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occurrence-matrices.Rmd
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occurrence-matrices.Rmd
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---
title: "Publication-ready occurrence matrices with rWCVP"
author: "Matilda Brown"
date: "24/05/2022"
---
<!-- GENERATED BY vignettes/articles/precompile.R -->
The [World Checklist of Vascular Plants (WCVP)](https://wcvp.science.kew.org) provides distribution data for the > 340,000 vascular plant species known to science. This distribution data can be used to build occurrence matrices for checklists of plant species, which `rWCVP` can help with.
As well as `rWCVP`, well use the `tidyverse` packages for data manipulation and plotting and the `gt` package for formatting tables.
```r
library(rWCVP)
library(tidyverse)
library(gt)
```
In this example I use the pipe operator (`%>%`) and `dplyr` syntax - if these are unfamiliar I suggest checking out https://dplyr.tidyverse.org/ and some of the help pages therein.
Now, let's get started!
## Finding an example group
For this example, we don't have a particular area or group of plants that we want to examine, but this gives us a chance to showcase one of other the functions in `rWCVP`!
We want a group of species that is a) not too large and b) distributed across a few WGSRPD Level 3 Areas. Brazil has good potential because it has five Level 3 Areas (a good number for this purpose because the table will fit on a portrait-oriented page). Let's see if there are some nice-sized example genera, using the `wcvp_summary` function:
```r
wcvp_summary(taxon="Myrtaceae", taxon_rank="family", area=get_wgsrpd3_codes("Brazil"),
grouping_var = "genus") %>%
wcvp_summary_gt()
```
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<table class="gt_table">
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<th colspan="6" class="gt_heading gt_title gt_font_normal" style><b> Myrtaceae of Brazil </b></th>
</tr>
<tr>
<th colspan="6" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style>Total number of species: 1127<br>Number of regionally endemic species: 878</th>
</tr>
</thead>
<thead class="gt_col_headings">
<tr>
<th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Genus</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Native</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Endemic</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Introduced</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Extinct</th>
<th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Total</th>
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<tr><td class="gt_row gt_left">Accara</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
<tr><td class="gt_row gt_left">Algrizea</td>
<td class="gt_row gt_right">2</td>
<td class="gt_row gt_right">2</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">2</td></tr>
<tr><td class="gt_row gt_left">Blepharocalyx</td>
<td class="gt_row gt_right">3</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">3</td></tr>
<tr><td class="gt_row gt_left">Calycolpus</td>
<td class="gt_row gt_right">8</td>
<td class="gt_row gt_right">4</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">8</td></tr>
<tr><td class="gt_row gt_left">Calycorectes</td>
<td class="gt_row gt_right">9</td>
<td class="gt_row gt_right">9</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">9</td></tr>
<tr><td class="gt_row gt_left">Campomanesia</td>
<td class="gt_row gt_right">41</td>
<td class="gt_row gt_right">31</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right" style="font-weight: bold;">42</td></tr>
<tr><td class="gt_row gt_left">Curitiba</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
<tr><td class="gt_row gt_left">Eugenia</td>
<td class="gt_row gt_right">430</td>
<td class="gt_row gt_right">338</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">431</td></tr>
<tr><td class="gt_row gt_left">Feijoa</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
<tr><td class="gt_row gt_left">Myrceugenia</td>
<td class="gt_row gt_right">34</td>
<td class="gt_row gt_right">30</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">34</td></tr>
<tr><td class="gt_row gt_left">Myrcia</td>
<td class="gt_row gt_right">440</td>
<td class="gt_row gt_right">351</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right" style="font-weight: bold;">441</td></tr>
<tr><td class="gt_row gt_left">Myrcianthes</td>
<td class="gt_row gt_right">7</td>
<td class="gt_row gt_right">3</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">7</td></tr>
<tr><td class="gt_row gt_left">Myrciaria</td>
<td class="gt_row gt_right">23</td>
<td class="gt_row gt_right">15</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">23</td></tr>
<tr><td class="gt_row gt_left">Myrrhinium</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
<tr><td class="gt_row gt_left">Neomitranthes</td>
<td class="gt_row gt_right">13</td>
<td class="gt_row gt_right">13</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">13</td></tr>
<tr><td class="gt_row gt_left">Pimenta</td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
<tr><td class="gt_row gt_left">Plinia</td>
<td class="gt_row gt_right">41</td>
<td class="gt_row gt_right">35</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">41</td></tr>
<tr><td class="gt_row gt_left">Psidium</td>
<td class="gt_row gt_right">57</td>
<td class="gt_row gt_right">36</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">57</td></tr>
<tr><td class="gt_row gt_left">Siphoneugena</td>
<td class="gt_row gt_right">10</td>
<td class="gt_row gt_right">8</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">10</td></tr>
<tr><td class="gt_row gt_left">Syzygium</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right">1</td>
<td class="gt_row gt_right"></td>
<td class="gt_row gt_right" style="font-weight: bold;">1</td></tr>
</tbody>
</table>
</div><!--/html_preserve-->
*Calycolpus* looks nice and tidy - let's see how the 8 species are distributed across the 5 areas. We can use the same function, but limit our taxon and change our grouping variable to area.
```r
wcvp_summary(taxon="Calycolpus", taxon_rank="genus", area=get_wgsrpd3_codes("Brazil"),
grouping_var = "area_code_l3") %>%
wcvp_summary_gt()
```
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