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Expand Up @@ -64,18 +64,18 @@ <h1 class="title">First Steps with TileDB</h1>
<h1>Getting started</h1>
<p>Once the TileDB R package is installed, it can be loaded via <code>library(tiledb)</code>. Installation is supported for Windows, Linux and macOS via the <a href="https://cran.r-project.org/package=tiledb">official CRAN package</a>, on Linux and macOS via <a href="https://anaconda.org/conda-forge/r-tiledb">the conda package</a> as well as from source.</p>
<p>Documentation for the TileDB R package is available via the <code>help()</code> function from within R as well as via the <a href="https://tiledb-inc.github.io/TileDB-R/">package documentation</a> and an [introductory notebook][tiledb_notebook]. Documentation about TileDB itself is <a href="https://docs.tiledb.com/main/">also available</a>.</p>
<p>Several “quickstart” examples that are discussed on the website are available in the <a href="https://github.com/TileDB-Inc/TileDB-R/tree/master/inst/examples">examples</a> directory. This vignette discusses similar examples.</p>
<p>In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as <code>s3://some/data/bucket</code> can be used where a local file would be used. See the script <a href="https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_S3.R">ex_S3.R</a> for an example.</p>
<p>Several “quickstart” examples that are discussed on the website are available in the <a href="https://github.com/TileDB-Inc/TileDB-R/tree/main/inst/examples">examples</a> directory. This vignette discusses similar examples.</p>
<p>In the following examples, the URIs describing arrays point to local file system object. When TileDB has been built with S3 support, and with proper AWS credentials in the usual environment variables, URIs such as <code>s3://some/data/bucket</code> can be used where a local file would be used. See the script <a href="https://github.com/TileDB-Inc/TileDB-R/blob/main/inst/examples/ex_S3.R">ex_S3.R</a> for an example.</p>
</section>
<section id="dense-arrays" class="level1">
<h1>Dense Arrays</h1>
<section id="preliminaries" class="level2">
<h2>Preliminaries</h2>
<p>These illustrations use the array created by the file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_1.R">ex_1.R</a> which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override).</p>
<p>These illustrations use the array created by the file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/main/inst/examples/ex_1.R">ex_1.R</a> which one can run from within R, or on the command-line. To follow along with discussion that follows, it helps to run the example once to create the array after possibly adjusting the array location path from its default value (using the current directory or, if set as an option, an override).</p>
</section>
<section id="basic-reading-of-dense-arrays" class="level2">
<h2>Basic Reading of Dense Arrays</h2>
<p>The file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_1.R">ex_1.R</a> in the examples directory is a simple yet complete example extending <a href="https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/quickstart_dense.R">quickstart_dense.R</a> by adding a second and third attribute. In this as well as the following examples we will use <code>tiledb_array()</code> to access the array; the older variants <code>tiledb_dense()</code> and <code>tiledb_sparse()</code> remain supported but are deprecated and may be removed at some point in the future.</p>
<p>The file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/main/inst/examples/ex_1.R">ex_1.R</a> in the examples directory is a simple yet complete example extending <a href="https://github.com/TileDB-Inc/TileDB-R/blob/main/inst/examples/quickstart_dense.R">quickstart_dense.R</a> by adding a second and third attribute. In this as well as the following examples we will use <code>tiledb_array()</code> to access the array; the older variants <code>tiledb_dense()</code> and <code>tiledb_sparse()</code> remain supported but are deprecated and may be removed at some point in the future.</p>
<p><em>Read 1-D</em></p>
<p>The first example extracts rows 1 to 2 and column 2 from an array. It also limits the selection to just one attribute (via <code>attrs</code>), asks for the return to be a <code>data.frame</code> (instead of a simpler list) and for the (row and column, if present as here) indices to not be printed (via <code>extended=FALSE</code>).</p>
<pre><code>&gt; A &lt;- tiledb_array(uri = uri, attrs = &quot;b&quot;,
Expand Down Expand Up @@ -189,7 +189,7 @@ <h2>Basic Reading and Writing of Sparse Arrays</h2>
</section>
<section id="datetime-attributes" class="level2">
<h2>Date(time) Attributes</h2>
<p>Similar to the dense array case described earlier, the file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/master/inst/examples/ex_2.R">ex_2.R</a> illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats.</p>
<p>Similar to the dense array case described earlier, the file <a href="https://github.com/TileDB-Inc/TileDB-R/blob/main/inst/examples/ex_2.R">ex_2.R</a> illustrates some basic operations on sparse arrays. It also shows date and datetime types instead of just integer and double precision floats.</p>
<pre><code>&gt; A &lt;- tiledb_array(uri = uri, as.data.frame = TRUE)
&gt; A[1577858403:1577858408]
rows cols a b d e
Expand All @@ -213,7 +213,7 @@ <h2>Date(time) Attributes</h2>
</section>
<section id="additional-information" class="level1">
<h1>Additional Information</h1>
<p>The TileDB R package is documented via R help functions (<em>e.g.</em> <code>help(&quot;tiledb_array&quot;)</code> shows information for the <code>tiledb_array()</code> function) as well as via a <a href="https://tiledb-inc.github.io/TileDB-R/">website regrouping all documentation</a>. Extended <a href="https://tiledb-inc.github.io/TileDB-R/documentation.html">API documentation</a> is available, as is a <a href="https://github.com/TileDB-Inc/TileDB-R/tree/master/inst/examples">examples/</a> directory.</p>
<p>The TileDB R package is documented via R help functions (<em>e.g.</em> <code>help(&quot;tiledb_array&quot;)</code> shows information for the <code>tiledb_array()</code> function) as well as via a <a href="https://tiledb-inc.github.io/TileDB-R/">website regrouping all documentation</a>. Extended <a href="https://tiledb-inc.github.io/TileDB-R/documentation.html">API documentation</a> is available, as is a <a href="https://github.com/TileDB-Inc/TileDB-R/tree/main/inst/examples">examples/</a> directory.</p>
<p>TileDB itself has extensive <a href="https://docs.tiledb.com/developer/installation">installation</a>, and <a href="https://docs.tiledb.com/developer/">overall documentation</a> as well as a <a href="https://forum.tiledb.com/">support forum</a>.</p>
</section>
</article>
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