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anu-bdsi · Sep 17, 2024 · bcb9017 · bcb9017
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-b5d8c031
+d4d84274
diff --git a/ad.html b/ad.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.31">
+<meta name="generator" content="quarto-1.5.30">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/exercises/handout1.pdf b/exercises/handout1.pdf
diff --git a/index.html b/index.html
diff --git a/next-time.html b/next-time.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.31">
+<meta name="generator" content="quarto-1.5.30">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 

diff --git a/search.json b/search.json
diff --git a/sitemap.xml b/sitemap.xml
@@ -1,27 +1,27 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide3.html</loc>
-    <lastmod>2024-09-14T10:33:59.287Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide2.html</loc>
+    <lastmod>2024-09-12T07:06:51.312Z</lastmod>
   </url>
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide1.html</loc>
-    <lastmod>2024-09-11T07:13:51.000Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/next-time.html</loc>
+    <lastmod>2024-09-12T01:44:48.014Z</lastmod>
   </url>
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/index.html</loc>
-    <lastmod>2024-09-14T10:45:12.258Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/ad.html</loc>
+    <lastmod>2024-09-11T04:38:29.569Z</lastmod>
   </url>
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/ad.html</loc>
-    <lastmod>2024-09-02T02:30:41.000Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/index.html</loc>
+    <lastmod>2024-09-14T10:45:12.000Z</lastmod>
   </url>
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/next-time.html</loc>
-    <lastmod>2024-09-12T01:44:48.000Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide1.html</loc>
+    <lastmod>2024-09-17T01:32:43.513Z</lastmod>
   </url>
   <url>
-    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide2.html</loc>
-    <lastmod>2024-09-12T07:06:51.000Z</lastmod>
+    <loc>https://anu-bdsi.github.io/workshop-experimental-design/slides/slide3.html</loc>
+    <lastmod>2024-09-14T10:33:59.000Z</lastmod>
   </url>
 </urlset>
diff --git a/slides/slide1.html b/slides/slide1.html
@@ -10,7 +10,7 @@
 <link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <link href="../site_libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
 <link href="../site_libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
-  <meta name="generator" content="quarto-1.5.31">
+  <meta name="generator" content="quarto-1.5.30">
 
   <meta name="author" content="Emi Tanaka">
   <title>ANU BDSI – Statistical anatomy of experiments</title>
@@ -1512,6 +1512,7 @@ <h2>Example</h2>
 <blockquote>
 <p>Researchers are studying the impact of a new irrigation method on tomato growth. They randomly select 40 plants of the same species and divide them into two groups. One group is watered using the new irrigation technique, while the other group is watered using a traditional method. The researchers record the dry weight of each tomato at harvest.</p>
 </blockquote>
+<div class="fragment">
 <ul>
 <li><strong>Aim</strong>: To assess the new irrigation method on tomato growth.<br> <span style="color:grey;"><i class="fas fa-exclamation-circle"></i> This aim should be more specific in practice.</span></li>
 <li><strong>Response</strong>: Dry weight of individual tomatoes at harvest.</li>
@@ -1523,6 +1524,7 @@ <h2>Example</h2>
 </ul></li>
 <li><strong>Design</strong>: Plants <i class="fas fa-arrow-right"></i> Irrigation treatment</li>
 </ul>
+</div>
 </section>
 <section id="summary" class="slide level2" data-background-color="#F5EDDE">
 <h2><i class="fas fa-sticky-note"></i> Summary</h2>

diff --git a/slides/slide2.html b/slides/slide2.html
@@ -10,7 +10,7 @@
 <link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <link href="../site_libs/quarto-contrib/fontawesome6-0.1.0/all.css" rel="stylesheet">
 <link href="../site_libs/quarto-contrib/fontawesome6-0.1.0/latex-fontsize.css" rel="stylesheet"><meta charset="utf-8">
-  <meta name="generator" content="quarto-1.5.31">
+  <meta name="generator" content="quarto-1.5.30">
 
   <meta name="author" content="Emi Tanaka">
   <title>ANU BDSI – Principles of experimental designs</title>
@@ -492,7 +492,7 @@
   };
 
   // Store cell data
-  globalThis.qwebrCellDetails = [{"code":"library(edibble)\nset.seed(1) # to replicate the result \ndesign(\"Randomised complete block design\") |> \n  set_units(pen = 3, \n            cow = nested_in(pen, 2)) |> \n  set_trts(supplement = c(\"new\", \"control\")) |> \n  allot_table(supplement ~ cow, order = \"random\")","id":1,"options":{"comment":"","fig-cap":"","out-width":"700px","results":"markup","output":"true","label":"unnamed-chunk-1","context":"interactive","classes":"","echo":"true","dpi":72,"fig-height":5,"warning":"true","out-height":"","read-only":"false","fig-width":7,"message":"true","autorun":"false"}},{"code":"library(edibble)\ntrt_str <- set_trts(fertilizer = c(\"A\", \"B\"),\n                    water = c(\"irrigate\", \"rainfed\"))\nunit_str1 <- set_units(plot = 12)\nunit_str2 <- set_units(strip = 6,\n                       plot = nested_in(strip, 2))\n\ndes1 <- (unit_str1 + trt_str) |> allot_table(fertilizer ~ plot, water ~ plot)\ndes2 <- (unit_str1 + trt_str) |> allot_table(fertilizer:water ~ plot)\ndes3 <- (unit_str2 + trt_str) |> allot_table(fertilizer:water ~ plot)\n\ndes1","id":2,"options":{"comment":"","fig-cap":"","out-width":"700px","results":"markup","output":"true","label":"unnamed-chunk-2","context":"interactive","classes":"","echo":"true","dpi":72,"fig-height":5,"warning":"true","out-height":"","read-only":"false","fig-width":7,"message":"true","autorun":"false"}},{"code":"design_anatomy(des3)","id":3,"options":{"label":"unnamed-chunk-3","context":"interactive","comment":"","output":"true","classes":"","message":"true","autorun":"false","fig-cap":"","warning":"true","out-width":"700px","results":"markup","out-height":"","read-only":"false","fig-width":7,"fig-height":5,"dpi":72}},{"code":"library(edibble)\ndes_invalid <- design(\"Invalid design\") |> \n  set_units(pen = 2, \n            cow = nested_in(pen, 3)) |> \n  set_trts(supp = c(\"new\", \"control\")) |> \n  allot_table(supp ~ pen)\n\ndesign_anatomy(des_invalid)","id":4,"options":{"label":"unnamed-chunk-4","context":"interactive","comment":"","output":"true","classes":"","message":"true","autorun":"false","fig-cap":"","warning":"true","out-width":"700px","results":"markup","out-height":"","read-only":"false","fig-width":7,"fig-height":5,"dpi":72}}];
+  globalThis.qwebrCellDetails = [{"id":1,"options":{"classes":"","out-height":"","label":"unnamed-chunk-1","autorun":"false","dpi":72,"context":"interactive","results":"markup","out-width":"700px","fig-cap":"","fig-height":5,"fig-width":7,"warning":"true","message":"true","output":"true","echo":"true","comment":"","read-only":"false"},"code":"library(edibble)\nset.seed(1) # to replicate the result \ndesign(\"Randomised complete block design\") |> \n  set_units(pen = 3, \n            cow = nested_in(pen, 2)) |> \n  set_trts(supplement = c(\"new\", \"control\")) |> \n  allot_table(supplement ~ cow, order = \"random\")"},{"id":2,"options":{"classes":"","out-height":"","label":"unnamed-chunk-2","autorun":"false","dpi":72,"context":"interactive","results":"markup","out-width":"700px","fig-cap":"","fig-height":5,"fig-width":7,"warning":"true","message":"true","output":"true","echo":"true","comment":"","read-only":"false"},"code":"library(edibble)\ntrt_str <- set_trts(fertilizer = c(\"A\", \"B\"),\n                    water = c(\"irrigate\", \"rainfed\"))\nunit_str1 <- set_units(plot = 12)\nunit_str2 <- set_units(strip = 6,\n                       plot = nested_in(strip, 2))\n\ndes1 <- (unit_str1 + trt_str) |> allot_table(fertilizer ~ plot, water ~ plot)\ndes2 <- (unit_str1 + trt_str) |> allot_table(fertilizer:water ~ plot)\ndes3 <- (unit_str2 + trt_str) |> allot_table(fertilizer:water ~ plot)\n\ndes1"},{"id":3,"options":{"message":"true","classes":"","results":"markup","out-height":"","fig-cap":"","label":"unnamed-chunk-3","autorun":"false","dpi":72,"out-width":"700px","warning":"true","context":"interactive","output":"true","fig-width":7,"fig-height":5,"comment":"","read-only":"false"},"code":"design_anatomy(des3)"},{"id":4,"options":{"message":"true","classes":"","results":"markup","out-height":"","fig-cap":"","label":"unnamed-chunk-4","autorun":"false","dpi":72,"out-width":"700px","warning":"true","context":"interactive","output":"true","fig-width":7,"fig-height":5,"comment":"","read-only":"false"},"code":"library(edibble)\ndes_invalid <- design(\"Invalid design\") |> \n  set_units(pen = 2, \n            cow = nested_in(pen, 3)) |> \n  set_trts(supp = c(\"new\", \"control\")) |> \n  allot_table(supp ~ pen)\n\ndesign_anatomy(des_invalid)"}];
 
   </script>
   <script type="module">

diff --git a/slides/slide3.html b/slides/slide3.html