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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
<link href="index_files/libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.2.269">
<title>ALA</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #767676;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #767676; padding-left: 4px; }
div.sourceCode
{ color: #545454; background-color: #fefefe; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #545454; } /* Normal */
code span.al { color: #7928a1; } /* Alert */
code span.an { color: #696969; } /* Annotation */
code span.at { color: #a55a00; } /* Attribute */
code span.bn { color: #7928a1; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #d91e18; } /* ControlFlow */
code span.ch { color: #008000; } /* Char */
code span.cn { color: #d91e18; } /* Constant */
code span.co { color: #696969; } /* Comment */
code span.cv { color: #696969; font-style: italic; } /* CommentVar */
code span.do { color: #696969; font-style: italic; } /* Documentation */
code span.dt { color: #7928a1; } /* DataType */
code span.dv { color: #7928a1; } /* DecVal */
code span.er { color: #7928a1; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #a55a00; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #696969; } /* Information */
code span.kw { color: #d91e18; } /* Keyword */
code span.op { color: #00769e; } /* Operator */
code span.ot { color: #d91e18; } /* Other */
code span.pp { color: #7928a1; } /* Preprocessor */
code span.sc { color: #00769e; } /* SpecialChar */
code span.ss { color: #008000; } /* SpecialString */
code span.st { color: #008000; } /* String */
code span.va { color: #a55a00; } /* Variable */
code span.vs { color: #008000; } /* VerbatimString */
code span.wa { color: #696969; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css" id="theme">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
.callout.callout-style-default {
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
}
.callout .callout-body-container {
flex-grow: 1;
}
.callout.callout-style-simple .callout-body {
font-size: 1rem;
font-weight: 400;
}
.callout.callout-style-default .callout-body {
font-size: 0.9rem;
font-weight: 400;
}
.callout.callout-captioned.callout-style-simple .callout-body {
margin-top: 0.2em;
}
.callout:not(.callout-captioned) .callout-body {
display: flex;
}
.callout:not(.no-icon).callout-captioned.callout-style-simple .callout-content {
padding-left: 1.6em;
}
.callout.callout-captioned .callout-header {
padding-top: 0.2em;
margin-bottom: -0.2em;
}
.callout.callout-captioned .callout-caption p {
margin-top: 0.5em;
margin-bottom: 0.5em;
}
.callout.callout-captioned.callout-style-simple .callout-content p {
margin-top: 0;
}
.callout.callout-captioned.callout-style-default .callout-content p {
margin-top: 0.7em;
}
.callout.callout-style-simple div.callout-caption {
border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
.callout.callout-style-default div.callout-caption {
border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-caption {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-captioned .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-captioned .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-captioned) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
background-image: url('data:image/png;base64,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');
}
div.callout-note.callout-style-default .callout-caption {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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<div class="slides">
<section id="title" class="slide level2" data-menu-title="Title" data-background-image="images/title_ridges.png">
<h2></h2>
<p><span class="title">Continental-scale biodiversity data assessment using the Atlas of Living Australia</span> <span class="subtitle">Shandiya Balasubramaniam <br> <i class="fa-brands fa-twitter" aria-label="twitter"></i> <span class="citation" data-cites="ShandiyaB">@ShandiyaB</span> <br> VicBioCon2023</span></p>
</section>
<section id="acknowledgement" class="slide level2" data-menu-title="Acknowledgement">
<h2></h2>
<p><span class="acknowledgement">I acknowledge the Traditional Owners of the lands on which I live and work, the Wurundjeri People of the Kulin Nation, and pay my respects to Elders past and present. I recognise the spiritual and cultural significance of land, water, and all that is in the environment to Traditional Owners, and their continuing connection to Country.</span></p>
<p><img data-src="images/ack_ridges.png" class="absolute" style="bottom: 10px; width: 1500px; "></p>
</section>
<section id="ala-home" class="slide level2 galah" data-menu-title="ALA Home">
<h2></h2>
<img data-src="images/ala-home.png" class="r-stretch quarto-figure-center"><div class="footer">
<p><a href="https://www.ala.org.au">ala.org.au</a></p>
</div>
<aside class="notes">
<p>The Atlas of Living Australia was launched in 2010 and is now the most comprehensive dataset on Australian biodiversity, with over 100 million records sourced from more than 800 data providers, which includes collections like iNaturalist, BirdLife, and the Victorian Biodiversity Atlas. So it aggregates data from natural history collections, government departments, researchers, community groups, and individuals, and makes it all available online for anyone to access.</p>
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</section>
<section>
<section id="galah" class="title-slide slide level1 galah-breaks center" data-menu-title="galah" data-background-color="#e9317f">
<h1>{galah}</h1>
<aside class="notes">
<p>The first project I wanted to introduce is the {galah} package, which acts as an interface to the biodiversity data in the ALA. The majority of these data consist of species occurrence records…</p>
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</section>
<section id="sp-occ" class="slide level2 galah" data-menu-title="Species Occurrence">
<h2></h2>
<h4 id="section">2020-09-23</h4>
<p><img data-src="images/whale.png" class="absolute" style="top: 20px; left: 380px; width: 700px; "> <img data-src="images/whale_map.png" class="absolute" style="left: 1000px; bottom: 200px; height: 500px; "></p>
<aside class="notes">
<p>…so, evidence of a taxon in a particular time and place. It’s possible to get these records through the website, but one of the main advantages of using {galah} is that it makes the query reproducible. It’s also implemented in both R and Python- the R version currently has more functionality but a fully-fledged Python release is going to be happening very soon.</p>
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</section>
<section id="counts" class="slide level2 galah" data-menu-title="atlas_counts()">
<h2>Counts of records</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-1" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-1-1">R</a></li><li><a href="#tabset-1-2">Python</a></li></ul>
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<div class="sourceCode cell-code" id="cb1" data-code-line-numbers="|1|3|4|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb1-2"><a href="#cb1-2"></a></span>
<span id="cb1-3"><a href="#cb1-3"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb1-4"><a href="#cb1-4"></a> <span class="fu">atlas_counts</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 1
count
<int>
1 113225978</code></pre>
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<div class="cell">
<div class="sourceCode cell-code" id="cb3" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1"></a><span class="im">import</span> galah</span>
<span id="cb3-2"><a href="#cb3-2"></a>galah.atlas_counts()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
</div>
<aside class="notes">
<p>I’ll run through some examples using the R syntax, but the Python code is here in this tab, and these slides are available online.</p>
<p>So, start by loading the package, and every query begins with galah_call(), which tells the API what we want. A lot of the syntax is similar to using dplyr, so if you’re familiar with the tidyverse this will be quite straightforward. The next line specifies what we want - here, atlas_counts() will retrieve counts of records. Voila, we’re told that there are just over 113 million records in the ALA. But we don’t always want everything, everywhere, all at once. So here are some functions that allow us to construct more specific queries</p>
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</section>
<section id="identify" class="slide level2 galah" data-menu-title="galah_identify()">
<h2>Identify taxa</h2>
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<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-2" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-2-1">R</a></li><li><a href="#tabset-2-2">Python</a></li></ul>
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<div class="sourceCode cell-code" id="cb4" data-code-line-numbers="|4|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb4-2"><a href="#cb4-2"></a></span>
<span id="cb4-3"><a href="#cb4-3"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb4-4"><a href="#cb4-4"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span></span>
<span id="cb4-5"><a href="#cb4-5"></a> <span class="fu">atlas_counts</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 1
count
<int>
1 1019663</code></pre>
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<div id="tabset-2-2">
<div class="cell">
<div class="sourceCode cell-code" id="cb6" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1"></a><span class="im">import</span> galah</span>
<span id="cb6-2"><a href="#cb6-2"></a>galah.atlas_counts(taxa<span class="op">=</span><span class="st">"pardalotus"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</div>
<p><img data-src="images/pardalotes/spotted.png" class="absolute" style="bottom: 50px; right: 100px; height: 150px; "> <img data-src="images/pardalotes/forty-spotted.png" class="absolute" style="bottom: 50px; right: 300px; height: 150px; "> <img data-src="images/pardalotes/striated.png" class="absolute" style="bottom: 50px; right: 500px; height: 150px; "> <img data-src="images/pardalotes/red-browed.png" class="absolute" style="bottom: 50px; right: 700px; height: 150px; "></p>
</div>
</div>
<aside class="notes">
<p>galah_identify() lets us specify one or more taxa - here, I’ve asked for the genus pardalotus. Over a million pardalote records</p>
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</section>
<section id="filter" class="slide level2 galah" data-menu-title="galah_filter()">
<h2>Filter records</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-3" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-3-1">R</a></li><li><a href="#tabset-3-2">Python</a></li></ul>
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<div id="tabset-3-1">
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb7" data-code-line-numbers="|5-6|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb7-2"><a href="#cb7-2"></a></span>
<span id="cb7-3"><a href="#cb7-3"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb7-4"><a href="#cb7-4"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span></span>
<span id="cb7-5"><a href="#cb7-5"></a> <span class="fu">galah_filter</span>(year <span class="sc">>=</span> <span class="dv">2020</span>, </span>
<span id="cb7-6"><a href="#cb7-6"></a> stateProvince <span class="sc">==</span> <span class="st">"Tasmania"</span>) <span class="sc">|></span> </span>
<span id="cb7-7"><a href="#cb7-7"></a> <span class="fu">atlas_counts</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 1
count
<int>
1 7016</code></pre>
</div>
</div>
</div>
</div>
<div id="tabset-3-2">
<div class="cell">
<div class="sourceCode cell-code" id="cb9" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1"></a><span class="im">import</span> galah</span>
<span id="cb9-2"><a href="#cb9-2"></a>galah.atlas_counts(</span>
<span id="cb9-3"><a href="#cb9-3"></a> taxa<span class="op">=</span><span class="st">"pardalotus"</span>,</span>
<span id="cb9-4"><a href="#cb9-4"></a> filters<span class="op">=</span>[<span class="st">"year >= 2020"</span>, <span class="st">"stateProvince == Tasmania"</span>]</span>
<span id="cb9-5"><a href="#cb9-5"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</div>
<p><img data-src="images/pardalotes/spotted.png" class="absolute" style="bottom: 50px; right: 100px; height: 150px; "> <img data-src="images/pardalotes/forty-spotted.png" class="absolute" style="bottom: 50px; right: 300px; height: 150px; "> <img data-src="images/pardalotes/striated.png" class="absolute" style="bottom: 50px; right: 500px; height: 150px; "></p>
</div>
</div>
<aside class="notes">
<p>galah_filter() applies filters to different fields - here, I’ve specified records from 2020 onwards, from Tasmania. Down to 7000 records. But maybe you want to know if there are different species in there, or if the counts change over the years…</p>
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overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="group" class="slide level2 galah" data-menu-title="galah_group_by()">
<h2>Group counts</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-4" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-4-1">R</a></li><li><a href="#tabset-4-2">Python</a></li></ul>
<div class="tab-content">
<div id="tabset-4-1">
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb10" data-code-line-numbers="|7|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb10-2"><a href="#cb10-2"></a></span>
<span id="cb10-3"><a href="#cb10-3"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb10-4"><a href="#cb10-4"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span></span>
<span id="cb10-5"><a href="#cb10-5"></a> <span class="fu">galah_filter</span>(year <span class="sc">>=</span> <span class="dv">2020</span>, </span>
<span id="cb10-6"><a href="#cb10-6"></a> stateProvince <span class="sc">==</span> <span class="st">"Tasmania"</span>) <span class="sc">|></span> </span>
<span id="cb10-7"><a href="#cb10-7"></a> <span class="fu">galah_group_by</span>(year, species) <span class="sc">|></span></span>
<span id="cb10-8"><a href="#cb10-8"></a> <span class="fu">atlas_counts</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 10 × 3
species year count
<chr> <chr> <int>
1 Pardalotus punctatus 2021 2321
2 Pardalotus punctatus 2020 1381
3 Pardalotus punctatus 2022 23
4 Pardalotus striatus 2021 1694
5 Pardalotus striatus 2020 1315
6 Pardalotus striatus 2022 19
7 Pardalotus striatus 2023 1
8 Pardalotus quadragintus 2021 133
9 Pardalotus quadragintus 2020 123
10 Pardalotus quadragintus 2022 6</code></pre>
</div>
</div>
</div>
</div>
<div id="tabset-4-2">
<div class="cell">
<div class="sourceCode cell-code" id="cb12" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1"></a><span class="im">import</span> galah</span>
<span id="cb12-2"><a href="#cb12-2"></a>galah.atlas_counts(</span>
<span id="cb12-3"><a href="#cb12-3"></a> taxa<span class="op">=</span><span class="st">"pardalotus"</span>,</span>
<span id="cb12-4"><a href="#cb12-4"></a> filters<span class="op">=</span>[<span class="st">"year >= 2020"</span>, <span class="st">"stateProvince == Tasmania"</span>],</span>
<span id="cb12-5"><a href="#cb12-5"></a> group_by<span class="op">=</span>[<span class="st">"year"</span>,<span class="st">"species"</span>]</span>
<span id="cb12-6"><a href="#cb12-6"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</div>
<p><img data-src="images/pardalotes/spotted-flip.png" class="absolute" style="left: 100px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/forty-spotted-flip.png" class="absolute" style="left: 300px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/striated-flip.png" class="absolute" style="left: 500px; bottom: 50px; height: 150px; "></p>
</div>
</div>
<aside class="notes">
<p>group_by() lets you group counts by the fields you specify - here, year and species. We can see that there are 3 species, and there’s quite a difference in the number of records.</p>
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overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="download" class="slide level2 galah" data-menu-title="atlas_occurrences()">
<h2>Download occurrences</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-5" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-5-1">R</a></li><li><a href="#tabset-5-2">Python</a></li></ul>
<div class="tab-content">
<div id="tabset-5-1">
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb13" data-code-line-numbers="|2,8|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb13-2"><a href="#cb13-2"></a><span class="fu">galah_config</span>(<span class="at">email =</span> <span class="st">"[email protected]"</span>)</span>
<span id="cb13-3"><a href="#cb13-3"></a></span>
<span id="cb13-4"><a href="#cb13-4"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb13-5"><a href="#cb13-5"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span></span>
<span id="cb13-6"><a href="#cb13-6"></a> <span class="fu">galah_filter</span>(year <span class="sc">>=</span> <span class="dv">2020</span>, </span>
<span id="cb13-7"><a href="#cb13-7"></a> stateProvince <span class="sc">==</span> <span class="st">"Tasmania"</span>) <span class="sc">|></span> </span>
<span id="cb13-8"><a href="#cb13-8"></a> <span class="fu">atlas_occurrences</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 7,016 × 8
decimal…¹ decim…² eventDate scien…³ taxon…⁴ recor…⁵ dataR…⁶ occur…⁷
<dbl> <dbl> <dttm> <chr> <chr> <chr> <chr> <chr>
1 -43.6 147. 2021-02-09 13:00:00 Pardal… https:… 5cb452… eBird … PRESENT
2 -43.6 147. 2021-02-09 13:00:00 Pardal… https:… 0308ea… eBird … PRESENT
3 -43.6 147. 2020-12-17 13:00:00 Pardal… https:… 586de7… eBird … PRESENT
4 -43.6 147. 2021-01-19 13:00:00 Pardal… https:… 3ce6c9… eBird … PRESENT
5 -43.6 147. 2020-12-16 13:00:00 Pardal… https:… d7ce89… eBird … PRESENT
6 -43.6 147. 2022-03-26 23:59:00 Pardal… https:… 859aae… iNatur… PRESENT
7 -43.6 147. 2020-12-16 13:00:00 Pardal… https:… cc741f… eBird … PRESENT
8 -43.6 147. 2020-12-16 13:00:00 Pardal… https:… 08e3d1… eBird … PRESENT
9 -43.5 147. 2021-02-08 13:00:00 Pardal… https:… 38f948… eBird … PRESENT
10 -43.5 147. 2020-12-15 13:00:00 Pardal… https:… a2c7b1… eBird … PRESENT
# … with 7,006 more rows, and abbreviated variable names ¹decimalLatitude,
# ²decimalLongitude, ³scientificName, ⁴taxonConceptID, ⁵recordID,
# ⁶dataResourceName, ⁷occurrenceStatus</code></pre>
</div>
</div>
</div>
</div>
<div id="tabset-5-2">
<div class="cell">
<div class="sourceCode cell-code" id="cb15" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb15-1"><a href="#cb15-1"></a><span class="im">import</span> galah</span>
<span id="cb15-2"><a href="#cb15-2"></a>galah.galah_config(email<span class="op">=</span><span class="st">"[email protected]"</span>)</span>
<span id="cb15-3"><a href="#cb15-3"></a>galah.atlas_occurrences(</span>
<span id="cb15-4"><a href="#cb15-4"></a> taxa<span class="op">=</span><span class="st">"pardalotus"</span>,</span>
<span id="cb15-5"><a href="#cb15-5"></a> filters<span class="op">=</span>[<span class="st">"year >= 2020"</span>, <span class="st">"stateProvince == Tasmania"</span>]</span>
<span id="cb15-6"><a href="#cb15-6"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</div>
<p><img data-src="images/pardalotes/spotted-flip.png" class="absolute" style="left: 100px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/forty-spotted-flip.png" class="absolute" style="left: 300px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/striated-flip.png" class="absolute" style="left: 500px; bottom: 50px; height: 150px; "></p>
</div>
</div>
<aside class="notes">
<p>To download these records and have a look at them in more detail, we can switch from atlas_counts() to atlas_occurrences(). Downloading records also requires that we provide the email we used to register with the ALA. This is a bit truncated, but we can see that the download consists of 7000+ rows and 8 columns.</p>
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position:absolute!important;
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width: 1px!important;
overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="select" class="slide level2 galah" data-menu-title="galah_select()">
<h2>Select fields</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-6" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-6-1">R</a></li><li><a href="#tabset-6-2">Python</a></li></ul>
<div class="tab-content">
<div id="tabset-6-1">
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb16" data-code-line-numbers="|8-10|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb16-2"><a href="#cb16-2"></a><span class="fu">galah_config</span>(<span class="at">email =</span> <span class="st">"[email protected]"</span>)</span>
<span id="cb16-3"><a href="#cb16-3"></a></span>
<span id="cb16-4"><a href="#cb16-4"></a><span class="fu">galah_call</span>() <span class="sc">|></span></span>
<span id="cb16-5"><a href="#cb16-5"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span></span>
<span id="cb16-6"><a href="#cb16-6"></a> <span class="fu">galah_filter</span>(year <span class="sc">>=</span> <span class="dv">2020</span>, </span>
<span id="cb16-7"><a href="#cb16-7"></a> stateProvince <span class="sc">==</span> <span class="st">"Tasmania"</span>) <span class="sc">|></span> </span>
<span id="cb16-8"><a href="#cb16-8"></a> <span class="fu">galah_select</span>(species, </span>
<span id="cb16-9"><a href="#cb16-9"></a> year, </span>
<span id="cb16-10"><a href="#cb16-10"></a> dataResourceName) <span class="sc">|></span> </span>
<span id="cb16-11"><a href="#cb16-11"></a> <span class="fu">atlas_occurrences</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 7,016 × 3
species year dataResourceName
<chr> <dbl> <chr>
1 Pardalotus punctatus 2021 eBird Australia
2 Pardalotus punctatus 2021 eBird Australia
3 Pardalotus punctatus 2021 eBird Australia
4 Pardalotus punctatus 2021 eBird Australia
5 Pardalotus punctatus 2020 eBird Australia
6 Pardalotus punctatus 2021 eBird Australia
7 Pardalotus punctatus 2021 eBird Australia
8 Pardalotus punctatus 2021 eBird Australia
9 Pardalotus punctatus 2021 eBird Australia
10 Pardalotus punctatus 2021 eBird Australia
# … with 7,006 more rows</code></pre>
</div>
</div>
</div>
</div>
<div id="tabset-6-2">
<div class="cell">
<div class="sourceCode cell-code" id="cb18" data-code-line-numbers="|"><pre class="sourceCode numberSource python number-lines code-with-copy"><code class="sourceCode python"><span id="cb18-1"><a href="#cb18-1"></a><span class="im">import</span> galah</span>
<span id="cb18-2"><a href="#cb18-2"></a>galah.galah_config(email<span class="op">=</span><span class="st">"[email protected]"</span>)</span>
<span id="cb18-3"><a href="#cb18-3"></a>galah.atlas_occurrences(</span>
<span id="cb18-4"><a href="#cb18-4"></a> taxa<span class="op">=</span><span class="st">"pardalotus"</span>,</span>
<span id="cb18-5"><a href="#cb18-5"></a> filters<span class="op">=</span>[<span class="st">"year >= 2020"</span>, <span class="st">"stateProvince == Tasmania"</span>],</span>
<span id="cb18-6"><a href="#cb18-6"></a> fields<span class="op">=</span>[<span class="st">"species"</span>,<span class="st">"year"</span>,<span class="st">"decimalLatitude"</span>,<span class="st">"decimalLongitude"</span>]</span>
<span id="cb18-7"><a href="#cb18-7"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</div>
</div>
</div>
<p><img data-src="images/pardalotes/spotted-flip.png" class="absolute" style="left: 100px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/forty-spotted-flip.png" class="absolute" style="left: 300px; bottom: 50px; height: 150px; "> <img data-src="images/pardalotes/striated-flip.png" class="absolute" style="left: 500px; bottom: 50px; height: 150px; "></p>
</div>
</div>
<aside class="notes">
<p>We might not want all the columns that are included in the default download, or we might want some different ones; we can specify this with galah_select() - here, we have records with information about species, year, and the data provider.</p>
<style type="text/css">
span.MJX_Assistive_MathML {
position:absolute!important;
clip: rect(1px, 1px, 1px, 1px);
padding: 1px 0 0 0!important;
border: 0!important;
height: 1px!important;
width: 1px!important;
overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="geolocate" class="slide level2 galah" data-menu-title="galah_geolocate()">
<h2>Geolocate</h2>
<div class="columns v-center-container">
<div class="column" style="width:100%;">
<div class="panel-tabset">
<ul id="tabset-7" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-7-1">R</a></li><li><a href="#tabset-7-2">Python</a></li></ul>
<div class="tab-content">
<div id="tabset-7-1">
<div class="cell columns column-output-location">
<div class="column">
<div class="sourceCode cell-code" id="cb19" data-code-line-numbers="|1-2|4-6|8-11|"><pre class="sourceCode numberSource r number-lines code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1"></a><span class="fu">library</span>(galah)</span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="fu">library</span>(sf)</span>
<span id="cb19-3"><a href="#cb19-3"></a></span>
<span id="cb19-4"><a href="#cb19-4"></a>melb <span class="ot"><-</span> <span class="fu">st_read</span>(<span class="st">"data/metro_region.shp"</span>, </span>
<span id="cb19-5"><a href="#cb19-5"></a> <span class="at">quiet =</span> <span class="cn">TRUE</span>) <span class="sc">|></span> </span>
<span id="cb19-6"><a href="#cb19-6"></a> <span class="fu">st_simplify</span>(<span class="at">dTolerance =</span> <span class="dv">1000</span>)</span>
<span id="cb19-7"><a href="#cb19-7"></a></span>
<span id="cb19-8"><a href="#cb19-8"></a><span class="fu">galah_call</span>() <span class="sc">|></span> </span>
<span id="cb19-9"><a href="#cb19-9"></a> <span class="fu">galah_identify</span>(<span class="st">"pardalotus"</span>) <span class="sc">|></span> </span>
<span id="cb19-10"><a href="#cb19-10"></a> <span class="fu">galah_geolocate</span>(melb) <span class="sc">|></span> </span>
<span id="cb19-11"><a href="#cb19-11"></a> <span class="fu">atlas_counts</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column fragment">
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 1 × 1
count
<int>
1 93217</code></pre>
</div>
</div>
</div>
<p><img data-src="images/metro_outline.png" class="absolute" style="bottom: 10px; right: 10px; "></p>
</div>
<div id="tabset-7-2">
<p>Watch this space!</p>
</div>
</div>
</div>
</div>
</div>
<aside class="notes">
<p>{galah} also lets you search within a bespoke location; with galah_geolocate, you can provide a shapefile, well known text string, bounding box, or simple features object. In this example here, we load the {sf} package, then read in a shapefile of the melbourne metro region. Then it’s’ just a case of providing this as an argument to galah_geolocate, and we have 93 thousand pardalotes ever recorded in Melbourne.</p>
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<p><a href="https://galah.ala.org.au">galah.ala.org.au</a></p>
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<aside class="notes">
<p>This is just some of the functionality of the package, there’s lots of other cool things that you can do with it, like apply data quality profiles, or query other living atlases, and that’s all documented on the website.</p>
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<h1>ALA labs</h1>
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<p>The second project I’d like to draw your attention to is ALA labs…</p>
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<p><a href="https://labs.ala.org.au">labs.ala.org.au</a></p>
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<p>…which is a resource for learning how to do things with data from the Atlas. The idea is to showcase and share tools for open, reproducible workflows</p>
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<p><video data-src="videos/alpha-hulls.mov" controls=""><a href="videos/alpha-hulls.mov">Video</a></video></p>
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<p><a href="https://labs.ala.org.au">labs.ala.org.au</a></p>
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<p>For example, Fonti and Margot wrote an article on convex and alpha hulls, which can be good options for visualising species distributions where there are very few existing observations. Recently, this method was used to estimate the impact of the 2020 bushfires on invertebrates in southern Australia. In this post, they walk though the process of downloading records of data-deficient species from the Atlas, and the steps involved in predicting species distributions using convex and alpha hulls, which can be a useful metric for conservation planning.</p>
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<p><a href="https://labs.ala.org.au">labs.ala.org.au</a></p>
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<aside class="notes">
<p>As you can see here, the science team at the Atlas have written articles describing a range of data visualisations and ecological analyses, and we’re continually adding to these. And if there’s something you think we should write about, let us know!</p>
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<h1>EcoAssets</h1>
<aside class="notes">
<p>The third project I’m introducing today is EcoAssets, which is a little bit different in terms of scale. EcoAssets brings together 3 research infrastructures…</p>
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<p><img data-src="images/logos/logo_ala.png" class="absolute" style="left: 200px; bottom: 350px; width: 300px; "> <img data-src="images/logos/logo_tern.png" class="absolute" style="left: 600px; bottom: 300px; width: 300px; "> <img data-src="images/logos/logo_imos.png" class="absolute" style="left: 1000px; bottom: 350px; width: 300px; "></p>
<aside class="notes">
<p>…the Atlas of Living Australia, the Terrestrial Ecosystem Research Network, and the Integrated Marine Observing System, to provide data in forms that support environmental reporting, such as the State of the Environment Report.</p>