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# Preface {-}

This book is designed as the lecture notes and textbook for
This book is designed as the supporting textbook for
[BIOF1001: Introduction to Biomedical Data Science](),
an undergraduate course (Year 1) at the University of Hong Kong.

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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 5 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies</title>
<meta name="description" content="This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook." />
<meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />

<meta property="og:title" content="Chapter 5 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies" />
<meta property="og:type" content="book" />
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<meta name="author" content="BIOF1001 teaching team" />


<meta name="date" content="2024-08-29" />
<meta name="date" content="2024-09-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="6.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>6.1.2</b> Statistical analysis</a></li>
<li class="chapter" data-level="6.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>6.1.3</b> Literature search</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a></li>
<li class="chapter" data-level="6.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.3</b> 1. Scenario</a></li>
<li class="chapter" data-level="6.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.4</b> 2. Hong Kong population</a>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a>
<ul>
<li class="chapter" data-level="6.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>6.4.1</b> Download population data</a></li>
<li class="chapter" data-level="6.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>6.4.2</b> Format data for plotting</a></li>
<li class="chapter" data-level="6.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>6.4.3</b> Plotting population data</a></li>
<li class="chapter" data-level="6.2.1" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.2.1</b> Scenario</a></li>
<li class="chapter" data-level="6.2.2" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.2.2</b> Hong Kong population</a></li>
<li class="chapter" data-level="6.2.3" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.2.3</b> Cancer registry data</a></li>
<li class="chapter" data-level="6.2.4" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.2.4</b> Existing cancer funding and publication data</a></li>
<li class="chapter" data-level="6.2.5" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.2.5</b> Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="6.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.5</b> 3. Cancer registry data</a>
<ul>
<li class="chapter" data-level="6.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>6.5.1</b> Download cancer registry data</a></li>
<li class="chapter" data-level="6.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>6.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
<li class="chapter" data-level="6.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>6.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
<li class="chapter" data-level="6.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>6.5.4</b> 3c. Mortality-incidence ratio</a></li>
<li class="chapter" data-level="6.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>6.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
<li class="chapter" data-level="6.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>6.5.6</b> 3e. Childhood versus elderly cancers</a></li>
</ul></li>
<li class="chapter" data-level="6.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.6</b> 4. Existing cancer funding and publication data</a>
<ul>
<li class="chapter" data-level="6.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>6.6.1</b> Download HMRF grants and Pubmed data</a></li>
<li class="chapter" data-level="6.6.2" data-path="cancer.html"><a href="cancer.html#make-word-cloud-for-grants"><i class="fa fa-check"></i><b>6.6.2</b> Make word cloud for grants</a></li>
<li class="chapter" data-level="6.6.3" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>6.6.3</b> Make compare grant funding with incidence and mortality</a></li>
</ul></li>
<li class="chapter" data-level="6.7" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.7</b> 5. Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>7</b> Population Genetics and Diseases</a>
<ul>
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Biomedical Data Science - introduction with case studies</title>
<meta name="description" content="This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook." />
<meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />

<meta property="og:title" content="Biomedical Data Science - introduction with case studies" />
<meta property="og:type" content="book" />
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<meta name="author" content="BIOF1001 teaching team" />


<meta name="date" content="2024-08-29" />
<meta name="date" content="2024-09-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="6.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>6.1.2</b> Statistical analysis</a></li>
<li class="chapter" data-level="6.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>6.1.3</b> Literature search</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a></li>
<li class="chapter" data-level="6.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.3</b> 1. Scenario</a></li>
<li class="chapter" data-level="6.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.4</b> 2. Hong Kong population</a>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a>
<ul>
<li class="chapter" data-level="6.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>6.4.1</b> Download population data</a></li>
<li class="chapter" data-level="6.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>6.4.2</b> Format data for plotting</a></li>
<li class="chapter" data-level="6.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>6.4.3</b> Plotting population data</a></li>
<li class="chapter" data-level="6.2.1" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.2.1</b> Scenario</a></li>
<li class="chapter" data-level="6.2.2" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.2.2</b> Hong Kong population</a></li>
<li class="chapter" data-level="6.2.3" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.2.3</b> Cancer registry data</a></li>
<li class="chapter" data-level="6.2.4" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.2.4</b> Existing cancer funding and publication data</a></li>
<li class="chapter" data-level="6.2.5" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.2.5</b> Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="6.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.5</b> 3. Cancer registry data</a>
<ul>
<li class="chapter" data-level="6.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>6.5.1</b> Download cancer registry data</a></li>
<li class="chapter" data-level="6.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>6.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
<li class="chapter" data-level="6.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>6.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
<li class="chapter" data-level="6.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>6.5.4</b> 3c. Mortality-incidence ratio</a></li>
<li class="chapter" data-level="6.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>6.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
<li class="chapter" data-level="6.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>6.5.6</b> 3e. Childhood versus elderly cancers</a></li>
</ul></li>
<li class="chapter" data-level="6.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.6</b> 4. Existing cancer funding and publication data</a>
<ul>
<li class="chapter" data-level="6.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>6.6.1</b> Download HMRF grants and Pubmed data</a></li>
<li class="chapter" data-level="6.6.2" data-path="cancer.html"><a href="cancer.html#make-word-cloud-for-grants"><i class="fa fa-check"></i><b>6.6.2</b> Make word cloud for grants</a></li>
<li class="chapter" data-level="6.6.3" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>6.6.3</b> Make compare grant funding with incidence and mortality</a></li>
</ul></li>
<li class="chapter" data-level="6.7" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.7</b> 5. Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>7</b> Population Genetics and Diseases</a>
<ul>
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<div id="header">
<h1 class="title">Biomedical Data Science - introduction with case studies</h1>
<p class="author"><em>BIOF1001 teaching team</em></p>
<p class="date"><em>2024-08-29</em></p>
<p class="date"><em>2024-09-01</em></p>
</div>
<div id="welcome" class="section level1 unnumbered hasAnchor">
<h1>Welcome<a href="index.html#welcome" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Appendix A: Install R &amp; RStudio | Biomedical Data Science - introduction with case studies</title>
<meta name="description" content="This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook." />
<meta name="generator" content="bookdown 0.35 and GitBook 2.6.7" />
<meta name="generator" content="bookdown 0.40 and GitBook 2.6.7" />

<meta property="og:title" content="Appendix A: Install R &amp; RStudio | Biomedical Data Science - introduction with case studies" />
<meta property="og:type" content="book" />
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<meta name="author" content="BIOF1001 teaching team" />


<meta name="date" content="2024-08-29" />
<meta name="date" content="2024-09-01" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<li class="chapter" data-level="6.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>6.1.2</b> Statistical analysis</a></li>
<li class="chapter" data-level="6.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>6.1.3</b> Literature search</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a></li>
<li class="chapter" data-level="6.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.3</b> 1. Scenario</a></li>
<li class="chapter" data-level="6.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.4</b> 2. Hong Kong population</a>
<li class="chapter" data-level="6.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>6.2</b> Case study 2: Cancer Epidemiology</a>
<ul>
<li class="chapter" data-level="6.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>6.4.1</b> Download population data</a></li>
<li class="chapter" data-level="6.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>6.4.2</b> Format data for plotting</a></li>
<li class="chapter" data-level="6.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>6.4.3</b> Plotting population data</a></li>
<li class="chapter" data-level="6.2.1" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>6.2.1</b> Scenario</a></li>
<li class="chapter" data-level="6.2.2" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>6.2.2</b> Hong Kong population</a></li>
<li class="chapter" data-level="6.2.3" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.2.3</b> Cancer registry data</a></li>
<li class="chapter" data-level="6.2.4" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.2.4</b> Existing cancer funding and publication data</a></li>
<li class="chapter" data-level="6.2.5" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.2.5</b> Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="6.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>6.5</b> 3. Cancer registry data</a>
<ul>
<li class="chapter" data-level="6.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>6.5.1</b> Download cancer registry data</a></li>
<li class="chapter" data-level="6.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>6.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
<li class="chapter" data-level="6.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>6.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
<li class="chapter" data-level="6.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>6.5.4</b> 3c. Mortality-incidence ratio</a></li>
<li class="chapter" data-level="6.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>6.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
<li class="chapter" data-level="6.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>6.5.6</b> 3e. Childhood versus elderly cancers</a></li>
</ul></li>
<li class="chapter" data-level="6.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>6.6</b> 4. Existing cancer funding and publication data</a>
<ul>
<li class="chapter" data-level="6.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>6.6.1</b> Download HMRF grants and Pubmed data</a></li>
<li class="chapter" data-level="6.6.2" data-path="cancer.html"><a href="cancer.html#make-word-cloud-for-grants"><i class="fa fa-check"></i><b>6.6.2</b> Make word cloud for grants</a></li>
<li class="chapter" data-level="6.6.3" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>6.6.3</b> Make compare grant funding with incidence and mortality</a></li>
</ul></li>
<li class="chapter" data-level="6.7" data-path="cancer.html"><a href="cancer.html#open-disucssion"><i class="fa fa-check"></i><b>6.7</b> 5. Open disucssion</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>7</b> Population Genetics and Diseases</a>
<ul>
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