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<!DOCTYPE html>
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<title>gretlR: A Seamless Integration of Gretl and R</title>
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<h1 class="title">gretlR: A Seamless Integration of Gretl and R</h1>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Sagiru Mati </p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">June 14, 2020</p>
</div>
</div>
</div>
</header>
<section id="about-gretlr" class="level1">
<h1>About gretlR</h1>
<p>gretlR is an R package that can run <code>gretl</code> program from R Markdown.</p>
</section>
<section id="installation" class="level1">
<h1>Installation</h1>
<p>gretlR can be installed using the following commands in R.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"gretlR"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> OR</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">'sagirumati/gretlR'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="usage" class="level1">
<h1>Usage</h1>
<p>Please load the gretlR package as follows:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>::: {.cell}</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="in">````{.cell-code}</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>```<span class="op">{</span>r gretlR<span class="op">}</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>library<span class="op">(</span>gretlR<span class="op">)</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>```</span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="in">````</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>:::</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Then create a chunk for <code>gretl</code> as shown below:</p>
<p>The above chunk creates a gretl program with the chunk’s content, then automatically run the gretl script, which will save gretl outputs in the new folder <code>gretlR</code> created in the current working directory.</p>
</section>
<section id="include_graph-function" class="level1">
<h1>include_graph function</h1>
<p>We can <em>dynamically and reproducibly</em> fetch the <code>gretl</code> graph object we created with the <code>gretl</code> chunk using the following R chunk:</p>
<p>For the scatter graph:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">include_graph</span>(<span class="at">chunk =</span> <span class="st">"gretlR"</span>,<span class="at">graph =</span> <span class="st">"scatter.png"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br><br><br><br></p>
<p>or the line graph:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">include_graph</span>(<span class="at">chunk =</span> <span class="st">"gretlR"</span>,<span class="at">graph =</span> <span class="st">"line.png"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="include_tex-function" class="level1">
<h1>include_tex function</h1>
<p>we can also include the equation of the OLS generated by the <code>gretl</code> chunk and save as <code>olsEquation.tex</code>.</p>
<p>If the output is <code>pdf</code>, one can use the raw <code>LaTeX</code> codes as follows:</p>
<p><code>\input{gretlr/gretlR/olsEquation.tex}</code></p>
<p>Or use <code>include_tex</code> function to include the equation as shown below:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">include_tex</span>(<span class="at">chunk =</span> <span class="st">"gretlR"</span>,<span class="at">tex =</span> <span class="st">"olsEquation"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">include_tex</span>(<span class="at">chunk =</span> <span class="st">"gretlR"</span>,<span class="at">tex =</span> <span class="st">"olsTAble"</span>,<span class="at">start =</span> <span class="dv">7</span>,<span class="at">end =</span> <span class="dv">24</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p><br><br><br><br></p>
<p>The OLS table output is saved by the <code>gretl</code> chunk as <code>olsTable.Rmd</code>. The entire OLS table output can included as child document as follows:</p>
</section>
<section id="import_kable-function" class="level1">
<h1>import_kable function</h1>
<p>The <code>gretl</code> chunk also saves the OSL table as <code>olsTable.csv</code>. The <code>import_kable</code> function can be used to import it as a table. further customisation can be done with <code>kableExtra</code> package.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">import_kable</span>(<span class="at">chunk =</span> <span class="st">"gretlR"</span>,<span class="at">file =</span> <span class="st">"olsTAble.csv"</span>,<span class="at">caption=</span><span class="st">"Table generated from gretl </span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="st"> chunk"</span>, <span class="at">start=</span><span class="dv">3</span>,<span class="at">end=</span><span class="dv">7</span>,<span class="at">digits=</span><span class="dv">2</span>) <span class="sc">|></span> </span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a>kableExtra<span class="sc">::</span><span class="fu">kable_styling</span>(<span class="at">latex_options =</span> <span class="fu">c</span>(<span class="st">"basic"</span>,<span class="st">"hold_position"</span>,<span class="st">"scale_down"</span>)) <span class="sc">|></span> </span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a> kableExtra<span class="sc">::</span><span class="fu">row_spec</span>(<span class="dv">0</span>,<span class="at">bold=</span>T)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="write_inp-function" class="level1">
<h1>write_inp function</h1>
<p>This function writes <code>gretl</code> file.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>code<span class="ot">=</span>r<span class="st">'(nulldata 500</span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="st">set seed 13</span></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="st">gretl1 = normal()</span></span>
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a><span class="st">gretl2 = normal()</span></span>
<span id="cb8-5"><a href="#cb8-5" aria-hidden="true" tabindex="-1"></a><span class="st">setobs 12 1980:01 --time-series</span></span>
<span id="cb8-6"><a href="#cb8-6" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl1 --time-series --with-lines --output="line.png"</span></span>
<span id="cb8-7"><a href="#cb8-7" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl2 gretl1 --output="scatter.png"</span></span>
<span id="cb8-8"><a href="#cb8-8" aria-hidden="true" tabindex="-1"></a><span class="st">)'</span></span>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true" tabindex="-1"></a><span class="fu">write_inp</span>(code,<span class="at">path=</span><span class="st">"gretlCodes"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="exec_inp-function" class="level1">
<h1>exec_inp function</h1>
<p>This function executes existing <code>gretl</code> files.</p>
<div class="sourceCode" 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>code<span class="ot">=</span>r<span class="st">'(nulldata 500</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="st">set seed 13</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="st">gretl1 = normal()</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="st">gretl2 = normal()</span></span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="st">setobs 12 1980:01 --time-series</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl1 --time-series --with-lines --output="line.png"</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl2 gretl1 --output="scatter.png"</span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="st"> )'</span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="fu">write_inp</span>(code,<span class="at">path=</span><span class="st">"SomeFolder/gretlCodes"</span>)</span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="fu">exec_inp</span>(<span class="st">"someFolder/gretlCodes"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="exec_gretl-function" class="level1">
<h1>exec_gretl function</h1>
<p>This function creates <code>gretl</code>file from R object or a set of character strings and executes it. It is a combination of <code>write_inp</code> and <code>exec_inp</code> functions.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>code<span class="ot">=</span>r<span class="st">'(nulldata 500</span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="st">set seed 13</span></span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="st">gretl1 = normal()</span></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="st">gretl2 = normal()</span></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="st">setobs 12 1980:01 --time-series</span></span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl1 --time-series --with-lines --output="line.png"</span></span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="st">gnuplot gretl2 gretl1 --output="scatter.png"</span></span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="st"> )'</span></span>
<span id="cb10-9"><a href="#cb10-9" aria-hidden="true" tabindex="-1"></a><span class="fu">exec_gretl</span>(code)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="demo" class="level1">
<h1>Demo</h1>
<p>Demo can be accessed via <code>demo(package="gretlR")</code>.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">demo</span>(exec_inp) </span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a><span class="fu">demo</span>(write_inp)</span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a><span class="fu">demo</span>(exec_gretl)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</section>
<section id="r-markdown-template" class="level1">
<h1>R Markdown template</h1>
<p>The R Markdown template for the <code>gretlR</code> can be accessed via <code>file -> New File -> R Markdown -> From Template -> gretlR</code></p>
<p><br><br><br><br></p>
<p>Please download a set of example files from <a href="https://github.com/sagirumati/gretlR/tree/master/inst/examples/">Github</a>.</p>
</section>
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return true;
}
}
return false;
}
const clipboard = new window.ClipboardJS('.code-copy-button', {
text: function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>