--- 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() ``` <!--html_preserve--><div id="acqmdkvyde" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#acqmdkvyde table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; 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} #acqmdkvyde .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #acqmdkvyde div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="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> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="match_type">match_type</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> <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="species">species</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacular_name">vernacular_name</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="issues">issues</th> </tr> </thead> <tbody class="gt_table_body"> <tr><td headers="search_term" class="gt_row gt_left">Petroica boodang</td> <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> <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 boodang</td> <td headers="vernacular_name" class="gt_row gt_left">Scarlet Robin</td> <td headers="issues" class="gt_row gt_left">noIssue</td></tr> </tbody> </table> </div><!--/html_preserve--> ``` 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() ``` <!--html_preserve--><div id="joyebwyjap" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#joyebwyjap table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; 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} #joyebwyjap .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #joyebwyjap div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="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> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="match_type">match_type</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> <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="species">species</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacular_name">vernacular_name</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="issues">issues</th> </tr> </thead> <tbody class="gt_table_body"> <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="inmqqegmgs" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#inmqqegmgs table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #inmqqegmgs thead, #inmqqegmgs tbody, #inmqqegmgs tfoot, #inmqqegmgs tr, #inmqqegmgs td, #inmqqegmgs th { border-style: none; } #inmqqegmgs p { margin: 0; padding: 0; } #inmqqegmgs .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #inmqqegmgs .gt_caption { padding-top: 4px; padding-bottom: 4px; } #inmqqegmgs .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #inmqqegmgs .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #inmqqegmgs .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #inmqqegmgs .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #inmqqegmgs .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #inmqqegmgs .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #inmqqegmgs .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #inmqqegmgs .gt_column_spanner_outer:first-child { padding-left: 0; } #inmqqegmgs .gt_column_spanner_outer:last-child { padding-right: 0; } #inmqqegmgs .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #inmqqegmgs .gt_spanner_row { border-bottom-style: hidden; } #inmqqegmgs .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #inmqqegmgs .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #inmqqegmgs .gt_from_md > :first-child { margin-top: 0; } #inmqqegmgs .gt_from_md > :last-child { margin-bottom: 0; } #inmqqegmgs .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #inmqqegmgs .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #inmqqegmgs .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #inmqqegmgs .gt_row_group_first td { border-top-width: 2px; } #inmqqegmgs .gt_row_group_first th { border-top-width: 2px; } #inmqqegmgs .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #inmqqegmgs .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #inmqqegmgs .gt_first_summary_row.thick { border-top-width: 2px; } #inmqqegmgs .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #inmqqegmgs .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #inmqqegmgs .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #inmqqegmgs .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #inmqqegmgs .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #inmqqegmgs .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #inmqqegmgs .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #inmqqegmgs .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #inmqqegmgs .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #inmqqegmgs .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #inmqqegmgs .gt_left { text-align: left; } #inmqqegmgs .gt_center { text-align: center; } #inmqqegmgs .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #inmqqegmgs .gt_font_normal { font-weight: normal; } #inmqqegmgs .gt_font_bold { font-weight: bold; } #inmqqegmgs .gt_font_italic { font-style: italic; } #inmqqegmgs .gt_super { font-size: 65%; } #inmqqegmgs .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #inmqqegmgs .gt_asterisk { font-size: 100%; vertical-align: 0; } #inmqqegmgs .gt_indent_1 { text-indent: 5px; } #inmqqegmgs .gt_indent_2 { text-indent: 10px; } #inmqqegmgs .gt_indent_3 { text-indent: 15px; } #inmqqegmgs .gt_indent_4 { text-indent: 20px; } #inmqqegmgs .gt_indent_5 { text-indent: 25px; } #inmqqegmgs .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #inmqqegmgs div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="search_term">search_term</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="issues">issues</th> </tr> </thead> <tbody class="gt_table_body"> <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() ``` <!--html_preserve--><div id="jsjykezbqx" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#jsjykezbqx table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #jsjykezbqx thead, #jsjykezbqx tbody, #jsjykezbqx tfoot, #jsjykezbqx tr, #jsjykezbqx td, #jsjykezbqx th { border-style: none; } #jsjykezbqx p { margin: 0; padding: 0; } #jsjykezbqx .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #jsjykezbqx .gt_caption { padding-top: 4px; padding-bottom: 4px; } #jsjykezbqx .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #jsjykezbqx .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #jsjykezbqx .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #jsjykezbqx .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #jsjykezbqx .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #jsjykezbqx .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #jsjykezbqx .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #jsjykezbqx .gt_column_spanner_outer:first-child { padding-left: 0; } #jsjykezbqx .gt_column_spanner_outer:last-child { padding-right: 0; } #jsjykezbqx .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #jsjykezbqx .gt_spanner_row { border-bottom-style: hidden; } #jsjykezbqx .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #jsjykezbqx .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #jsjykezbqx .gt_from_md > :first-child { margin-top: 0; } #jsjykezbqx .gt_from_md > :last-child { margin-bottom: 0; } #jsjykezbqx .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #jsjykezbqx .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #jsjykezbqx .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #jsjykezbqx .gt_row_group_first td { border-top-width: 2px; } #jsjykezbqx .gt_row_group_first th { border-top-width: 2px; } #jsjykezbqx .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #jsjykezbqx .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #jsjykezbqx .gt_first_summary_row.thick { border-top-width: 2px; } #jsjykezbqx .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #jsjykezbqx .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #jsjykezbqx .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #jsjykezbqx .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #jsjykezbqx .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #jsjykezbqx .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #jsjykezbqx .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #jsjykezbqx .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #jsjykezbqx .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #jsjykezbqx .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #jsjykezbqx .gt_left { text-align: left; } #jsjykezbqx .gt_center { text-align: center; } #jsjykezbqx .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #jsjykezbqx .gt_font_normal { font-weight: normal; } #jsjykezbqx .gt_font_bold { font-weight: bold; } #jsjykezbqx .gt_font_italic { font-style: italic; } #jsjykezbqx .gt_super { font-size: 65%; } #jsjykezbqx .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #jsjykezbqx .gt_asterisk { font-size: 100%; vertical-align: 0; } #jsjykezbqx .gt_indent_1 { text-indent: 5px; } #jsjykezbqx .gt_indent_2 { text-indent: 10px; } #jsjykezbqx .gt_indent_3 { text-indent: 15px; } #jsjykezbqx .gt_indent_4 { text-indent: 20px; } #jsjykezbqx .gt_indent_5 { text-indent: 25px; } #jsjykezbqx .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #jsjykezbqx div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="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> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="match_type">match_type</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> <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> <tbody class="gt_table_body"> <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 132981 ``` ``` r galah_call(type = "species") |> identify("Muscicapa chrysoptera", "Guniibuu") |> collect() |> gt::gt() ``` <!--html_preserve--><div id="zjycmsxubq" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#zjycmsxubq table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #zjycmsxubq thead, #zjycmsxubq tbody, #zjycmsxubq tfoot, #zjycmsxubq tr, #zjycmsxubq td, #zjycmsxubq th { border-style: none; } #zjycmsxubq p { margin: 0; padding: 0; } #zjycmsxubq .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #zjycmsxubq .gt_caption { padding-top: 4px; padding-bottom: 4px; } #zjycmsxubq .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #zjycmsxubq .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #zjycmsxubq .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #zjycmsxubq .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #zjycmsxubq .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #zjycmsxubq .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #zjycmsxubq .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: 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border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #zjycmsxubq .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #zjycmsxubq .gt_from_md > :first-child { margin-top: 0; } #zjycmsxubq .gt_from_md > :last-child { margin-bottom: 0; } #zjycmsxubq .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #zjycmsxubq .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #zjycmsxubq .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #zjycmsxubq .gt_row_group_first td { border-top-width: 2px; } #zjycmsxubq .gt_row_group_first th { border-top-width: 2px; } #zjycmsxubq .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #zjycmsxubq .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #zjycmsxubq .gt_first_summary_row.thick { border-top-width: 2px; } #zjycmsxubq .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #zjycmsxubq .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #zjycmsxubq .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #zjycmsxubq .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #zjycmsxubq .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #zjycmsxubq .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #zjycmsxubq .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #zjycmsxubq .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #zjycmsxubq .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #zjycmsxubq .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #zjycmsxubq .gt_left { text-align: left; } #zjycmsxubq .gt_center { text-align: center; } #zjycmsxubq .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #zjycmsxubq .gt_font_normal { font-weight: normal; } #zjycmsxubq .gt_font_bold { font-weight: bold; } #zjycmsxubq .gt_font_italic { font-style: italic; } #zjycmsxubq .gt_super { font-size: 65%; } #zjycmsxubq .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #zjycmsxubq .gt_asterisk { font-size: 100%; vertical-align: 0; } #zjycmsxubq .gt_indent_1 { text-indent: 5px; } #zjycmsxubq .gt_indent_2 { text-indent: 10px; } #zjycmsxubq .gt_indent_3 { text-indent: 15px; } #zjycmsxubq .gt_indent_4 { text-indent: 20px; } #zjycmsxubq .gt_indent_5 { text-indent: 25px; } #zjycmsxubq .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #zjycmsxubq div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="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="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> <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="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 & Horsfield, 1827)</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">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() ``` ``` ## Retrying in 1 seconds. ``` <!--html_preserve--><div id="czodxzmlln" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#czodxzmlln table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #czodxzmlln thead, #czodxzmlln tbody, #czodxzmlln tfoot, #czodxzmlln tr, #czodxzmlln td, #czodxzmlln th { border-style: none; } #czodxzmlln p { margin: 0; padding: 0; } #czodxzmlln .gt_table { display: table; 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.katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #czodxzmlln div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="recordID">recordID</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="scientificName">scientificName</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="taxonConceptID">taxonConceptID</th> <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="decimalLatitude">decimalLatitude</th> <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="decimalLongitude">decimalLongitude</th> <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="eventDate">eventDate</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="occurrenceStatus">occurrenceStatus</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="dataResourceName">dataResourceName</th> </tr> </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">005ef5cf-aae1-411c-8476-8ac01dc80e9b</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">-36.82343</td> <td headers="decimalLongitude" class="gt_row gt_right">175.0731</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 Fungal and Plant Disease Collection</td></tr> <tr><td headers="recordID" class="gt_row gt_left">0084789b-e04d-4742-95b5-2e3761d9fd9c</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">-38.03175</td> <td headers="decimalLongitude" class="gt_row gt_right">176.4870</td> <td headers="eventDate" class="gt_row gt_right">2019-05-14</td> <td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td> <td headers="dataResourceName" class="gt_row gt_left">New Zealand Fungal and Plant Disease Collection</td></tr> <tr><td headers="recordID" class="gt_row gt_left">00efd1aa-ebf2-4afb-bd4d-b76af6ff0207</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">-41.09759</td> <td headers="decimalLongitude" class="gt_row gt_right">172.9346</td> <td headers="eventDate" class="gt_row gt_right">2014-05-01</td> <td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td> <td headers="dataResourceName" class="gt_row gt_left">New Zealand Fungal and Plant Disease Collection</td></tr> <tr><td headers="recordID" class="gt_row gt_left">0688cd3a-2954-45f7-9775-f83331d86519</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">-36.92053</td> <td headers="decimalLongitude" class="gt_row gt_right">174.4585</td> <td headers="eventDate" class="gt_row gt_right">1942-07-12</td> <td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td> <td headers="dataResourceName" class="gt_row gt_left">New Zealand Fungal and Plant Disease Collection</td></tr> <tr><td headers="recordID" class="gt_row gt_left">08010c5f-19ee-46e2-b6e0-973a5e79d135</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">-42.24482</td> <td headers="decimalLongitude" class="gt_row gt_right">171.3296</td> <td headers="eventDate" class="gt_row gt_right">1986-04-20</td> <td headers="occurrenceStatus" class="gt_row gt_left">PRESENT</td> <td headers="dataResourceName" class="gt_row gt_left">New Zealand Fungal and Plant Disease Collection</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 132981 ``` 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 88434 ``` 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() ``` <!--html_preserve--><div id="klsdkrynmr" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#klsdkrynmr table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #klsdkrynmr thead, #klsdkrynmr tbody, #klsdkrynmr tfoot, #klsdkrynmr tr, #klsdkrynmr td, #klsdkrynmr th { border-style: none; } #klsdkrynmr p { margin: 0; padding: 0; } #klsdkrynmr .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: 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padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #klsdkrynmr .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #klsdkrynmr .gt_column_spanner_outer:first-child { padding-left: 0; } #klsdkrynmr .gt_column_spanner_outer:last-child { padding-right: 0; } #klsdkrynmr .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #klsdkrynmr .gt_spanner_row { border-bottom-style: hidden; } #klsdkrynmr .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #klsdkrynmr .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #klsdkrynmr .gt_from_md > :first-child { margin-top: 0; } #klsdkrynmr .gt_from_md > :last-child { margin-bottom: 0; } #klsdkrynmr .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #klsdkrynmr .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #klsdkrynmr .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #klsdkrynmr .gt_row_group_first td { border-top-width: 2px; } #klsdkrynmr .gt_row_group_first th { border-top-width: 2px; } #klsdkrynmr .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #klsdkrynmr .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #klsdkrynmr .gt_first_summary_row.thick { border-top-width: 2px; } #klsdkrynmr .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #klsdkrynmr .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #klsdkrynmr .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #klsdkrynmr .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #klsdkrynmr .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #klsdkrynmr .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #klsdkrynmr .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #klsdkrynmr .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #klsdkrynmr .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #klsdkrynmr .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #klsdkrynmr .gt_left { text-align: left; } #klsdkrynmr .gt_center { text-align: center; } #klsdkrynmr .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #klsdkrynmr .gt_font_normal { font-weight: normal; } #klsdkrynmr .gt_font_bold { font-weight: bold; } #klsdkrynmr .gt_font_italic { font-style: italic; } #klsdkrynmr .gt_super { font-size: 65%; } #klsdkrynmr .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #klsdkrynmr .gt_asterisk { font-size: 100%; vertical-align: 0; } #klsdkrynmr .gt_indent_1 { text-indent: 5px; } #klsdkrynmr .gt_indent_2 { text-indent: 10px; } #klsdkrynmr .gt_indent_3 { text-indent: 15px; } #klsdkrynmr .gt_indent_4 { text-indent: 20px; } #klsdkrynmr .gt_indent_5 { text-indent: 25px; } #klsdkrynmr .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #klsdkrynmr div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="species">species</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacularName">vernacularName</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="species" class="gt_row gt_left">Petroica boodang</td> <td headers="vernacularName" class="gt_row gt_left">Scarlet Robin</td> <td headers="count" class="gt_row gt_right">129172</td></tr> <tr><td headers="species" class="gt_row gt_left">Petroica boodang</td> <td headers="vernacularName" class="gt_row gt_left">Eastern Scarlet Robin</td> <td headers="count" class="gt_row gt_right">3593</td></tr> <tr><td headers="species" class="gt_row gt_left">Petroica boodang</td> <td headers="vernacularName" class="gt_row gt_left">South-western Scarlet Robin</td> <td headers="count" class="gt_row gt_right">166</td></tr> <tr><td headers="species" class="gt_row gt_left">Petroica boodang</td> <td headers="vernacularName" class="gt_row gt_left">Tasmanian Scarlet Robin</td> <td headers="count" class="gt_row gt_right">50</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> <td headers="count" class="gt_row gt_right">119914</td></tr> <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">88434</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">60101</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">15640</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">21</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">6705</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() ``` <!--html_preserve--><div id="ykgigelmue" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#ykgigelmue table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #ykgigelmue thead, #ykgigelmue tbody, #ykgigelmue tfoot, #ykgigelmue tr, #ykgigelmue td, #ykgigelmue th { border-style: none; } #ykgigelmue p { margin: 0; padding: 0; } #ykgigelmue .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #ykgigelmue .gt_caption { padding-top: 4px; padding-bottom: 4px; } #ykgigelmue .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #ykgigelmue .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #ykgigelmue .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #ykgigelmue .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ykgigelmue .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #ykgigelmue .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #ykgigelmue .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #ykgigelmue .gt_column_spanner_outer:first-child { padding-left: 0; } #ykgigelmue .gt_column_spanner_outer:last-child { padding-right: 0; } #ykgigelmue .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #ykgigelmue .gt_spanner_row { border-bottom-style: hidden; } #ykgigelmue .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #ykgigelmue .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #ykgigelmue .gt_from_md > :first-child { margin-top: 0; } #ykgigelmue .gt_from_md > :last-child { margin-bottom: 0; } #ykgigelmue .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #ykgigelmue .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #ykgigelmue .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #ykgigelmue .gt_row_group_first td { border-top-width: 2px; } #ykgigelmue .gt_row_group_first th { border-top-width: 2px; } #ykgigelmue .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #ykgigelmue .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #ykgigelmue .gt_first_summary_row.thick { border-top-width: 2px; } #ykgigelmue .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ykgigelmue .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #ykgigelmue .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #ykgigelmue .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #ykgigelmue .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #ykgigelmue .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ykgigelmue .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #ykgigelmue .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #ykgigelmue .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #ykgigelmue .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #ykgigelmue .gt_left { text-align: left; } #ykgigelmue .gt_center { text-align: center; } #ykgigelmue .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #ykgigelmue .gt_font_normal { font-weight: normal; } #ykgigelmue .gt_font_bold { font-weight: bold; } #ykgigelmue .gt_font_italic { font-style: italic; } #ykgigelmue .gt_super { font-size: 65%; } #ykgigelmue .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #ykgigelmue .gt_asterisk { font-size: 100%; vertical-align: 0; } #ykgigelmue .gt_indent_1 { text-indent: 5px; } #ykgigelmue .gt_indent_2 { text-indent: 10px; } #ykgigelmue .gt_indent_3 { text-indent: 15px; } #ykgigelmue .gt_indent_4 { text-indent: 20px; } #ykgigelmue .gt_indent_5 { text-indent: 25px; } #ykgigelmue .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #ykgigelmue div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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">9061922</td></tr> <tr><td headers="phylum" class="gt_row gt_left">Mollusca</td> <td headers="count" class="gt_row gt_right">1498353</td></tr> <tr><td headers="phylum" class="gt_row gt_left">Annelida</td> <td headers="count" class="gt_row gt_right">320916</td></tr> <tr><td headers="phylum" class="gt_row gt_left">Cnidaria</td> <td headers="count" class="gt_row gt_right">283139</td></tr> <tr><td headers="phylum" class="gt_row gt_left">Echinodermata</td> <td headers="count" class="gt_row gt_right">206043</td></tr> <tr><td headers="phylum" class="gt_row gt_left">Porifera</td> <td headers="count" class="gt_row gt_right">132106</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="yireotxtgc" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#yireotxtgc table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #yireotxtgc thead, #yireotxtgc tbody, #yireotxtgc tfoot, #yireotxtgc tr, #yireotxtgc td, #yireotxtgc th { border-style: none; } #yireotxtgc p { margin: 0; padding: 0; } #yireotxtgc .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #yireotxtgc .gt_caption { padding-top: 4px; padding-bottom: 4px; } #yireotxtgc .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #yireotxtgc .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #yireotxtgc .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #yireotxtgc .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #yireotxtgc .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #yireotxtgc .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #yireotxtgc .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #yireotxtgc .gt_column_spanner_outer:first-child { padding-left: 0; } #yireotxtgc .gt_column_spanner_outer:last-child { padding-right: 0; } #yireotxtgc .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #yireotxtgc .gt_spanner_row { border-bottom-style: hidden; } #yireotxtgc .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #yireotxtgc .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #yireotxtgc .gt_from_md > :first-child { margin-top: 0; } #yireotxtgc .gt_from_md > :last-child { margin-bottom: 0; } #yireotxtgc .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #yireotxtgc .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #yireotxtgc .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #yireotxtgc .gt_row_group_first td { border-top-width: 2px; } #yireotxtgc .gt_row_group_first th { border-top-width: 2px; } #yireotxtgc .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #yireotxtgc .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #yireotxtgc .gt_first_summary_row.thick { border-top-width: 2px; } #yireotxtgc .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #yireotxtgc .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #yireotxtgc .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #yireotxtgc .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #yireotxtgc .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #yireotxtgc .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #yireotxtgc .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #yireotxtgc .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #yireotxtgc .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #yireotxtgc .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #yireotxtgc .gt_left { text-align: left; } #yireotxtgc .gt_center { text-align: center; } #yireotxtgc .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #yireotxtgc .gt_font_normal { font-weight: normal; } #yireotxtgc .gt_font_bold { font-weight: bold; } #yireotxtgc .gt_font_italic { font-style: italic; } #yireotxtgc .gt_super { font-size: 65%; } #yireotxtgc .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #yireotxtgc .gt_asterisk { font-size: 100%; vertical-align: 0; } #yireotxtgc .gt_indent_1 { text-indent: 5px; } #yireotxtgc .gt_indent_2 { text-indent: 10px; } #yireotxtgc .gt_indent_3 { text-indent: 15px; } #yireotxtgc .gt_indent_4 { text-indent: 20px; } #yireotxtgc .gt_indent_5 { text-indent: 25px; } #yireotxtgc .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #yireotxtgc div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="scientificName">scientificName</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="taxonRank">taxonRank</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="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">30041</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">6550</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">883</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> <td headers="count" class="gt_row gt_right">311</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Erythropitta) erythrogaster</td> <td headers="taxonRank" class="gt_row gt_left">species</td> <td headers="count" class="gt_row gt_right">181</td></tr> <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">83</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta</td> <td headers="taxonRank" class="gt_row gt_left">genus</td> <td headers="count" class="gt_row gt_right">68</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) versicolor intermedia</td> <td headers="taxonRank" class="gt_row gt_left">subspecies</td> <td headers="count" class="gt_row gt_right">42</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) versicolor simillima</td> <td headers="taxonRank" class="gt_row gt_left">subspecies</td> <td headers="count" class="gt_row gt_right">38</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Pitta) iris johnstoneiana</td> <td headers="taxonRank" class="gt_row gt_left">subspecies</td> <td headers="count" class="gt_row gt_right">27</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Pitta (Erythropitta) erythrogaster digglesi</td> <td headers="taxonRank" class="gt_row gt_left">subspecies</td> <td headers="count" class="gt_row gt_right">6</td></tr> </tbody> </table> </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() ``` <!--html_preserve--><div id="sucnbpnwsl" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#sucnbpnwsl table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #sucnbpnwsl thead, #sucnbpnwsl tbody, #sucnbpnwsl tfoot, #sucnbpnwsl tr, #sucnbpnwsl td, #sucnbpnwsl th { border-style: none; } #sucnbpnwsl p { margin: 0; padding: 0; } 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border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #sucnbpnwsl .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #sucnbpnwsl .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #sucnbpnwsl .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #sucnbpnwsl .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #sucnbpnwsl .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #sucnbpnwsl .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #sucnbpnwsl .gt_left { text-align: left; } #sucnbpnwsl .gt_center { text-align: center; } #sucnbpnwsl .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #sucnbpnwsl .gt_font_normal { font-weight: normal; } #sucnbpnwsl .gt_font_bold { font-weight: bold; } #sucnbpnwsl .gt_font_italic { font-style: italic; } #sucnbpnwsl .gt_super { font-size: 65%; } #sucnbpnwsl .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #sucnbpnwsl .gt_asterisk { font-size: 100%; vertical-align: 0; } #sucnbpnwsl .gt_indent_1 { text-indent: 5px; } #sucnbpnwsl .gt_indent_2 { text-indent: 10px; } #sucnbpnwsl .gt_indent_3 { text-indent: 15px; } #sucnbpnwsl .gt_indent_4 { text-indent: 20px; } #sucnbpnwsl .gt_indent_5 { text-indent: 25px; } #sucnbpnwsl .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #sucnbpnwsl div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="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> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="match_type">match_type</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> <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="species">species</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="vernacular_name">vernacular_name</th> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="issues">issues</th> </tr> </thead> <tbody class="gt_table_body"> <tr><td headers="search_term" class="gt_row gt_left">Sarcophilus</td> <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> <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">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> <td headers="family" class="gt_row gt_left">Dasyuridae</td> <td headers="genus" class="gt_row gt_left">Sarcophilus</td> <td headers="species" class="gt_row gt_left">NA</td> <td headers="vernacular_name" class="gt_row gt_left">NA</td> <td headers="issues" class="gt_row gt_left">noIssue, noIssue, noIssue, noIssue, noIssue, noIssue</td></tr> <tr><td headers="search_term" class="gt_row gt_left">Bettongia gaimardi</td> <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, noIssue, noIssue, noIssue, noIssue, 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 & 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, noIssue, noIssue, noIssue, noIssue, 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, noIssue, noIssue, noIssue, noIssue, 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 & 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, noIssue, noIssue, noIssue, noIssue, 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> <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">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, noIssue, noIssue, noIssue, noIssue, noIssue</td></tr> </tbody> </table> </div><!--/html_preserve--> ``` r galah_call() |> identify(tas_endemic) |> group_by(scientificName) |> count() |> collect() |> arrange(scientificName) |> gt::gt() ``` <!--html_preserve--><div id="ovcdvwclsl" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#ovcdvwclsl table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #ovcdvwclsl thead, #ovcdvwclsl tbody, #ovcdvwclsl tfoot, #ovcdvwclsl tr, #ovcdvwclsl td, #ovcdvwclsl th { border-style: none; } #ovcdvwclsl p { margin: 0; padding: 0; } #ovcdvwclsl .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #ovcdvwclsl .gt_caption { padding-top: 4px; padding-bottom: 4px; } #ovcdvwclsl .gt_title { color: #333333; font-size: 125%; font-weight: initial; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; border-bottom-color: #FFFFFF; border-bottom-width: 0; } #ovcdvwclsl .gt_subtitle { color: #333333; font-size: 85%; font-weight: initial; padding-top: 3px; padding-bottom: 5px; padding-left: 5px; padding-right: 5px; border-top-color: #FFFFFF; border-top-width: 0; } #ovcdvwclsl .gt_heading { background-color: #FFFFFF; text-align: center; border-bottom-color: #FFFFFF; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #ovcdvwclsl .gt_bottom_border { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ovcdvwclsl .gt_col_headings { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; } #ovcdvwclsl .gt_col_heading { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 6px; padding-left: 5px; padding-right: 5px; overflow-x: hidden; } #ovcdvwclsl .gt_column_spanner_outer { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: normal; text-transform: inherit; padding-top: 0; padding-bottom: 0; padding-left: 4px; padding-right: 4px; } #ovcdvwclsl .gt_column_spanner_outer:first-child { padding-left: 0; } #ovcdvwclsl .gt_column_spanner_outer:last-child { padding-right: 0; } #ovcdvwclsl .gt_column_spanner { border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: bottom; padding-top: 5px; padding-bottom: 5px; overflow-x: hidden; display: inline-block; width: 100%; } #ovcdvwclsl .gt_spanner_row { border-bottom-style: hidden; } #ovcdvwclsl .gt_group_heading { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; text-align: left; } #ovcdvwclsl .gt_empty_group_heading { padding: 0.5px; color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; vertical-align: middle; } #ovcdvwclsl .gt_from_md > :first-child { margin-top: 0; } #ovcdvwclsl .gt_from_md > :last-child { margin-bottom: 0; } #ovcdvwclsl .gt_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; margin: 10px; border-top-style: solid; border-top-width: 1px; border-top-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3; vertical-align: middle; overflow-x: hidden; } #ovcdvwclsl .gt_stub { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; } #ovcdvwclsl .gt_stub_row_group { color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #ovcdvwclsl .gt_row_group_first td { border-top-width: 2px; } #ovcdvwclsl .gt_row_group_first th { border-top-width: 2px; } #ovcdvwclsl .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #ovcdvwclsl .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #ovcdvwclsl .gt_first_summary_row.thick { border-top-width: 2px; } #ovcdvwclsl .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ovcdvwclsl .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #ovcdvwclsl .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #ovcdvwclsl .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #ovcdvwclsl .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #ovcdvwclsl .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #ovcdvwclsl .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #ovcdvwclsl .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #ovcdvwclsl .gt_sourcenotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #ovcdvwclsl .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #ovcdvwclsl .gt_left { text-align: left; } #ovcdvwclsl .gt_center { text-align: center; } #ovcdvwclsl .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #ovcdvwclsl .gt_font_normal { font-weight: normal; } #ovcdvwclsl .gt_font_bold { font-weight: bold; } #ovcdvwclsl .gt_font_italic { font-style: italic; } #ovcdvwclsl .gt_super { font-size: 65%; } #ovcdvwclsl .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #ovcdvwclsl .gt_asterisk { font-size: 100%; vertical-align: 0; } #ovcdvwclsl .gt_indent_1 { text-indent: 5px; } #ovcdvwclsl .gt_indent_2 { text-indent: 10px; } #ovcdvwclsl .gt_indent_3 { text-indent: 15px; } #ovcdvwclsl .gt_indent_4 { text-indent: 20px; } #ovcdvwclsl .gt_indent_5 { text-indent: 25px; } #ovcdvwclsl .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #ovcdvwclsl div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="scientificName">scientificName</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="scientificName" class="gt_row gt_left">Aquila (Uroaetus) audax fleayi</td> <td headers="count" class="gt_row gt_right">5035</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Bettongia gaimardi</td> <td headers="count" class="gt_row gt_right">1964</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">15719</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata kingi</td> <td headers="count" class="gt_row gt_right">16</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Melanodryas (Amaurodryas) vittata vittata</td> <td headers="count" class="gt_row gt_right">46</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Platycercus (Platycercus) caledonicus</td> <td headers="count" class="gt_row gt_right">51180</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> <tr><td headers="scientificName" class="gt_row gt_left">Sarcophilus</td> <td headers="count" class="gt_row gt_right">3</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Sarcophilus harrisii</td> <td headers="count" class="gt_row gt_right">36376</td></tr> <tr><td headers="scientificName" class="gt_row gt_left">Tyto novaehollandiae castanops</td> <td headers="count" class="gt_row gt_right">67</td></tr> </tbody> </table> </div><!--/html_preserve-->