](https://github.com/ropensci/taxizedb) is starting to really
  take shape due to help from [Zebulun
  Arendsee](https://github.com/arendsee). `taxizedb` will make taxonomic
  name work much faster for large datasets. It's worth checking out.

## Thanks!

A huge thanks goes to all `taxize` users and contributors. It's awesome
to see how useful `taxize` has been through the years, and we look
forward to making it even better moving forward.


taxize was seven years old this last Saturday! What is taxize? taxize 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.

Messaggi di Rogue Scholar

taxize: seven years of taxonomy in R