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<h1 class="title">Spatial data</h1>

<section class="slide level2">

<section><section id="course-logistics-reminder" class="title-slide slide level1"><h1>Course Logistics Reminder</h1></section><section id="project-proposal" class="slide level2">

<h2>Project Proposal</h2>

<p>Start thinking about:</p>

<li>Question you want to answer</li>

<li>Problem you want to solve</li>

</section><section id="link-to-this-script" class="slide level2">

<h2>Link to this script</h2>

<p><a href="PS_08_sf.Rmd"><i class="fa fa-desktop"></i> If interested, you can download the R script associated with this presentation here</a>.</p>

</section><section id="section" class="slide level2" data-background-iframe="https://cran.r-project.org/web/views/">

</section><section id="code-reading-challenge" class="slide level2">

<h2>Code Reading Challenge</h2>

<p>Write out in a sentence what this code is doing. Make sure to catch the key points in your sentence</p>

<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(downloader)</a>

<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">library</span>(sf)</a>

<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw">library</span>(fs)</a>

<a class="sourceLine" id="cb1-4" data-line-number="4">dams_path &lt;-<span class="st"> &quot;https://research.idwr.idaho.gov/gis/Spatial/DamSafety/dam.zip&quot;</span></a>

<a class="sourceLine" id="cb1-5" data-line-number="5">df &lt;-<span class="st"> </span><span class="kw">tempfile</span>(); uf &lt;-<span class="st"> </span><span class="kw">tempfile</span>()</a>

<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="kw">download</span>(dams_path, df, <span class="dt">mode =</span> <span class="st">&quot;wb&quot;</span>)</a>

<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="kw">unzip</span>(df, <span class="dt">exdir =</span> uf)</a>

<a class="sourceLine" id="cb1-8" data-line-number="8">dams &lt;-<span class="st"> </span><span class="kw">read_sf</span>(uf)</a>

<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="kw">file_delete</span>(df); <span class="kw">dir_delete</span>(uf)</a></code></pre></div>

<section><section id="working-with-spatial-data-in-r" class="title-slide slide level1"><h1>Working with Spatial Data in R</h1></section><section id="available-packages" class="slide level2">

<h2>Available Packages</h2>

<li><code>sp</code> First major spatial data package/format</li>

<li><code>rgdal</code> reading and writing spatial data</li>

<li><code>rgeos</code> Interface to open-source geometry engine (GEOS)</li>

<li><code>sf</code> Spatial Features in the ‘tidyverse’</li>

<li><code>raster</code> gridded data (like satellite imagery)</li>

<li>and a few others…</li>

</section><section id="what-is-a-spatial-feature-sf" class="slide level2">

<h2>What is a Spatial Feature (sf)?</h2>

<p>Typically an object in the real world, such as a building or a tree.</p>

<p>Features could include:</p>

<li>a forest (polygon)</li>

<li>a tree in the forest (point or polygon)</li>

<li>a branch on the tree (line?)</li>

<li>a complete image (multipoint, polygon, raster)</li>

<li>a satellite image pixel of that forest (point or polgyon or raster)</li>

</section><section id="spatial-features" class="slide level2">

<h2>Spatial Features</h2>

<p>What information do we need to store in order to define points, lines, polygons in geographic space?</p>

<li>lat/lon coordinates</li>

<li>projection</li>

<li>what type (point/line/poly)</li>

<li>if polygon, is it a hole or not</li>

<li>attribute data</li>

<li>… ?</li>

</section><section id="geometry" class="slide level2">

<h2>Geometry</h2>

<p>Features have a <em>geometry</em> describing <em>where</em> on Earth the feature is located, and they have attributes, which describe other properties.</p>

<p>A Tree:</p>

<li>delineation of its crown</li>

<li>its stem</li>

<li>point indicating its centre</li>

<p>Attributes:</p>

<li>species</li>

<li>height</li>

<li>diameter</li>

<li>date of observation</li>

<li>…</li>

</section><section id="spatial-feature-standard" class="slide level2">

<h2>Spatial Feature Standard</h2>

<p>“<em>A simple feature is defined by the OpenGIS Abstract specification to have both spatial and non-spatial attributes. Spatial attributes are geometry valued, and simple features are based on 2D geometry with linear interpolation between vertices.</em>”</p>

</section><section id="dimensions" class="slide level2">

<h2>Dimensions</h2>

<p>All geometries composed of points: coordinates in 2-, 3- or 4-dimensional space.</p>

<li><strong>X</strong> coordinate in X direction (typically longitude or similar)</li>

<li><strong>Y</strong> coordinate in Y direction (typically latitude or similar)</li>

<li><strong>Z</strong> coordinate denoting altitude</li>

<li><strong>M</strong> coordinate (rarely used), denoting some <em>measure</em> that is associated with the point, rather than with the feature as a whole (in which case it would be a feature attribute); examples could be time of measurement, or measurement error.</li>

</section><section id="dimensions-1" class="slide level2">

<h2>Dimensions</h2>

<p>The four possible cases then are:</p>

<ol type="1">

<li>2D (XY): x and y, easting and northing, or longitude and latitude</li>

<li>3D (XYZ): three-dimensional points</li>

<li>3D (XYM): three-dimensional points where 3rd is some attribute space</li>

<li>4D (XYZM): four-dimensional points as XYZM (the third axis is Z, fourth M)</li>

</section><section id="common-simple-feature-sf-types" class="slide level2">

<h2>Common Simple Feature (SF) types</h2>

<p><img data-src="https://geocompr.robinlovelace.net/figures/sf-classes.png" /></p>

</section><section id="seven-common-simple-feature-sf-geometry-types" class="slide level2">

<h2>Seven common Simple Feature (SF) geometry types</h2>

<tr class="header">

<th>type</th>

<th>description</th>

<tr class="odd">

<td><code>POINT</code></td>

<td>a single point</td>

<tr class="even">

<td><code>LINESTRING</code></td>

<td>sequence of points connected by lines</td>

<tr class="odd">

<td><code>POLYGON</code></td>

<td>sequence of points form a closed ring</td>

<tr class="even">

<td><code>MULTIPOINT</code></td>

<td>set of points</td>

<tr class="odd">

<td><code>MULTILINESTRING</code></td>

<td>set of linestrings</td>

<tr class="even">

<td><code>MULTIPOLYGON</code></td>

<td>set of polygons</td>

<tr class="odd">

<td><code>GEOMETRYCOLLECTION</code></td>

<td>set of geometries</td>

<p>Some formats only include these (e.g. <a href="https://tools.ietf.org/html/rfc7946">GeoJSON</a>)</p>

</section><section id="uncommon-geometry-types" class="slide level2">

<h2>Uncommon Geometry Types</h2>

<p>10 more geometries 10 are rare:</p>

<li><code>CIRCULARSTRING</code></li>

<li><code>COMPOUNDCURVE</code></li>

<li><code>CURVEPOLYGON</code></li>

<li><code>MULTICURVE</code></li>

<li><code>MULTISURFACE</code></li>

<li><code>CURVE</code></li>

<li><code>SURFACE</code></li>

<li><code>POLYHEDRALSURFACE</code></li>

<li><code>TIN</code></li>

<li><code>TRIANGLE</code></li>

<p>There are currently two main approaches in R to handle geographic vector data.</p>

</section><section id="sp-package" class="slide level2">

<h2><code>sp</code> package</h2>

<p>First package for spatial data: <a href="https://cran.r-project.org/package=sp"><code>sp</code></a>. Provides classes and methods to create <em>points</em>, <em>lines</em>, <em>polygons</em>, and <em>grids</em> and to operate on them.</p>

<p>~350 of the spatial analysis packages use <code>sp</code> data types, so it is important to know how to convert <strong>sp</strong> to and from <strong>sf</strong> objects.</p>

</section><section id="sf-package" class="slide level2">

<h2><code>sf</code> package</h2>

<p><a href="https://cran.r-project.org/package=sf"><code>sf</code></a> implements a formal standard called <a href="https://en.wikipedia.org/wiki/Simple_Features">“Simple Features”</a> that specifies a storage and access model of spatial geometries (point, line, polygon).</p>

<p>A feature geometry is called simple when it consists of points connected by straight line pieces, and does not intersect itself.</p>

<p>This standard has been adopted widely, not only by spatial databases such as PostGIS, but also more recent standards such as GeoJSON.</p>

</section><section id="how-simple-features-in-r-are-organized" class="slide level2">

<h2>How simple features in R are organized</h2>

<p>All spatial functions and methods in <code>sf</code> prefixed by <code>st_</code> (refering to <em>spatial and temporal</em>)</p>

<p>Simple features are implemented as R native data, using simple data structures (S3 classes, lists, matrix, vector).</p>

</section><section class="slide level2">

<p>Stored as <code>data.frame</code> objects (or very similar <code>tbl_df</code>) with <em>feature geometries in a <code>data.frame</code> column</em>.</p>

<p>Since geometries are not single-valued, they are put in a list-column, a list of length equal to the number of records in the <code>data.frame</code>, with each list element holding the simple feature geometry of that feature.</p>

</section><section id="components" class="slide level2">

<h2>Components</h2>

<li><code>sf</code>, the table (<code>data.frame</code>) with feature attributes and feature geometries, which contains</li>

<li><code>sfc</code>, the list-column with the geometries for each feature (record), which is composed of</li>

<li><code>sfg</code>, the feature geometry of an individual simple feature.</li>

</section><section class="slide level2">

<p>If you work with PostGis or GeoJSON you may have come across the <a href="https://en.wikipedia.org/wiki/Well-known_text">WKT (well-known text)</a> format, for example like these:</p>

<pre><code>POINT (30 10)

LINESTRING (30 10, 10 30, 40 40)

POLYGON ((30 10, 40 40, 20 40, 10 20, 30 10))</code></pre>

<p><code>sf</code> implements this standard natively in R. Data are structured and conceptualized very differently from the <code>sp</code> approach.</p>

</section><section id="i.-create-geometric-objects-topology" class="slide level2">

<h2>I. Create geometric objects (topology)</h2>

<p>Geometric objects (simple features) can be created from a numeric vector, matrix or a list with the coordinates. They are called <code>sfg</code> objects for Simple Feature Geometry.</p>

<p>Create a LINESTRING <code>sfg</code> object:</p>

<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">xy=<span class="kw">matrix</span>(<span class="kw">runif</span>(<span class="dv">6</span>), <span class="dt">ncol=</span><span class="dv">2</span>)</a>

<a class="sourceLine" id="cb3-2" data-line-number="2">xy</a></code></pre></div>

<pre><code>## [,1] [,2]

## [1,] 0.3046195 0.5242276

## [2,] 0.2268402 0.9591672

## [3,] 0.6675886 0.9305813</code></pre>

<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1">lnstr_sfg &lt;-<span class="st"> </span><span class="kw">st_linestring</span>(xy) </a>

<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="kw">class</span>(lnstr_sfg)</a></code></pre></div>

<pre><code>## [1] &quot;XY&quot; &quot;LINESTRING&quot; &quot;sfg&quot;</code></pre>

<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">lnstr_sfg</a></code></pre></div>

<pre><code>## LINESTRING (0.3046195 0.5242276, 0.2268402 0.9591672, 0.6675886 0.9305813)</code></pre>

</section><section id="ii.-combine-all-individual-single-feature-objects-for-the-special-column." class="slide level2">

<h2>II. Combine all individual single feature objects for the special column.</h2>

<p>Create a <code>sfc</code> (Simple Feature Collection) object of individual features:</p>

<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">lnstr_sfc &lt;-<span class="st"> </span><span class="kw">st_sfc</span>(lnstr_sfg) <span class="co"># just one feature here</span></a>

<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw">class</span>(lnstr_sfc)</a></code></pre></div>

<pre><code>## [1] &quot;sfc_LINESTRING&quot; &quot;sfc&quot;</code></pre>

<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">lnstr_sfc</a></code></pre></div>

<pre><code>## Geometry set for 1 feature

## geometry type: LINESTRING

## dimension: XY

## bbox: xmin: 0.2268402 ymin: 0.5242276 xmax: 0.6675886 ymax: 0.9591672

## epsg (SRID): NA

## proj4string: NA</code></pre>

<pre><code>## LINESTRING (0.3046195 0.5242276, 0.2268402 0.95...</code></pre>

<p>The <code>sfc</code> object also holds the bounding box and the projection information.</p>

</section><section id="iii.-add-attributes." class="slide level2">

<h2>III. Add attributes.</h2>

<p>Add attributes (in a <code>data.frame</code>) to the <code>sfc</code> object to make a <code>sf</code> (Simple Features) object:</p>

<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">dfr=<span class="kw">data.frame</span>(<span class="dt">type=</span><span class="st">&quot;random&quot;</span>)</a>

<a class="sourceLine" id="cb14-2" data-line-number="2">lnstr_sf &lt;-<span class="st"> </span><span class="kw">st_sf</span>(dfr , lnstr_sfc)</a>

<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="kw">class</span>(lnstr_sf)</a></code></pre></div>

<pre><code>## [1] &quot;sf&quot; &quot;data.frame&quot;</code></pre>

<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1">lnstr_sf</a></code></pre></div>

<pre><code>## Simple feature collection with 1 feature and 1 field

## geometry type: LINESTRING