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Condors.pdf
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<title>report</title>
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<section id="condor-populations-project-3" class="level1">
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<h1>Condor Populations Project 3</h1>
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<p>Michael Thomas, Emily, Menna</p>
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<div class="cell">
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<div class="sourceCode cell-code" 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">source</span>(<span class="st">"project.R"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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</div>
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<section id="part-a.-suppose-year-1-immature-and-adult-birds-have-the-same-mortality-rate-0.086." class="level2">
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<h2 class="anchored" data-anchor-id="part-a.-suppose-year-1-immature-and-adult-birds-have-the-same-mortality-rate-0.086.">Part A. Suppose year 1, immature, and adult birds have the same mortality rate, 0.086.</h2>
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<div class="cell">
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<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">simulate_condor_population</span>(<span class="fl">0.086</span>, <span class="fl">0.086</span>, <span class="fl">0.086</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output-display">
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<div>
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<figure class="figure">
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<p><img src="Report_files/figure-html/unnamed-chunk-2-1.png" class="img-fluid figure-img" width="672"></p>
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</figure>
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</div>
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</div>
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</div>
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</section>
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<section id="part-b.-suppose-year-1-and-immature-birds-have-a-mortality-rate-of-0.138-while-adult-condors-have-a-mortality-of-half-that-amount-0.069." class="level2">
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<h2 class="anchored" data-anchor-id="part-b.-suppose-year-1-and-immature-birds-have-a-mortality-rate-of-0.138-while-adult-condors-have-a-mortality-of-half-that-amount-0.069.">Part B. Suppose year 1 and immature birds have a mortality rate of 0.138, while adult condors have a mortality of half that amount, 0.069.</h2>
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<div class="cell">
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<div class="sourceCode cell-code" 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">simulate_condor_population</span>(<span class="fl">0.138</span>, <span class="fl">0.138</span>, <span class="fl">0.069</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output-display">
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<div>
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<figure class="figure">
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<p><img src="Report_files/figure-html/unnamed-chunk-3-1.png" class="img-fluid figure-img" width="672"></p>
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</figure>
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</div>
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</div>
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</div>
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</section>
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<section id="part-c.-bustamante-1996-found-a-mortality-of-65.9-for-year-1-bearded-vultures.-use-this-mortality-and-immature-and-adult-mortality-of-0.086." class="level2">
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<h2 class="anchored" data-anchor-id="part-c.-bustamante-1996-found-a-mortality-of-65.9-for-year-1-bearded-vultures.-use-this-mortality-and-immature-and-adult-mortality-of-0.086.">Part C. (Bustamante 1996) found a mortality of 65.9% for year-1 bearded vultures. Use this mortality and immature and adult mortality of 0.086.</h2>
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<div class="cell">
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<div class="sourceCode cell-code" 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">simulate_condor_population</span>(<span class="fl">0.659</span>, <span class="fl">0.086</span>, <span class="fl">0.086</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output-display">
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<div>
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<figure class="figure">
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<p><img src="Report_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid figure-img" width="672"></p>
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</figure>
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<section id="part-d.-consider-year-1-immature-and-adult-mortalities-of-0.659-0.138-and-0.069-respectively." class="level2">
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<h2 class="anchored" data-anchor-id="part-d.-consider-year-1-immature-and-adult-mortalities-of-0.659-0.138-and-0.069-respectively.">Part D. Consider year 1, immature, and adult mortalities of 0.659, 0.138, and 0.069, respectively.</h2>
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<div class="cell">
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<div class="sourceCode cell-code" 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">simulate_condor_population</span>(<span class="fl">0.659</span>, <span class="fl">0.138</span>, <span class="fl">0.069</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<figure class="figure">
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<p><img src="Report_files/figure-html/unnamed-chunk-5-1.png" class="img-fluid figure-img" width="672"></p>
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</figure>
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<section id="part-e.-consider-year-1-immature-and-adult-mortalities-of-0.659-0.099-and-0.099-respectively." class="level2">
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<h2 class="anchored" data-anchor-id="part-e.-consider-year-1-immature-and-adult-mortalities-of-0.659-0.099-and-0.099-respectively.">Part E. Consider year 1, immature, and adult mortalities of 0.659, 0.099, and 0.099, respectively.</h2>
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<div class="cell">
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<div class="sourceCode cell-code" 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">simulate_condor_population</span>(<span class="fl">0.659</span>, <span class="fl">0.099</span>, <span class="fl">0.099</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div>
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<p><img src="Report_files/figure-html/unnamed-chunk-6-1.png" class="img-fluid figure-img" width="672"></p>
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</figure>
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<section id="part-f.-under-the-assumptions-of-part-d-suppose-that-a-program-of-double-clutching-persists-for-five-years.-afterwards-all-captive-birds-are-returned-to-the-wild.-compare-the-number-of-wild-condors-for-this-scenario-to-that-in-part-d." class="level2">
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<h2 class="anchored" data-anchor-id="part-f.-under-the-assumptions-of-part-d-suppose-that-a-program-of-double-clutching-persists-for-five-years.-afterwards-all-captive-birds-are-returned-to-the-wild.-compare-the-number-of-wild-condors-for-this-scenario-to-that-in-part-d.">Part F. Under the assumptions of Part d, suppose that a program of double-clutching persists for five years. Afterwards, all captive birds are returned to the wild. Compare the number of wild condors for this scenario to that in Part d. </h2>
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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);
|
||||||
|
if (note) {
|
||||||
|
return note.innerHTML;
|
||||||
|
} else {
|
||||||
|
return "";
|
||||||
|
}
|
||||||
|
});
|
||||||
|
}
|
||||||
|
const xrefs = window.document.querySelectorAll('a.quarto-xref');
|
||||||
|
const processXRef = (id, note) => {
|
||||||
|
// Strip column container classes
|
||||||
|
const stripColumnClz = (el) => {
|
||||||
|
el.classList.remove("page-full", "page-columns");
|
||||||
|
if (el.children) {
|
||||||
|
for (const child of el.children) {
|
||||||
|
stripColumnClz(child);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
stripColumnClz(note)
|
||||||
|
if (id === null || id.startsWith('sec-')) {
|
||||||
|
// Special case sections, only their first couple elements
|
||||||
|
const container = document.createElement("div");
|
||||||
|
if (note.children && note.children.length > 2) {
|
||||||
|
container.appendChild(note.children[0].cloneNode(true));
|
||||||
|
for (let i = 1; i < note.children.length; i++) {
|
||||||
|
const child = note.children[i];
|
||||||
|
if (child.tagName === "P" && child.innerText === "") {
|
||||||
|
continue;
|
||||||
|
} else {
|
||||||
|
container.appendChild(child.cloneNode(true));
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (window.Quarto?.typesetMath) {
|
||||||
|
window.Quarto.typesetMath(container);
|
||||||
|
}
|
||||||
|
return container.innerHTML
|
||||||
|
} else {
|
||||||
|
if (window.Quarto?.typesetMath) {
|
||||||
|
window.Quarto.typesetMath(note);
|
||||||
|
}
|
||||||
|
return note.innerHTML;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
// Remove any anchor links if they are present
|
||||||
|
const anchorLink = note.querySelector('a.anchorjs-link');
|
||||||
|
if (anchorLink) {
|
||||||
|
anchorLink.remove();
|
||||||
|
}
|
||||||
|
if (window.Quarto?.typesetMath) {
|
||||||
|
window.Quarto.typesetMath(note);
|
||||||
|
}
|
||||||
|
// TODO in 1.5, we should make sure this works without a callout special case
|
||||||
|
if (note.classList.contains("callout")) {
|
||||||
|
return note.outerHTML;
|
||||||
|
} else {
|
||||||
|
return note.innerHTML;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
for (var i=0; i<xrefs.length; i++) {
|
||||||
|
const xref = xrefs[i];
|
||||||
|
tippyHover(xref, undefined, function(instance) {
|
||||||
|
instance.disable();
|
||||||
|
let url = xref.getAttribute('href');
|
||||||
|
let hash = undefined;
|
||||||
|
if (url.startsWith('#')) {
|
||||||
|
hash = url;
|
||||||
|
} else {
|
||||||
|
try { hash = new URL(url).hash; } catch {}
|
||||||
|
}
|
||||||
|
if (hash) {
|
||||||
|
const id = hash.replace(/^#\/?/, "");
|
||||||
|
const note = window.document.getElementById(id);
|
||||||
|
if (note !== null) {
|
||||||
|
try {
|
||||||
|
const html = processXRef(id, note.cloneNode(true));
|
||||||
|
instance.setContent(html);
|
||||||
|
} finally {
|
||||||
|
instance.enable();
|
||||||
|
instance.show();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
// See if we can fetch this
|
||||||
|
fetch(url.split('#')[0])
|
||||||
|
.then(res => res.text())
|
||||||
|
.then(html => {
|
||||||
|
const parser = new DOMParser();
|
||||||
|
const htmlDoc = parser.parseFromString(html, "text/html");
|
||||||
|
const note = htmlDoc.getElementById(id);
|
||||||
|
if (note !== null) {
|
||||||
|
const html = processXRef(id, note);
|
||||||
|
instance.setContent(html);
|
||||||
|
}
|
||||||
|
}).finally(() => {
|
||||||
|
instance.enable();
|
||||||
|
instance.show();
|
||||||
|
});
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
// See if we can fetch a full url (with no hash to target)
|
||||||
|
// This is a special case and we should probably do some content thinning / targeting
|
||||||
|
fetch(url)
|
||||||
|
.then(res => res.text())
|
||||||
|
.then(html => {
|
||||||
|
const parser = new DOMParser();
|
||||||
|
const htmlDoc = parser.parseFromString(html, "text/html");
|
||||||
|
const note = htmlDoc.querySelector('main.content');
|
||||||
|
if (note !== null) {
|
||||||
|
// This should only happen for chapter cross references
|
||||||
|
// (since there is no id in the URL)
|
||||||
|
// remove the first header
|
||||||
|
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
|
||||||
|
note.children[0].remove();
|
||||||
|
}
|
||||||
|
const html = processXRef(null, note);
|
||||||
|
instance.setContent(html);
|
||||||
|
}
|
||||||
|
}).finally(() => {
|
||||||
|
instance.enable();
|
||||||
|
instance.show();
|
||||||
|
});
|
||||||
|
}
|
||||||
|
}, function(instance) {
|
||||||
|
});
|
||||||
|
}
|
||||||
|
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";
|
||||||
|
div.style.left = 0;
|
||||||
|
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;
|
||||||
|
};
|
||||||
|
// Handle positioning of the toggle
|
||||||
|
window.addEventListener(
|
||||||
|
"resize",
|
||||||
|
throttle(() => {
|
||||||
|
elRect = undefined;
|
||||||
|
if (selectedAnnoteEl) {
|
||||||
|
selectCodeLines(selectedAnnoteEl);
|
||||||
|
}
|
||||||
|
}, 10)
|
||||||
|
);
|
||||||
|
function throttle(fn, ms) {
|
||||||
|
let throttle = false;
|
||||||
|
let timer;
|
||||||
|
return (...args) => {
|
||||||
|
if(!throttle) { // first call gets through
|
||||||
|
fn.apply(this, args);
|
||||||
|
throttle = true;
|
||||||
|
} else { // all the others get throttled
|
||||||
|
if(timer) clearTimeout(timer); // cancel #2
|
||||||
|
timer = setTimeout(() => {
|
||||||
|
fn.apply(this, args);
|
||||||
|
timer = throttle = false;
|
||||||
|
}, ms);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
}
|
||||||
|
// 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>
|
||||||
39
Report.qmd
Normal file
39
Report.qmd
Normal file
|
|
@ -0,0 +1,39 @@
|
||||||
|
# Condor Populations Project 3
|
||||||
|
|
||||||
|
Emily Fowler, Menna Ellaqanny, Michael Thomas
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
source("project.R")
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part A. Suppose year 1, immature, and adult birds have the same mortality rate, 0.086.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
simulate_condor_population(0.086, 0.086, 0.086)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part B. Suppose year 1 and immature birds have a mortality rate of 0.138, while adult condors have a mortality of half that amount, 0.069.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
simulate_condor_population(0.138, 0.138, 0.069)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part C. (Bustamante 1996) found a mortality of 65.9% for year-1 bearded vultures. Use this mortality and immature and adult mortality of 0.086.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
simulate_condor_population(0.659, 0.086, 0.086)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part D. Consider year 1, immature, and adult mortalities of 0.659, 0.138, and 0.069, respectively.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
simulate_condor_population(0.659, 0.138, 0.069)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part E. Consider year 1, immature, and adult mortalities of 0.659, 0.099, and 0.099, respectively.
|
||||||
|
|
||||||
|
```{r}
|
||||||
|
simulate_condor_population(0.659, 0.099, 0.099)
|
||||||
|
```
|
||||||
|
|
||||||
|
## Part F. Under the assumptions of Part d, suppose that a program of double-clutching persists for five years. Afterwards, all captive birds are returned to the wild. Compare the number of wild condors for this scenario to that in Part d.
|
||||||
102
project.R
Normal file
102
project.R
Normal file
|
|
@ -0,0 +1,102 @@
|
||||||
|
####################
|
||||||
|
# Global Constants #
|
||||||
|
####################
|
||||||
|
|
||||||
|
# age at which birds in captivity begin breeding (become adults)
|
||||||
|
captive_begin_breeding <- 7
|
||||||
|
# age at which birds in the wild begin breeding (become adults)
|
||||||
|
wild_begin_breeding <- 8
|
||||||
|
# if the captive population exceeds this amount, then the entire year one
|
||||||
|
# population will be released
|
||||||
|
max_in_captivity <- 150
|
||||||
|
# carrying capacity in the wild
|
||||||
|
wild_carrying_capacity <- 400
|
||||||
|
# percentage of children which will make it to year 1 in captivity,
|
||||||
|
# per mating pair
|
||||||
|
captive_productivity_rate <- 0.9
|
||||||
|
# percentage of children which will make it to year 1 in captivity,
|
||||||
|
# per mating pair (with double clutching)
|
||||||
|
captive_productivity_rate_dc <- 1.8
|
||||||
|
# percentage of children which will make it to year 1, per mating pair
|
||||||
|
wild_productivity_rate <- 0.3729
|
||||||
|
|
||||||
|
################################
|
||||||
|
# Global Simulation Parameters #
|
||||||
|
################################
|
||||||
|
|
||||||
|
# number of years to simulate
|
||||||
|
simulation_years <- 50
|
||||||
|
|
||||||
|
######################
|
||||||
|
# Derived Parameters #
|
||||||
|
######################
|
||||||
|
|
||||||
|
# rate at which captive immature birds will become adults
|
||||||
|
# an approximation which assumes an equal distribution of immature bird ages
|
||||||
|
captive_immature_to_adult_rate <- 1 / (captive_begin_breeding - 2)
|
||||||
|
# rate at which wild immature birds will become adults
|
||||||
|
# an approximation which assumes an equal distribution of immature bird ages
|
||||||
|
wild_immature_to_adult_rate <- 1 / (wild_begin_breeding - 2)
|
||||||
|
|
||||||
|
# Simulates the Condor population over time using the given parameters.
|
||||||
|
# * `rd1` - death rate of year one birds
|
||||||
|
# * `rdI` - death rate of immature birds
|
||||||
|
# * `rdA` - death rate of adult birds
|
||||||
|
simulate_condor_population <- function(rd1, rdI, rdA) {
|
||||||
|
# captive population groups
|
||||||
|
c_Y0 <- c(10)
|
||||||
|
c_Y1 <- c(10)
|
||||||
|
c_I <- c(10)
|
||||||
|
c_A <- c(10)
|
||||||
|
|
||||||
|
# wild population groups
|
||||||
|
w_Y0 <- c()
|
||||||
|
w_Y1 <- c()
|
||||||
|
w_I <- c()
|
||||||
|
w_A <- c()
|
||||||
|
|
||||||
|
years <- seq(1, simulation_years)
|
||||||
|
|
||||||
|
for (t in 2:simulation_years) {
|
||||||
|
# model captive population changes (year 1, immature, and adult)
|
||||||
|
c_Y1[t] <- c_Y0[t - 1] - # last year's population
|
||||||
|
rd1 * c_Y0[t - 1] # outflow to deaths
|
||||||
|
|
||||||
|
c_I[t] <- c_I[t - 1] - # last year's population
|
||||||
|
rdI * c_I[t - 1] - # outflow to deaths
|
||||||
|
captive_immature_to_adult_rate * c_I[t - 1] + # outflow to adult
|
||||||
|
c_Y1[t - 1] # inflow from year 1
|
||||||
|
|
||||||
|
c_A[t] <- c_A[t - 1] - # last year's population
|
||||||
|
rdA * c_A[t - 1] + # outflow to deaths
|
||||||
|
captive_immature_to_adult_rate * c_I[t - 1] # inflow from immature
|
||||||
|
|
||||||
|
# model new births in captive population
|
||||||
|
c_Y0[t] <- captive_productivity_rate * (c_A[t] / 2)
|
||||||
|
|
||||||
|
# sum of all population groups
|
||||||
|
captive_population <- c_Y0[t] + c_Y1[t] + c_I[t] + c_A[t]
|
||||||
|
released_to_wild <- if (captive_population > max_in_captivity) {
|
||||||
|
c_Y1[t]
|
||||||
|
} else {
|
||||||
|
0.8 * c_Y1[t]
|
||||||
|
}
|
||||||
|
# subtract the released birds from the captive year one population
|
||||||
|
c_Y1[t] <- c_Y1[t] - released_to_wild
|
||||||
|
}
|
||||||
|
|
||||||
|
captive_population <- c_Y0 + c_Y1 + c_I + c_A
|
||||||
|
plot(
|
||||||
|
years,
|
||||||
|
c_Y0,
|
||||||
|
ylim = c(0, 50),
|
||||||
|
col = "red",
|
||||||
|
main = "Condor Population in Captivity",
|
||||||
|
xlab = "Time (years)",
|
||||||
|
ylab = "Population"
|
||||||
|
)
|
||||||
|
points(years, c_Y1, col = "orange")
|
||||||
|
points(years, c_I, col = "darkgreen")
|
||||||
|
points(years, c_A, col = "blue")
|
||||||
|
points(years, captive_population)
|
||||||
|
}
|
||||||
Loading…
Reference in a new issue