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<!DOCTYPE html>

<title>An example Quarto Markdown file</title>

<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 -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */

vertical-align: middle;

}

/* CSS for syntax highlighting */

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;

}

pre.numberSource { margin-left: 3em; padding-left: 4px; }

div.sourceCode

{ }

@media screen {

pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }

}

/* CSS for citations */

div.csl-bib-body { }

div.csl-entry {

clear: both;

}

.hanging-indent div.csl-entry {

margin-left:2em;

text-indent:-2em;

}

div.csl-left-margin {

min-width:2em;

float:left;

}

div.csl-right-inline {

margin-left:2em;

padding-left:1em;

}

div.csl-indent {

margin-left: 2em;

}</style>

</head>

<body>

<div class="quarto-alternate-formats"><h2>Other Formats</h2><ul><li><a href="demo-q.pdf"><i class="bi bi-file-pdf"></i>PDF</a></li></ul></div></div>

\newcommand{\trans}{^\mathsf{T}}

\newcommand{\eps}{\epsilon}

<h1 class="title">An example Quarto Markdown file</h1>

<p class="subtitle lead">Illustrating use of R, bash, Python, and Julia code chunks</p>

</div>

<div>

<div class="quarto-title-meta-heading">Author</div>

<p>Christopher Paciorek </p>

</div>

<div>

<div class="quarto-title-meta-heading">Published</div>

<p class="date">September 1, 2023</p>

</div>

</header>

<h1>1) How to generate a document from this file</h1>

<p>From the command line, you can render the file as follows:</p>

<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> render demo.qmd <span class="at">--to</span> html</span>

<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> render demo.qmd <span class="at">--to</span> pdf</span>

<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> render demo.qmd <span class="co"># output depends on 'format' declaration at the top of the document (defaults to html)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>Alternatively, start R and run the desired line from amongst the following possibilities in R:</p>

<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(quarto)</span>

<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">quarto_render</span>(<span class="st">"demo.qmd"</span>) <span class="co"># defaults to html</span></span>

<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">quarto_render</span>(<span class="st">"demo.qmd"</span>, <span class="at">output_format =</span> <span class="st">"pdf"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>Or in RStudio (version at least 2022.07), click on the ‘Render’ button and choose to knit to HTML, PDF, or Word (for R Markdown).</p>

</section>

<h1>2) Some basic Markdown formatting</h1>

<p>Here’s an <em>introduction</em> to our <strong>critical</strong> discovery. Here we have some code to display inline but not evaluate: <code>exp(7)</code> and we can embed the code in a static code block as follows:</p>

<pre><code>a = 7 %% 5

b = exp(a)</code></pre>

<p>This document will focus on embedding math and code and not on standard Markdown formatting. There are lots of sources of information on Markdown. <a href="https://rmarkdown.rstudio.com">RStudio has good information on R Markdown</a> (including Markdown formatting).</p>

<p>For documents whose output format is HTML, you can use HTML formatting within your Markdown-based text.</p>

</section>

<h1>3) Embedding equations using LaTeX</h1>

<p>This can be done with the following syntax. Note that you can’t have a space after the initial $ for the inline equations.</p>

<p>Here is an inline equation <span class="math inline">$f(x) = \int f(y, x) dy$</span>.</p>

<p>Here’s a displayed equation</p>

<p><span class="math display">\[

f_\theta(x) = \int f_\theta(y, x) dy.

\]</span></p>

<h2 class="anchored" data-anchor-id="latex-macros">3.1) LaTeX macros</h2>

<p>You can define LaTeX macros in separate files and then use them as follows.</p>

<p>The macros for PDF rendering should be placed in a .tex file as shown in <a href="macros.tex">macros.tex</a>. The macros for HTML rendering should be placed in a .md file, formatted as shown in <a href="macros.md">macros.md</a>.</p>

<p>(Unfortunately, it does seem to me that you need to have two separate files with the same macro definitions if rendering to both pdf and html.)</p>

<p>Then make sure to include those files as seen in the header of the qmd document like this:</p>

<pre><code>format:

pdf:

include-before-body:

- file: macros.tex

html:

include-before-body:

- file: macros.md</code></pre>

<p>We can then use a macro in this equation:</p>

<p><span class="math display">\[

A = X \trans Y

\]</span></p>

</section>

<h1>4) Embedding R code</h1>

<p>Here’s an R code chunk</p>

</div>

</div>

<p>When running R code, output is printed interspersed with the code, as one would generally want. Also, later chunks have access to result from earlier chunks (i.e., state is preserved between chunks).</p>

<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">hist</span>(<span class="fu">rnorm</span>(<span class="dv">20</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>And here’s some inline R code: What is 3 plus 5? 8.</p>

</section>

<h1>5) Controlling code chunk behavior</h1>

<p>While you can specify the chunk label and chunk options using R Markdown syntax inside the braces in the first chunk line above, with Quarto, an alternative, nice way to specify chunk labels and other options is within the chunk, like this:</p>

<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: put-options-in-chunk</span></span>

<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>b <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="dv">5</span>)</span>

</div>

<p>You have control over whether code in chunks is echoed into the document and evaluated using the <code>include</code>, <code>echo</code>, and <code>eval</code> tags.</p>

<p>Here we print out the code, but we don’t evaluate it:</p>

<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: evalChunk</span></span>

<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="co">#| eval: false</span></span>

<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(<span class="st">"This code is printed in the document, but the code is not evaluated."</span>)</span>

</div>

<p>Here’s the result of a chunk with <code>echo</code> set to <code>false</code> so the code itself does not show up in the rendered document.</p>

<pre><code>This code is not printed in the document, but results of evaluating the code are printed.</code></pre>

</div>

<p>Here’s a chunk with <code>include</code> set to <code>false</code>, hence neither the code nor output from running the code show up in the rendered output.</p>

<p>Results of intensive calculations can be saved using the <code>cache: true</code> tag so they don’t need to be rerun every time you compile the document.</p>

<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: slow-step</span></span>

<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="co">#| cache: true</span></span>

<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">mean</span>(<span class="fu">rnorm</span>(<span class="fl">5e7</span>))</span>

</div>

<p>You can use variables (an R variable here) to control the chunk options. Note that the variable <code>myControlVar</code> is defined in the first chunk of this document. Here it is used to turn off evaluation of the chunk code.</p>

<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: use-var-in-chunk-option</span></span>

<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="co">#| eval: !expr '!myControlVar'</span></span>

<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="fu">print</span>(<span class="st">"hi"</span>)</span>

</div>

<p>You can control which executable is used to execute a given chunk of code by (particularly useful for Python and bash and for debugging), using the <code>engine.path</code> chunk option.</p>

<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="in">```{python}</span></span>

<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| eval: false</span></span>

<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a><span class="co">#| engine.path: /usr/bin/python2</span></span>

<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span> a</span>

</div>

<p>It’s not uncommon to have various Python executables installed (different versions, in Conda/Mamba environments, etc.) on your system or to be unclear about which shell is being used to execute a shell chunk. Manually setting <code>engine.path</code> can help figure things out or work around problems.</p>

</section>

<h1>6) Embedding bash, Python, and Julia code</h1>

<p>Using code chunks from various languages, including bash, Python, and Julia is very similar to using R chunks. In addition, controlling and annotating chunks works the same.</p>

<p>A bash chunk:</p>

<pre><code>-rw-r--r-- 1 paciorek scfstaff 7088 Sep 28 15:20 test.html

-rw-r--r-- 1 paciorek scfstaff 1166 Sep 27 17:21 test.ipynb

-rw-r--r-- 1 paciorek scfstaff 7167 Jul 17 2015 test-line-formatting.Rnw

-rw-r--r-- 1 paciorek scfstaff 14477 Sep 28 15:19 test.pdf

-rw-r--r-- 1 paciorek scfstaff 64072 Sep 27 16:07 testq.html

-rw-r--r-- 1 paciorek scfstaff 419 Sep 28 15:19 test.qmd

-rw-r--r-- 1 paciorek scfstaff 387 Sep 27 17:22 test.qmd~

-rw-r--r-- 1 paciorek scfstaff 15865 Sep 27 16:05 testq.qmd

-rw------- 1 paciorek scfstaff 5285 Sep 28 15:16 test.tex~

test_files:

total 9

drwxr-sr-x 15 paciorek scfstaff 15 Sep 27 15:21 libs

testq_cache:

total 9

drwxr-sr-x 2 paciorek scfstaff 6 Sep 27 15:57 html

testq_files:

total 1

drwxr-sr-x 2 paciorek scfstaff 3 Sep 27 15:57 figure-html

drwxr-sr-x 5 paciorek scfstaff 5 Sep 27 16:07 libs

Filesystem Size Used Avail Use% Mounted on

/dev/sda2 59G 31G 26G 55% /

tmpfs 16G 406M 16G 3% /dev/shm

tmpfs 3.2G 26M 3.2G 1% /run

tmpfs 5.0M 4.0K 5.0M 1% /run/lock

/dev/sdb1 111G 4.6G 101G 5% /tmp

/dev/sda3 59G 12G 45G 21% /var

/dev/sda5 2.6T 180G 2.3T 8% /var/tmp

/dev/sda1 499M 6.1M 493M 2% /boot/efi

oz.berkeley.edu:/pool0/system 6.0T 3.9T 2.2T 65% /system

oz.berkeley.edu:/pool0/scratch 35T 33T 2.6T 93% /scratch

oz.berkeley.edu:/pool0/accounts 71T 8.1T 63T 12% /accounts

tmpfs 3.2G 300K 3.2G 1% /run/user/3189

/tmp</code></pre>

</div>

<p>Unfortunately, output from bash chunks occurs after all the code is printed. Also, state is not preserved between chunks.</p>

<p>We can see that state is not preserved here, where the current working directory is NOT the directory that we changed to in the chunk above.</p>

<div class="sourceCode cell-code" id="cb20"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="bu">pwd</span> <span class="co"># result would be /tmp if state were preserved </span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code>/accounts/vis/paciorek/staff/tutorials/tutorial-dynamic-docs</code></pre>

</div>

<p>Inline bash code won’t work: <code>bash wc demo.Rmd</code>, unlike with R code.</p>

<p>If you are using the <code>jupyter</code> engine and want to have both bash and Python chunks in a document, or you don’t want to have to install a bash Jupyter kernel, you can use ipython magic to run bash code within a Python chunk:</p>

<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="op">!</span>echo <span class="st">"hello from python"</span></span>

</div>

<p>One can also use <code>zsh</code> or other shell chunks, replacing the “bash” label with “zsh” or the other shell.</p>

</section>

<h2 class="anchored" data-anchor-id="embedding-python-code">6.2) Embedding Python code</h2>

<p>You can embed Python code. As with R, state is preserved so later chunks can use objects from earlier chunks.</p>

<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> numpy <span class="im">as</span> np</span>

<span id="cb23-2"><a href="#cb23-2" aria-hidden="true" tabindex="-1"></a>x <span class="op">=</span> np.array((<span class="dv">3</span>, <span class="dv">5</span>, <span class="dv">7</span>))</span>

<span id="cb23-3"><a href="#cb23-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(x.<span class="bu">sum</span>())</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>x.<span class="bu">min</span>() <span class="co"># this will print with more recent versions of rmarkdown </span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a> <span class="bu">print</span>(<span class="st">"state is preserved if we see the value of `x[2]` next"</span>)</span>

<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a> <span class="bu">print</span>(x[<span class="dv">2</span>])</span>

<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a><span class="cf">except</span> <span class="pp">NameError</span>:</span>

<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a> <span class="bu">print</span>(<span class="st">'state is not preserved: x does not exist'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code>state is preserved if we see the value of `x[2]` next

7</code></pre>

</div>

<p>When using the <code>jupyter</code> rendering engine, all output is printed after all the code from the chunk. When using <code>knitr</code> engine, output appears directly after the code producing the output. However, output appears after any comments that follow the code, which might not be what you want.</p>

<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="dv">1</span>)</span>

<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Whether "1" and "2" are printed after all the code or interspersed</span></span>

<span id="cb29-3"><a href="#cb29-3" aria-hidden="true" tabindex="-1"></a><span class="co"># depends on the engine used.</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<div class="sourceCode cell-code" id="cb31"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>There is no facility for inline Python code: <code>python print(3+5)</code></p>

<p>To display code from a file of Python code, you can use functionality in the <code>inspect</code> module. This code would display the definition of <code>doubled()</code> from the <code>my_code</code> module.</p>

<div class="sourceCode cell-code" id="cb33"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb33-1"><a href="#cb33-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> my_code</span>

<span id="cb33-2"><a href="#cb33-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> inspect</span>

<span id="cb33-3"><a href="#cb33-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(inspect.getsource(my_code.doubled))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>This will work for functions and for class definitions.</p>

</section>

<h2 class="anchored" data-anchor-id="embedding-julia-code">6.3) Embedding Julia code</h2>

<p>You can embed Julia code. As with R and Python, state is preserved so later chunks can use objects from earlier chunks.</p>

</div>

<span id="cb36-2"><a href="#cb36-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">println</span>(<span class="st">"state is preserved if we see the value of `x[2]` next"</span>)</span>

<span id="cb36-3"><a href="#cb36-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(x[<span class="fl">2</span>])</span>

<span id="cb36-4"><a href="#cb36-4" aria-hidden="true" tabindex="-1"></a>catch</span>

<span id="cb36-5"><a href="#cb36-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(<span class="st">"state is not preserved: x does not exist"</span>)</span>

<pre><code>state is preserved if we see the value of `x[2]` next

5</code></pre>

</div>

<p>There is no facility for inline Julia code: <code>julia print(3+5)</code></p>

</section>

<h1>7) Reading code from an external file</h1>

<p>It’s sometimes nice to draw code in from a separate file. Before invoking a chunk, we need to read the chunks from the source file, which contains the chunks tagged with some special formatting.</p>

<p>This only works with the <code>knitr</code> engine.</p>

<span id="cb38-2"><a href="#cb38-2" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: read-chunk</span></span>

<span id="cb38-3"><a href="#cb38-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>

<span id="cb38-4"><a href="#cb38-4" aria-hidden="true" tabindex="-1"></a><span class="fu">read_chunk</span>(<span class="st">'demo.R'</span>) <span class="do">## contains external_chunk_1 and external_chunk_2 of R code</span></span>

<span id="cb38-5"><a href="#cb38-5" aria-hidden="true" tabindex="-1"></a><span class="fu">read_chunk</span>(<span class="st">'demo.py'</span>) <span class="do">## contains external_chunk_3 of Python code</span></span>

</div>

<p>Note that a good place for reading the source file via <code>read_chunk()</code> is in an initial setup chunk at the beginning of the document.</p>

<p>Here are two R chunks whose code is in <code>demo.R</code>.</p>

</div>

</div>

<p>And here is a Python chunk whose code is in <code>demo.py</code>.</p>

<span id="cb43-2"><a href="#cb43-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(<span class="bu">len</span>(a))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>To display function or class definitions from a file of Python code, you can use functionality in the <code>inspect</code> module. This code would display the definition of <code>doubled()</code> from the <code>my_code</code> module.</p>

<div class="sourceCode cell-code" id="cb45"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb45-1"><a href="#cb45-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> my_code</span>

<span id="cb45-2"><a href="#cb45-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> inspect</span>

<span id="cb45-3"><a href="#cb45-3" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(inspect.getsource(my_code.doubled))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

</section>

<h1>8) Formatting of long lines of code and of output</h1>

<p>Having long lines be nicely formatted and other aspects of formatting can be a challenge. Also, results can differ depending on your output format (e.g., PDF vs. HTML). In general the code in this section will often overflow the page width in PDF but not in HTML, but even in the HTML the line breaks may be awkwardly positioned.</p>

<p>Here are some examples that overflow in PDF output.</p>

<div class="sourceCode cell-code" id="cb46"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb46-1"><a href="#cb46-1" aria-hidden="true" tabindex="-1"></a>b <span class="ot"><-</span> <span class="st">"Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively"</span></span>

<span id="cb46-2"><a href="#cb46-2" aria-hidden="true" tabindex="-1"></a><span class="do">## Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively</span></span>

<span id="cb46-4"><a href="#cb46-4" aria-hidden="true" tabindex="-1"></a><span class="do">## This should work to give decent formatting in HTML but doesn't in PDF.</span></span>

<pre><code>Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively</code></pre>

</div>

<div class="sourceCode cell-code" id="cb48"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb48-1"><a href="#cb48-1" aria-hidden="true" tabindex="-1"></a>vecWithALongName <span class="ot">=</span> <span class="fu">rnorm</span>(<span class="dv">100</span>)</span>

<span id="cb48-2"><a href="#cb48-2" aria-hidden="true" tabindex="-1"></a>a <span class="ot">=</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span> vecWithALongName <span class="sc">*</span> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>))</span>

<span id="cb48-3"><a href="#cb48-3" aria-hidden="true" tabindex="-1"></a>a <span class="ot">=</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName)) <span class="co"># this is a comment that goes over the line by a good long ways</span></span>

<span id="cb48-4"><a href="#cb48-4" aria-hidden="true" tabindex="-1"></a>a <span class="ot">=</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)) <span class="co"># this is a comment that goes over the line by a good long long long long long long long long ways</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>In contrast, long output is usually fine, even in PDF.</p>

<div class="sourceCode cell-code" id="cb49"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb49-1"><a href="#cb49-1" aria-hidden="true" tabindex="-1"></a><span class="fu">rnorm</span>(<span class="dv">30</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code> [1] -1.04437702 0.51995461 0.15155954 0.55836893 -1.87940055 -0.99908618

[7] -0.47083913 0.88461719 -2.47235000 1.55333948 1.41114869 1.91056609

[13] -0.62932679 1.22380063 1.12960580 -0.84659648 -0.65229492 1.83760743

[19] -1.32678114 0.50964439 -0.80747544 -0.03085863 -0.91200119 0.82473210

[25] 0.70518136 -0.84725563 -1.07806906 1.38768940 1.11856234 0.24872574</code></pre>

</div>

<p>Adding the <code>tidy: true</code> chunk option and setting the width (as shown in the Rmd version of this document) can help with long comment lines or lines of code, but doesn’t help for some of the cases above.</p>

<div class="sourceCode cell-code" id="cb51"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb51-1"><a href="#cb51-1" aria-hidden="true" tabindex="-1"></a><span class="do">## Long strings and long comments:</span></span>

<span id="cb51-3"><a href="#cb51-3" aria-hidden="true" tabindex="-1"></a>b <span class="ot"><-</span> <span class="st">"Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively"</span></span>

<span id="cb51-4"><a href="#cb51-4" aria-hidden="true" tabindex="-1"></a><span class="do">## Statistics at UC Berkeley: We are a community engaged in research and</span></span>

<span id="cb51-5"><a href="#cb51-5" aria-hidden="true" tabindex="-1"></a><span class="do">## education in probability and statistics. In addition to developing</span></span>

<span id="cb51-6"><a href="#cb51-6" aria-hidden="true" tabindex="-1"></a><span class="do">## fundamental theory and methodology, we are actively</span></span>

<span id="cb51-8"><a href="#cb51-8" aria-hidden="true" tabindex="-1"></a><span class="do">## This should work to give decent formatting in HTML but doesn't in PDF:</span></span>

</div>

<div class="sourceCode cell-code" id="cb53"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb53-1"><a href="#cb53-1" aria-hidden="true" tabindex="-1"></a><span class="do">## Now consider long lines of code:</span></span>

<span id="cb53-3"><a href="#cb53-3" aria-hidden="true" tabindex="-1"></a>vecWithALongName <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="dv">100</span>)</span>

<span id="cb53-4"><a href="#cb53-4" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span></span>

<span id="cb53-5"><a href="#cb53-5" aria-hidden="true" tabindex="-1"></a> vecWithALongName <span class="sc">*</span> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>))</span>

<span id="cb53-6"><a href="#cb53-6" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName)) <span class="co"># this is a comment that goes over the line by a good long ways</span></span>

<span id="cb53-7"><a href="#cb53-7" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span></span>

<span id="cb53-8"><a href="#cb53-8" aria-hidden="true" tabindex="-1"></a> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)) <span class="co"># this is a comment that goes over the line by a good long long long long long long long long ways</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>To address the problems seen above, sometimes you can format things manually for better results. You may need to tag the chunk with <code>tidy: false</code>, but I have not done that here.</p>

<div class="sourceCode cell-code" id="cb54"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb54-1"><a href="#cb54-1" aria-hidden="true" tabindex="-1"></a><span class="do">## Breaking up a string:</span></span>

<span id="cb54-3"><a href="#cb54-3" aria-hidden="true" tabindex="-1"></a>b <span class="ot"><-</span> <span class="st">"Statistics at UC Berkeley: We are a community engaged in research</span></span>

<span id="cb54-4"><a href="#cb54-4" aria-hidden="true" tabindex="-1"></a><span class="st"> and education in probability and statistics. In addition to developing </span></span>

<span id="cb54-5"><a href="#cb54-5" aria-hidden="true" tabindex="-1"></a><span class="st">fundamental theory and methodology, we are actively"</span></span>

<span id="cb54-7"><a href="#cb54-7" aria-hidden="true" tabindex="-1"></a><span class="do">## Breaking up a comment:</span></span>

<span id="cb54-9"><a href="#cb54-9" aria-hidden="true" tabindex="-1"></a><span class="do">## Statistics at UC Berkeley: We are a community engaged in research and </span></span>

<span id="cb54-10"><a href="#cb54-10" aria-hidden="true" tabindex="-1"></a><span class="do">## education in probability and statistics. In addition to developing </span></span>

<span id="cb54-11"><a href="#cb54-11" aria-hidden="true" tabindex="-1"></a><span class="do">## fundamental theory and methodology, we are actively</span></span>

<span id="cb54-13"><a href="#cb54-13" aria-hidden="true" tabindex="-1"></a><span class="do">## Breaking up code lines:</span></span>

<span id="cb54-15"><a href="#cb54-15" aria-hidden="true" tabindex="-1"></a>vecWithALongName <span class="ot">=</span> <span class="fu">rnorm</span>(<span class="dv">100</span>)</span>

<span id="cb54-16"><a href="#cb54-16" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span> </span>

<span id="cb54-17"><a href="#cb54-17" aria-hidden="true" tabindex="-1"></a> vecWithALongName <span class="sc">*</span> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>))</span>

<span id="cb54-18"><a href="#cb54-18" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName)) <span class="co"># this is a comment that </span></span>

<span id="cb54-20"><a href="#cb54-20" aria-hidden="true" tabindex="-1"></a>a <span class="ot"><-</span> <span class="fu">length</span>(<span class="fu">mean</span>(<span class="dv">5</span> <span class="sc">*</span> vecWithALongName <span class="sc">+</span> vecWithALongName <span class="sc">-</span> <span class="fu">exp</span>(vecWithALongName) <span class="sc">+</span> </span>

<span id="cb54-21"><a href="#cb54-21" aria-hidden="true" tabindex="-1"></a> vecWithALongName, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)) <span class="co"># this is a comment that goes over the line </span></span>

</div>

</section>

<p>In bash, we have similar problems with lines overflowing in PDF output, but bash allows us to use a backslash to break lines of code. However that strategy doesn’t help with long lines of output.</p>

<div class="sourceCode cell-code" id="cb55"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb55-1"><a href="#cb55-1" aria-hidden="true" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively"</span> <span class="op">></span> tmp.txt</span>

<span id="cb55-3"><a href="#cb55-3" aria-hidden="true" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"Second try: Statistics at UC Berkeley: We are a community engaged </span><span class="dt">\</span></span>

<span id="cb55-4"><a href="#cb55-4" aria-hidden="true" tabindex="-1"></a><span class="st">in research and education in probability and statistics. In addition to </span><span class="dt">\</span></span>

<span id="cb55-5"><a href="#cb55-5" aria-hidden="true" tabindex="-1"></a><span class="st">developing fundamental theory and methodology, we are actively"</span> <span class="dt">\</span></span>

<pre><code>Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively

Second try: Statistics at UC Berkeley: We are a community engaged in research and education in probability and statistics. In addition to developing fundamental theory and methodology, we are actively</code></pre>

</div>

<p>We also have problems with long comments, so we would need to manually format them.</p>

<p>Here is a long comment line that overflows in PDF:</p>

<div class="sourceCode cell-code" id="cb57"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb57-1"><a href="#cb57-1" aria-hidden="true" tabindex="-1"></a><span class="co"># asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

<p>Instead manually break the comment into multiple lines:</p>

<div class="sourceCode cell-code" id="cb58"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb58-1"><a href="#cb58-1" aria-hidden="true" tabindex="-1"></a><span class="co"># asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla </span></span>

<span id="cb58-2"><a href="#cb58-2" aria-hidden="true" tabindex="-1"></a><span class="co"># lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa </span></span>

<span id="cb58-3"><a href="#cb58-3" aria-hidden="true" tabindex="-1"></a><span class="co"># adlfjaf jkladf afdl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

</section>

<h2 class="anchored" data-anchor-id="python-code">8.3) Python code</h2>

<p>In Python, there is similar trouble with lines overflowing in PDF output too.</p>

<div class="sourceCode cell-code" id="cb59"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb59-1"><a href="#cb59-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This overflows the page:</span></span>

<span id="cb59-3"><a href="#cb59-3" aria-hidden="true" tabindex="-1"></a>b <span class="op">=</span> <span class="st">"asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl"</span></span>

<span id="cb59-4"><a href="#cb59-4" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(b)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code>asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl</code></pre>

</div>

<div class="sourceCode cell-code" id="cb61"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb61-1"><a href="#cb61-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This code overflows the page:</span></span>

<span id="cb61-3"><a href="#cb61-3" aria-hidden="true" tabindex="-1"></a>zoo <span class="op">=</span> {<span class="st">"lion"</span>: <span class="st">"Simba"</span>, <span class="st">"panda"</span>: <span class="va">None</span>, <span class="st">"whale"</span>: <span class="st">"Moby"</span>, <span class="st">"numAnimals"</span>: <span class="dv">3</span>, <span class="st">"bear"</span>: <span class="st">"Yogi"</span>, <span class="st">"killer whale"</span>: <span class="st">"shamu"</span>, <span class="st">"bunny:"</span>: <span class="st">"bugs"</span>}</span>

<span id="cb61-4"><a href="#cb61-4" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(zoo)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code>{'lion': 'Simba', 'panda': None, 'whale': 'Moby', 'numAnimals': 3, 'bear': 'Yogi', 'killer whale': 'shamu', 'bunny:': 'bugs'}</code></pre>

</div>

<p>To fix the issue, we can manually break the code into multiple lines, but long output still overflows.</p>

<div class="sourceCode cell-code" id="cb63"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb63-1"><a href="#cb63-1" aria-hidden="true" tabindex="-1"></a>zoo <span class="op">=</span> {<span class="st">"lion"</span>: <span class="st">"Simba"</span>, <span class="st">"panda"</span>: <span class="va">None</span>, <span class="st">"whale"</span>: <span class="st">"Moby"</span>, </span>

<span id="cb63-2"><a href="#cb63-2" aria-hidden="true" tabindex="-1"></a> <span class="st">"numAnimals"</span>: <span class="dv">3</span>, <span class="st">"bear"</span>: <span class="st">"Yogi"</span>, <span class="st">"killer whale"</span>: <span class="st">"shamu"</span>, </span>

<span id="cb63-3"><a href="#cb63-3" aria-hidden="true" tabindex="-1"></a> <span class="st">"bunny:"</span>: <span class="st">"bugs"</span>}</span>

<span id="cb63-4"><a href="#cb63-4" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(zoo)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

<pre><code>{'lion': 'Simba', 'panda': None, 'whale': 'Moby', 'numAnimals': 3, 'bear': 'Yogi', 'killer whale': 'shamu', 'bunny:': 'bugs'}</code></pre>

</div>

<p>Long comments overflow as well, but you can always manually break into multiple lines.</p>

<div class="sourceCode cell-code" id="cb65"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb65-1"><a href="#cb65-1" aria-hidden="true" tabindex="-1"></a><span class="co"># asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl</span></span>

<span id="cb65-3"><a href="#cb65-3" aria-hidden="true" tabindex="-1"></a><span class="co"># asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad</span></span>

<span id="cb65-4"><a href="#cb65-4" aria-hidden="true" tabindex="-1"></a><span class="co"># kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>

</div>

</section>

<h1>9) References</h1>

<p>We’ll just see how you use BibTeX style references. <span class="citation" data-cites="Bane:etal:2008">Banerjee et al. (<a href="#ref-Bane:etal:2008" role="doc-biblioref">2008</a>)</span> proposed a useful method. This was confirmed <span class="citation" data-cites="Cres:Joha:2008">(<a href="#ref-Cres:Joha:2008" role="doc-biblioref">Cressie and Johannesson 2008</a>)</span>.</p>

<p>Note the indication of the <code>refs.bib</code> file in the initial lines of this document so that the bibliographic information for these citations can be found.</p>

<p>The list of references is placed at the end of the document. You’d presumably want a section header like this:</p>

</section>

</section>

<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography"><h2 class="anchored quarto-appendix-heading">Literature cited</h2><div id="refs" class="references csl-bib-body hanging-indent" role="list">

Banerjee, S., A. E. Gelfand, A. O. Finley, and H. Sang. 2008. <span>“Gaussian Predictive Process Models for Large Spatial Data Sets.”</span> <em>Journal of the Royal Statistical Society B</em> 70 (4): 825–48.

</div>

Cressie, N., and G. Johannesson. 2008. <span>“Fixed Rank Kriging for Very Large Spatial Data Sets.”</span> <em>Journal of the Royal Statistical Society B</em> 70 (1): 209–26.

</div>

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