Y2023 docs initial release

docs/image-digital.html

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-  <title>Chapter 6 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies</title>
+  <title>Chapter 5 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies</title>
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-  <meta name="twitter:title" content="Chapter 6 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies" />
+  <meta name="twitter:title" content="Chapter 5 Medical Image and Digital Health | Biomedical Data Science - introduction with case studies" />
 
   <meta name="twitter: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="author" content="BIOF1001 teaching team" />
 
 
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+<meta name="date" content="2023-09-01" />
 
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 <ul>
 <li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#introduction-for-readers"><i class="fa fa-check"></i>Introduction for readers</a>
 <ul>
-<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#what-we-hope-you-will-learn-from-this-course-book"><i class="fa fa-check"></i>What we hope you will learn from this course / book</a></li>
+<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#what-you-will-learn-from-this-coursebook"><i class="fa fa-check"></i>What you will learn from this course/book</a></li>
 <li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#what-we-recommend-you-do-while-reading-this-book"><i class="fa fa-check"></i>What we recommend you do while reading this book</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#other-reference-books"><i class="fa fa-check"></i>Other reference books</a></li>
 <li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#acknowledgements"><i class="fa fa-check"></i>Acknowledgements</a></li>
-<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#last-notes"><i class="fa fa-check"></i>Last notes</a></li>
 </ul></li>
 <li class="part"><span><b>I Data Science Foundations</b></span></li>
 <li class="chapter" data-level="1" data-path="introR.html"><a href="introR.html"><i class="fa fa-check"></i><b>1</b> Introduction to R programming</a>
@@ -259,25 +263,49 @@
 </ul></li>
 </ul></li>
 <li class="part"><span><b>II Biomedical Data Modules</b></span></li>
-<li class="chapter" data-level="5" data-path="genomics.html"><a href="genomics.html"><i class="fa fa-check"></i><b>5</b> Personalised Genomic Medicine</a>
+<li class="chapter" data-level="5" data-path="image-digital.html"><a href="image-digital.html"><i class="fa fa-check"></i><b>5</b> Medical Image and Digital Health</a></li>
+<li class="chapter" data-level="6" data-path="infectious-dis.html"><a href="infectious-dis.html"><i class="fa fa-check"></i><b>6</b> Infectious Disease Informatics</a></li>
+<li class="chapter" data-level="7" data-path="cancer.html"><a href="cancer.html"><i class="fa fa-check"></i><b>7</b> Cancer genomics and epidemiology</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="genomics.html"><a href="genomics.html#genomics-case1"><i class="fa fa-check"></i><b>5.1</b> Case study 1: splicing fedility prediction</a>
+<li class="chapter" data-level="7.1" data-path="cancer.html"><a href="cancer.html#cancer-case1"><i class="fa fa-check"></i><b>7.1</b> Case study 1: analysis of cBioportal mutation data</a>
 <ul>
-<li class="chapter" data-level="5.1.1" data-path="genomics.html"><a href="genomics.html#questions-for-discussion"><i class="fa fa-check"></i><b>5.1.1</b> Questions for Discussion</a></li>
-<li class="chapter" data-level="5.1.2" data-path="genomics.html"><a href="genomics.html#hands-on-with-regression-model"><i class="fa fa-check"></i><b>5.1.2</b> Hands-on with regression model</a></li>
-<li class="chapter" data-level="5.1.3" data-path="genomics.html"><a href="genomics.html#open-question"><i class="fa fa-check"></i><b>5.1.3</b> Open question</a></li>
+<li class="chapter" data-level="7.1.1" data-path="cancer.html"><a href="cancer.html#exploratory-analysis"><i class="fa fa-check"></i><b>7.1.1</b> Exploratory analysis</a></li>
+<li class="chapter" data-level="7.1.2" data-path="cancer.html"><a href="cancer.html#statistical-analysis"><i class="fa fa-check"></i><b>7.1.2</b> Statistical analysis</a></li>
+<li class="chapter" data-level="7.1.3" data-path="cancer.html"><a href="cancer.html#literature-search"><i class="fa fa-check"></i><b>7.1.3</b> Literature search</a></li>
 </ul></li>
-<li class="chapter" data-level="5.2" data-path="genomics.html"><a href="genomics.html#genomics-case2"><i class="fa fa-check"></i><b>5.2</b> Case study 2: analysis of cBioportal mutation data</a>
+<li class="chapter" data-level="7.2" data-path="cancer.html"><a href="cancer.html#cancer-case2"><i class="fa fa-check"></i><b>7.2</b> Case study 2: Cancer Epidemiology</a></li>
+<li class="chapter" data-level="7.3" data-path="cancer.html"><a href="cancer.html#scenario"><i class="fa fa-check"></i><b>7.3</b> 1. Scenario</a></li>
+<li class="chapter" data-level="7.4" data-path="cancer.html"><a href="cancer.html#hong-kong-population"><i class="fa fa-check"></i><b>7.4</b> 2. Hong Kong population</a>
+<ul>
+<li class="chapter" data-level="7.4.1" data-path="cancer.html"><a href="cancer.html#download-population-data"><i class="fa fa-check"></i><b>7.4.1</b> Download population data</a></li>
+<li class="chapter" data-level="7.4.2" data-path="cancer.html"><a href="cancer.html#format-data-for-plotting"><i class="fa fa-check"></i><b>7.4.2</b> Format data for plotting</a></li>
+<li class="chapter" data-level="7.4.3" data-path="cancer.html"><a href="cancer.html#plotting-population-data"><i class="fa fa-check"></i><b>7.4.3</b> Plotting population data</a></li>
+</ul></li>
+<li class="chapter" data-level="7.5" data-path="cancer.html"><a href="cancer.html#cancer-registry-data"><i class="fa fa-check"></i><b>7.5</b> 3. Cancer registry data</a>
+<ul>
+<li class="chapter" data-level="7.5.1" data-path="cancer.html"><a href="cancer.html#download-cancer-registry-data"><i class="fa fa-check"></i><b>7.5.1</b> Download cancer registry data</a></li>
+<li class="chapter" data-level="7.5.2" data-path="cancer.html"><a href="cancer.html#a.-visualise-changes-in-incidence-and-mortality"><i class="fa fa-check"></i><b>7.5.2</b> 3a. Visualise changes in incidence and mortality</a></li>
+<li class="chapter" data-level="7.5.3" data-path="cancer.html"><a href="cancer.html#b.-calculate-cancer-risk-and-mortality-rate"><i class="fa fa-check"></i><b>7.5.3</b> 3b. Calculate cancer risk and mortality rate</a></li>
+<li class="chapter" data-level="7.5.4" data-path="cancer.html"><a href="cancer.html#c.-mortality-incidence-ratio"><i class="fa fa-check"></i><b>7.5.4</b> 3c. Mortality-incidence ratio</a></li>
+<li class="chapter" data-level="7.5.5" data-path="cancer.html"><a href="cancer.html#d.-paired-t-test-on-mortality-incidence-ratio-change"><i class="fa fa-check"></i><b>7.5.5</b> 3d. Paired t-test on mortality-incidence ratio change</a></li>
+<li class="chapter" data-level="7.5.6" data-path="cancer.html"><a href="cancer.html#e.-childhood-versus-elderly-cancers"><i class="fa fa-check"></i><b>7.5.6</b> 3e. Childhood versus elderly cancers</a></li>
+</ul></li>
+<li class="chapter" data-level="7.6" data-path="cancer.html"><a href="cancer.html#existing-cancer-funding-and-publication-data"><i class="fa fa-check"></i><b>7.6</b> 4. Existing cancer funding and publication data</a>
+<ul>
+<li class="chapter" data-level="7.6.1" data-path="cancer.html"><a href="cancer.html#download-hmrf-grants-and-pubmed-data"><i class="fa fa-check"></i><b>7.6.1</b> Download HMRF grants and Pubmed data</a></li>
+<li class="chapter" data-level="7.6.2" data-path="cancer.html"><a href="cancer.html#make-word-cloud-for-grants"><i class="fa fa-check"></i><b>7.6.2</b> Make word cloud for grants</a></li>
+<li class="chapter" data-level="7.6.3" data-path="cancer.html"><a href="cancer.html#make-compare-grant-funding-with-incidence-and-mortality"><i class="fa fa-check"></i><b>7.6.3</b> Make compare grant funding with incidence and mortality</a></li>
+</ul></li>
+<li class="chapter" data-level="7.7" data-path="cancer.html"><a href="cancer.html#task-to-be-completed-in-tutotial-2-by-300pm-and-shared-with-other-tutorial-group"><i class="fa fa-check"></i><b>7.7</b> 5. Task (to be completed in Tutotial 2 by 3:00pm and shared with other tutorial group)</a></li>
+</ul></li>
+<li class="chapter" data-level="8" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>8</b> Population Genetics and Diseases</a>
+<ul>
+<li class="chapter" data-level="8.1" data-path="pop-genetics.html"><a href="pop-genetics.html#case-study-1-heritability-and-human-traits"><i class="fa fa-check"></i><b>8.1</b> Case study 1: Heritability and human traits</a>
 <ul>
-<li class="chapter" data-level="5.2.1" data-path="genomics.html"><a href="genomics.html#exploratory-analysis"><i class="fa fa-check"></i><b>5.2.1</b> Exploratory analysis</a></li>
-<li class="chapter" data-level="5.2.2" data-path="genomics.html"><a href="genomics.html#statistical-analysis"><i class="fa fa-check"></i><b>5.2.2</b> Statistical analysis</a></li>
-<li class="chapter" data-level="5.2.3" data-path="genomics.html"><a href="genomics.html#literature-search"><i class="fa fa-check"></i><b>5.2.3</b> Literature search</a></li>
+<li class="chapter" data-level="8.1.1" data-path="pop-genetics.html"><a href="pop-genetics.html#part-1"><i class="fa fa-check"></i><b>8.1.1</b> Part 1</a></li>
+<li class="chapter" data-level="8.1.2" data-path="pop-genetics.html"><a href="pop-genetics.html#part-2"><i class="fa fa-check"></i><b>8.1.2</b> Part 2</a></li>
 </ul></li>
 </ul></li>
-<li class="chapter" data-level="6" data-path="image-digital.html"><a href="image-digital.html"><i class="fa fa-check"></i><b>6</b> Medical Image and Digital Health</a></li>
-<li class="chapter" data-level="7" data-path="infectious-dis.html"><a href="infectious-dis.html"><i class="fa fa-check"></i><b>7</b> Infectious Disease Informatics</a></li>
-<li class="chapter" data-level="8" data-path="pop-genetics.html"><a href="pop-genetics.html"><i class="fa fa-check"></i><b>8</b> Population Genetics and Diseases</a></li>
-<li class="chapter" data-level="9" data-path="epidemiology.html"><a href="epidemiology.html"><i class="fa fa-check"></i><b>9</b> Epidemiology of Cancer and Other Diseases</a></li>
 <li class="part"><span><b>III Appendix</b></span></li>
 <li class="chapter" data-level="" data-path="install.html"><a href="install.html"><i class="fa fa-check"></i>Appendix A: Install R &amp; RStudio</a>
 <ul>
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-<div id="image-digital" class="section level1 hasAnchor" number="6">
-<h1><span class="header-section-number">Chapter 6</span> Medical Image and Digital Health<a href="image-digital.html#image-digital" class="anchor-section" aria-label="Anchor link to header"></a></h1>
+<div id="image-digital" class="section level1 hasAnchor" number="5">
+<h1><span class="header-section-number">Chapter 5</span> Medical Image and Digital Health<a href="image-digital.html#image-digital" class="anchor-section" aria-label="Anchor link to header"></a></h1>
+<!-- # Medical Image and Digital Health {#image-digital} -->
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