---
title: "Taxonomic filtering"
author: "Callum Waite & Shandiya Balasubramaniam"
date: '2023-10-13'
output:
  rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Taxonomic filtering}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Taxonomic complexity can confound the process of searching, filtering, and downloading records using `galah`, but there are a few ways to ensure records are not missed.


```r
library(galah)
library(dplyr)
```




```r
galah_config(email = "your_email_here", verbose = FALSE)
```

### search_taxa()

`search_taxa()` enables users to look up taxonomic names before downloading data, which allows for disambiguating homonyms and checking that the search term matches the taxon name in the ALA . `search_taxa()` returns the scientific name, authorship, rank, and full classification for the taxon matched to the provided search term.


```r
search_taxa("Petroica boodang") |> gt::gt()
```

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<td headers="scientific_name" class="gt_row gt_left">Petroica (Petroica) boodang</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Lesson, 1838)</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/a3e5376b-f9e6-4bdf-adae-1e7add9f5c29</td>
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<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Passeriformes</td>
<td headers="family" class="gt_row gt_left">Petroicidae</td>
<td headers="genus" class="gt_row gt_left">Petroica</td>
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```r
# Muscicapa chrysoptera is a synonym for the Flame Robin, Petroica phoenicea
# Guniibuu is the Yuwaalaraay Indigenous name for the Red-Capped Robin, Petroica goodenovii
search_taxa("Muscicapa chrysoptera", "Guniibuu") |> gt::gt()
```

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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="family">family</th>
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="species">species</th>
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    </tr>
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    <tr><td headers="search_term" class="gt_row gt_left">Muscicapa chrysoptera</td>
<td headers="scientific_name" class="gt_row gt_left">Petroica (Littlera) phoenicea</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">Gould, 1837</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/fe74e658-4848-437a-a23d-f1001a198552</td>
<td headers="rank" class="gt_row gt_left">species</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Passeriformes</td>
<td headers="family" class="gt_row gt_left">Petroicidae</td>
<td headers="genus" class="gt_row gt_left">Petroica</td>
<td headers="species" class="gt_row gt_left">Petroica phoenicea</td>
<td headers="vernacular_name" class="gt_row gt_left">Flame Robin</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->
<br>
Where homonyms exist, `search_taxa()` will prompt users to clarify the search term by providing one or more taxonomic ranks in a `tibble`. This example differentiates among the genus Morganella in three kingdoms:


```r
search_taxa("Morganella") |> gt::gt()
```

```
## Warning: Search returned multiple taxa due to a homonym issue.
## ℹ Please provide another rank in your search to clarify taxa.
## ℹ Use a `tibble` to clarify taxa, see `?search_taxa`.
## ✖ Homonym issue with "Morganella".
```

<!--html_preserve--><div id="watnbtggoz" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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    </tr>
  </thead>
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    <tr><td headers="search_term" class="gt_row gt_left">Morganella</td>
<td headers="issues" class="gt_row gt_left">homonym</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->


```r
search_taxa(tibble(kingdom = "Fungi", genus = "Morganella")) |> gt::gt()
```

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    <tr class="gt_col_headings">
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="search_term">search_term</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="scientific_name">scientific_name</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="scientific_name_authorship">scientific_name_authorship</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="taxon_concept_id">taxon_concept_id</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="rank">rank</th>
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="order">order</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="family">family</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="genus">genus</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="issues">issues</th>
    </tr>
  </thead>
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    <tr><td headers="search_term" class="gt_row gt_left">Fungi_Morganella</td>
<td headers="scientific_name" class="gt_row gt_left">Morganella</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">Zeller</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://id.biodiversity.org.au/node/fungi/60091999</td>
<td headers="rank" class="gt_row gt_left">genus</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Fungi</td>
<td headers="phylum" class="gt_row gt_left">Basidiomycota</td>
<td headers="class" class="gt_row gt_left">Agaricomycetes</td>
<td headers="order" class="gt_row gt_left">Agaricales</td>
<td headers="family" class="gt_row gt_left">Agaricaceae</td>
<td headers="genus" class="gt_row gt_left">Morganella</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->
<br>

### identify()

`identify()` is similar to `search_taxa()`, except that it can be used within a piped workflow to retrieve counts, species, or records e.g.


```r
galah_call() |>
  identify("Petroica boodang") |>
  count() |>
  collect()
```

```
## # A tibble: 1 × 1
##    count
##    <int>
## 1 119417
```


```r
galah_call(type = "species") |>
  identify("Muscicapa chrysoptera", "Guniibuu") |>
  collect() |> 
  gt::gt()
```

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  padding-bottom: 8px;
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  padding-right: 5px;
}

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  padding-bottom: 8px;
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  <thead>
    
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="species_name">species_name</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="scientific_name_authorship">scientific_name_authorship</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="taxon_rank">taxon_rank</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="kingdom">kingdom</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="phylum">phylum</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="class">class</th>
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="family">family</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="genus">genus</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacular_name">vernacular_name</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/10dbd908-00f3-4ec2-9a9c-a2fd4782eaf1</td>
<td headers="species_name" class="gt_row gt_left">Petroica (Petroica) goodenovii</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Vigors &amp; Horsfield, 1827)</td>
<td headers="taxon_rank" class="gt_row gt_left">species</td>
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<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Passeriformes</td>
<td headers="family" class="gt_row gt_left">Petroicidae</td>
<td headers="genus" class="gt_row gt_left">Petroica</td>
<td headers="vernacular_name" class="gt_row gt_left">Red-capped Robin</td></tr>
    <tr><td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/fe74e658-4848-437a-a23d-f1001a198552</td>
<td headers="species_name" class="gt_row gt_left">Petroica (Littlera) phoenicea</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">Gould, 1837</td>
<td headers="taxon_rank" class="gt_row gt_left">species</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Passeriformes</td>
<td headers="family" class="gt_row gt_left">Petroicidae</td>
<td headers="genus" class="gt_row gt_left">Petroica</td>
<td headers="vernacular_name" class="gt_row gt_left">Flame Robin</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->


```r
galah_call() |>
  identify(tibble(kingdom = "Fungi", genus = "Morganella")) |>
  collect() |>
  head() |> 
  gt::gt()
```

<!--html_preserve--><div id="dcqwoxuqqh" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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  <thead>
    
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      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="eventDate">eventDate</th>
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  </thead>
  <tbody class="gt_table_body">
    <tr><td headers="recordID" class="gt_row gt_left">001ec30d-3376-4f63-ba32-b48bc3dd137d</td>
<td headers="scientificName" class="gt_row gt_left">Morganella purpurascens</td>
<td headers="taxonConceptID" class="gt_row gt_left">https://id.biodiversity.org.au/node/fungi/60092001</td>
<td headers="decimalLatitude" class="gt_row gt_right">-33.66218</td>
<td headers="decimalLongitude" class="gt_row gt_right">150.2708</td>
<td headers="eventDate" class="gt_row gt_right">2021-04-10</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
<td headers="dataResourceName" class="gt_row gt_left">NSW BioNet Atlas</td></tr>
    <tr><td headers="recordID" class="gt_row gt_left">02ba39cd-8077-4868-a0ff-e50765089788</td>
<td headers="scientificName" class="gt_row gt_left">Morganella compacta</td>
<td headers="taxonConceptID" class="gt_row gt_left">NZOR-6-128055</td>
<td headers="decimalLatitude" class="gt_row gt_right">-41.28082</td>
<td headers="decimalLongitude" class="gt_row gt_right">174.7943</td>
<td headers="eventDate" class="gt_row gt_right">NA</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
<td headers="dataResourceName" class="gt_row gt_left">New Zealand Virtual Herbarium</td></tr>
    <tr><td headers="recordID" class="gt_row gt_left">0422009d-c1f0-4e2e-8d29-e88df6de2049</td>
<td headers="scientificName" class="gt_row gt_left">Morganella compacta</td>
<td headers="taxonConceptID" class="gt_row gt_left">NZOR-6-128055</td>
<td headers="decimalLatitude" class="gt_row gt_right">-36.44838</td>
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<td headers="eventDate" class="gt_row gt_right">NA</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
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    <tr><td headers="recordID" class="gt_row gt_left">04aeeb8d-0538-477c-aff1-29574eafa349</td>
<td headers="scientificName" class="gt_row gt_left">Morganella compacta</td>
<td headers="taxonConceptID" class="gt_row gt_left">NZOR-6-128055</td>
<td headers="decimalLatitude" class="gt_row gt_right">-36.84225</td>
<td headers="decimalLongitude" class="gt_row gt_right">174.4695</td>
<td headers="eventDate" class="gt_row gt_right">1993-06-19</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
<td headers="dataResourceName" class="gt_row gt_left">New Zealand Virtual Herbarium</td></tr>
    <tr><td headers="recordID" class="gt_row gt_left">092b6f3e-ef27-4cbf-bb28-b172c1b200c5</td>
<td headers="scientificName" class="gt_row gt_left">Morganella purpurascens</td>
<td headers="taxonConceptID" class="gt_row gt_left">https://id.biodiversity.org.au/node/fungi/60092001</td>
<td headers="decimalLatitude" class="gt_row gt_right">-26.77940</td>
<td headers="decimalLongitude" class="gt_row gt_right">152.8803</td>
<td headers="eventDate" class="gt_row gt_right">2009-02-19</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
<td headers="dataResourceName" class="gt_row gt_left">National Herbarium of Victoria (MEL) AVH data</td></tr>
    <tr><td headers="recordID" class="gt_row gt_left">0be95d59-29a4-4475-8586-a497cac607f7</td>
<td headers="scientificName" class="gt_row gt_left">Morganella compacta</td>
<td headers="taxonConceptID" class="gt_row gt_left">NZOR-6-128055</td>
<td headers="decimalLatitude" class="gt_row gt_right">-43.15002</td>
<td headers="decimalLongitude" class="gt_row gt_right">171.7305</td>
<td headers="eventDate" class="gt_row gt_right">NA</td>
<td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td>
<td headers="dataResourceName" class="gt_row gt_left">New Zealand Virtual Herbarium</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->


### filter()

`filter()` subsets records by searching for exact matches to an expression, and 
may also be used for taxonomic filtering e.g.


```r
galah_call() |>
  filter(species == "Petroica boodang") |>
  count() |>
  collect()
```

```
## # A tibble: 1 × 1
##    count
##    <int>
## 1 119417
```

Alternatively, we could use `filter()` after first checking taxonomy with 
`search_taxa()`, in place of `identify()`:


```r
robins <- search_taxa("Muscicapa chrysoptera", "Guniibuu") 

galah_call() |>
  filter(taxonConceptID == robins$taxon_concept_id) |>
  count() |>
  collect()
```

```
## # A tibble: 1 × 1
##   count
##   <int>
## 1 81570
```

It is also possible to specify several species at once using `filter()`:


```r
aus_petroica <- c("Petroica boodang", "Petroica goodenovii", 
                  "Petroica phoenicea", "Petroica rosea",
                  "Petroica rodinogaster", "Petroica multicolor")

galah_call() |>
  filter(species %in% aus_petroica) |>
  group_by(species, vernacularName) |>
  count() |> 
  collect() |>
  gt::gt()
```

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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacularName">vernacularName</th>
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<td headers="vernacularName" class="gt_row gt_left">Eastern Scarlet Robin</td>
<td headers="count" class="gt_row gt_right">3496</td></tr>
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<td headers="vernacularName" class="gt_row gt_left">South-western Scarlet Robin</td>
<td headers="count" class="gt_row gt_right">160</td></tr>
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<td headers="vernacularName" class="gt_row gt_left">Tasmanian Scarlet Robin</td>
<td headers="count" class="gt_row gt_right">26</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica goodenovii</td>
<td headers="vernacularName" class="gt_row gt_left">Red-capped Robin</td>
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    <tr><td headers="species" class="gt_row gt_left">Petroica phoenicea</td>
<td headers="vernacularName" class="gt_row gt_left">Flame Robin</td>
<td headers="count" class="gt_row gt_right">81570</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica rosea</td>
<td headers="vernacularName" class="gt_row gt_left">Rose Robin</td>
<td headers="count" class="gt_row gt_right">52414</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica rodinogaster</td>
<td headers="vernacularName" class="gt_row gt_left">Pink Robin</td>
<td headers="count" class="gt_row gt_right">13417</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica rodinogaster</td>
<td headers="vernacularName" class="gt_row gt_left">Mainland Pink Robin</td>
<td headers="count" class="gt_row gt_right">60</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica rodinogaster</td>
<td headers="vernacularName" class="gt_row gt_left">Tasmanian Pink Robin</td>
<td headers="count" class="gt_row gt_right">14</td></tr>
    <tr><td headers="species" class="gt_row gt_left">Petroica multicolor</td>
<td headers="vernacularName" class="gt_row gt_left">Pacific Robin</td>
<td headers="count" class="gt_row gt_right">6699</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->

This can be useful in searching for paraphyletic or polyphyletic groups, which 
cannot be done using `identify()`. For example, to get counts of non-chordates:


```r
galah_call() |>
  filter(kingdom == "Animalia", phylum != "Chordata") |>
  group_by(phylum) |>
  count() |>
  collect() |>
  head() |> 
  gt::gt()
```

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}

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  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: bottom;
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  padding-bottom: 6px;
  padding-left: 5px;
  padding-right: 5px;
  overflow-x: hidden;
}

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#lgbkmpqmhm .gt_spanner_row {
  border-bottom-style: hidden;
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#lgbkmpqmhm .gt_group_heading {
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  border-top-width: 2px;
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  border-bottom-style: solid;
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  border-bottom-color: #D3D3D3;
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#lgbkmpqmhm .gt_from_md > :first-child {
  margin-top: 0;
}

#lgbkmpqmhm .gt_from_md > :last-child {
  margin-bottom: 0;
}

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  padding-top: 8px;
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}

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  padding-right: 5px;
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}

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}

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  padding-right: 5px;
}

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  padding-left: 5px;
  padding-right: 5px;
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}

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}

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}

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  text-indent: 20px;
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#lgbkmpqmhm .gt_indent_5 {
  text-indent: 25px;
}
</style>
<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
  <thead>
    
    <tr class="gt_col_headings">
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="phylum">phylum</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="count">count</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td headers="phylum" class="gt_row gt_left">Arthropoda</td>
<td headers="count" class="gt_row gt_right">8567585</td></tr>
    <tr><td headers="phylum" class="gt_row gt_left">Mollusca</td>
<td headers="count" class="gt_row gt_right">1378754</td></tr>
    <tr><td headers="phylum" class="gt_row gt_left">Annelida</td>
<td headers="count" class="gt_row gt_right">316619</td></tr>
    <tr><td headers="phylum" class="gt_row gt_left">Cnidaria</td>
<td headers="count" class="gt_row gt_right">273227</td></tr>
    <tr><td headers="phylum" class="gt_row gt_left">Echinodermata</td>
<td headers="count" class="gt_row gt_right">196016</td></tr>
    <tr><td headers="phylum" class="gt_row gt_left">Porifera</td>
<td headers="count" class="gt_row gt_right">130249</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->

### filter(), identify(), and taxonomic ranks

Deciding between using `filter()` and `identify()` in a query comes down to how 
a record has been classified, and whether or not you have the correct *unique* 
name and classification of the taxa of interest.

The ALA has fields for the primary taxonomic ranks (`kingdom`, `phylum`, `class`, 
`order`, `family`, `genus`, `species`) and some secondary ranks (e.g. `subfamily`, 
`subgenus`), all of which may be used with `galah_filter()` and `galah_identify()`. 
Additionally, there is a field named `scientificName`, which refers to the lowest 
taxonomic rank to which a record has been identified e.g.


```r
galah_call() |>
  identify(tibble(genus = "Pitta")) |>
  group_by(scientificName, taxonRank) |>
  count() |>
  collect() |>
  filter(!is.na(scientificName)) |>
  gt::gt()
```

<!--html_preserve--><div id="aydpywfhin" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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  <thead>
    
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="taxonRank">taxonRank</th>
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    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) versicolor</td>
<td headers="taxonRank" class="gt_row gt_left">species</td>
<td headers="count" class="gt_row gt_right">26085</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) iris</td>
<td headers="taxonRank" class="gt_row gt_left">species</td>
<td headers="count" class="gt_row gt_right">5722</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Erythropitta)</td>
<td headers="taxonRank" class="gt_row gt_left">subgenus</td>
<td headers="count" class="gt_row gt_right">728</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) versicolor versicolor</td>
<td headers="taxonRank" class="gt_row gt_left">subspecies</td>
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    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Erythropitta) erythrogaster</td>
<td headers="taxonRank" class="gt_row gt_left">species</td>
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    <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) iris iris</td>
<td headers="taxonRank" class="gt_row gt_left">subspecies</td>
<td headers="count" class="gt_row gt_right">76</td></tr>
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<td headers="taxonRank" class="gt_row gt_left">genus</td>
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<td headers="taxonRank" class="gt_row gt_left">subspecies</td>
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<td headers="taxonRank" class="gt_row gt_left">subspecies</td>
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<td headers="taxonRank" class="gt_row gt_left">subspecies</td>
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</div><!--/html_preserve-->

If, for instance, you have the correct species or subspecies name, then searching 
for matches against the `species` and `subspecies` fields, respectively, will 
provide more precise results. This is because the field `scientificName` may 
include subgenera. If you've used `search_taxa()` to get the ALA-matched name of 
a taxon and only want records identified to a particular level of classification, 
searching for matches against `scientificName` is recommended.

Paraphyletic or polyphyletic groups may contain taxa identified to different 
taxonomic levels. In this case, it is simpler to use `search_taxa()` and 
`identify()` rather than `filter()`. In the example below, `search_taxa()` 
matches terms to one genus, three species, and two subspecies. This can then be 
used in a piped workflow with `identify()`.


```r
tas_endemic <- c("Sarcophilus", # Tasmanian Devil
                 "Bettongia gaimardi", # Tasmanian Bettong
                 "Melanodryas vittata", # Dusky Robin
                 "Platycercus caledonicus",# Green Rosella
                 "Aquila audax fleayi", # Tasmanian Wedge-Tailed Eagle
                 "Tyto novaehollandiae castanops") # Tasmanian Masked Owl

search_taxa(tas_endemic) |> gt::gt()
```

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<td headers="scientific_name" class="gt_row gt_left">Sarcophilus</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">Cuvier, 1837</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/06455b77-7d50-4ec7-9122-8ab48cfb0c1c</td>
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<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Mammalia</td>
<td headers="order" class="gt_row gt_left">Dasyuromorphia</td>
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<td headers="genus" class="gt_row gt_left">Sarcophilus</td>
<td headers="species" class="gt_row gt_left">NA</td>
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<td headers="scientific_name" class="gt_row gt_left">Bettongia gaimardi</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Desmarest, 1822)</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/8f7da937-6338-4c39-8b11-4f83807afe11</td>
<td headers="rank" class="gt_row gt_left">species</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Mammalia</td>
<td headers="order" class="gt_row gt_left">Diprotodontia</td>
<td headers="family" class="gt_row gt_left">Potoroidae</td>
<td headers="genus" class="gt_row gt_left">Bettongia</td>
<td headers="species" class="gt_row gt_left">Bettongia gaimardi</td>
<td headers="vernacular_name" class="gt_row gt_left">Tasmanian Bettong</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
    <tr><td headers="search_term" class="gt_row gt_left">Melanodryas vittata</td>
<td headers="scientific_name" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Quoy &amp; Gaimard, 1830)</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/0f04889f-5489-4369-a545-8a041fba9f6d</td>
<td headers="rank" class="gt_row gt_left">species</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Passeriformes</td>
<td headers="family" class="gt_row gt_left">Petroicidae</td>
<td headers="genus" class="gt_row gt_left">Melanodryas</td>
<td headers="species" class="gt_row gt_left">Melanodryas vittata</td>
<td headers="vernacular_name" class="gt_row gt_left">Dusky Robin</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
    <tr><td headers="search_term" class="gt_row gt_left">Platycercus caledonicus</td>
<td headers="scientific_name" class="gt_row gt_left">Platycercus (Platycercus) caledonicus</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Gmelin, 1788)</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/c6e478fe-f199-463f-8576-a77108fd73e2</td>
<td headers="rank" class="gt_row gt_left">species</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Psittaciformes</td>
<td headers="family" class="gt_row gt_left">Psittacidae</td>
<td headers="genus" class="gt_row gt_left">Platycercus</td>
<td headers="species" class="gt_row gt_left">Platycercus caledonicus</td>
<td headers="vernacular_name" class="gt_row gt_left">Green Rosella</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
    <tr><td headers="search_term" class="gt_row gt_left">Aquila audax fleayi</td>
<td headers="scientific_name" class="gt_row gt_left">Aquila (Uroaetus) audax fleayi</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">Condon &amp; Amadon, 1954</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/ac93f7f0-0686-4589-801a-5832378cb7c1</td>
<td headers="rank" class="gt_row gt_left">subspecies</td>
<td headers="match_type" class="gt_row gt_left">exactMatch</td>
<td headers="kingdom" class="gt_row gt_left">Animalia</td>
<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Accipitriformes</td>
<td headers="family" class="gt_row gt_left">Accipitridae</td>
<td headers="genus" class="gt_row gt_left">Aquila</td>
<td headers="species" class="gt_row gt_left">Aquila audax</td>
<td headers="vernacular_name" class="gt_row gt_left">Tasmanian Wedge-tailed Eagle</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
    <tr><td headers="search_term" class="gt_row gt_left">Tyto novaehollandiae castanops</td>
<td headers="scientific_name" class="gt_row gt_left">Tyto novaehollandiae castanops</td>
<td headers="scientific_name_authorship" class="gt_row gt_left">(Gould, 1837)</td>
<td headers="taxon_concept_id" class="gt_row gt_left">https://biodiversity.org.au/afd/taxa/2c30d58b-572b-4dab-8644-b222c28eb0ec</td>
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<td headers="phylum" class="gt_row gt_left">Chordata</td>
<td headers="class" class="gt_row gt_left">Aves</td>
<td headers="order" class="gt_row gt_left">Strigiformes</td>
<td headers="family" class="gt_row gt_left">Tytonidae</td>
<td headers="genus" class="gt_row gt_left">Tyto</td>
<td headers="species" class="gt_row gt_left">Tyto novaehollandiae</td>
<td headers="vernacular_name" class="gt_row gt_left">Tasmanian Masked Owl</td>
<td headers="issues" class="gt_row gt_left">noIssue</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->

```r
galah_call() |>
  identify(tas_endemic) |>
  group_by(scientificName) |>
  count() |>
  collect() |>
  arrange(scientificName) |>
  gt::gt()
```

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      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="count">count</th>
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    <tr><td headers="scientificName" class="gt_row gt_left">Aquila (Uroaetus) audax fleayi</td>
<td headers="count" class="gt_row gt_right">4935</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Bettongia gaimardi</td>
<td headers="count" class="gt_row gt_right">1941</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Bettongia gaimardi cuniculus</td>
<td headers="count" class="gt_row gt_right">41</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Bettongia gaimardi gaimardi</td>
<td headers="count" class="gt_row gt_right">9</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata</td>
<td headers="count" class="gt_row gt_right">14131</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata kingi</td>
<td headers="count" class="gt_row gt_right">15</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata vittata</td>
<td headers="count" class="gt_row gt_right">39</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Platycercus (Platycercus) caledonicus</td>
<td headers="count" class="gt_row gt_right">43463</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Platycercus (Platycercus) caledonicus brownii</td>
<td headers="count" class="gt_row gt_right">24</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Platycercus (Platycercus) caledonicus caledonicus</td>
<td headers="count" class="gt_row gt_right">33</td></tr>
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<td headers="count" class="gt_row gt_right">3</td></tr>
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<td headers="count" class="gt_row gt_right">36302</td></tr>
    <tr><td headers="scientificName" class="gt_row gt_left">Tyto novaehollandiae castanops</td>
<td headers="count" class="gt_row gt_right">63</td></tr>
  </tbody>
  
  
</table>
</div><!--/html_preserve-->
