Built site for gh-pages

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@@ -1 +1 @@
-1457aeff
+b7fefde3

01-technical-background.html

@@ -365,7 +365,7 @@
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 // Store cell data
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+globalThis.qwebrCellDetails = [{"id":1,"options":{"dpi":72,"fig-cap":"","editor-quick-suggestions":"false","label":"unnamed-chunk-1","classes":"","output":"true","autorun":"false","editor-font-scale":"1","context":"interactive","message":"true","out-height":"","warning":"true","read-only":"false","fig-height":5,"comment":"","fig-width":7,"editor-word-wrap":"true","editor-max-height":"","out-width":"700px","results":"markup"},"code":"lambda = 1\nx <- seq(0, 10, by = 0.1)\ny <- dexp(x, rate = lambda)\nplot(x, y, type ='l')"},{"id":2,"options":{"dpi":72,"fig-cap":"","editor-quick-suggestions":"false","label":"unnamed-chunk-2","classes":"","output":"true","autorun":"false","editor-font-scale":"1","context":"interactive","message":"true","out-height":"","warning":"true","read-only":"false","fig-height":5,"comment":"","fig-width":7,"editor-word-wrap":"true","editor-max-height":"","out-width":"700px","results":"markup"},"code":"alpha = 1\nbeta = 1\ny = dweibull(x, shape = alpha, scale = beta)\nplot(x, y, type = 'l')"}];
 
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@@ -1667,6 +1667,12 @@
   <a href="./chapters/week-05.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Survival analysis I</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./chapters/week-06.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Survival analysis II</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

chapters/week-01.html

@@ -179,6 +179,12 @@
   <a href="../chapters/week-05.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Survival analysis I</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chapters/week-06.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Survival analysis II</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

chapters/week-02.html

@@ -356,7 +356,7 @@
 };
 
 // Store cell data
-globalThis.qwebrCellDetails = [{"options":{"editor-word-wrap":"true","comment":"","fig-width":7,"message":"true","fig-height":5,"out-height":"","fig-cap":"","autorun":"false","context":"interactive","editor-font-scale":"1","results":"markup","warning":"true","editor-max-height":"","dpi":72,"editor-quick-suggestions":"false","output":"true","read-only":"false","label":"unnamed-chunk-1","classes":"","out-width":"700px"},"code":"set.seed(1000)\ninstall.packages(\"tidyverse\")\nlibrary(tidyverse)\nm1 <- 0\nm2 <- 0.2\ns <- 0.5\nn <- 10 # number of samples we observe in 1 expt (replicates)\nnsim <- 1000 # number of simulated expts\n\n# compute sampling distributions\nx1 <- replicate(nsim, mean(rnorm(n, m1, s)))\nx2 <- replicate(nsim, mean(rnorm(n, m2, s)))\n\ndr <- sqrt(n) * (x2 - x1) / (2 * s^2) > qnorm(0.95)\npower <- mean(dr)\n\nd <- tibble(x = c(x1, x2), grp = factor(c(rep(1, nsim), rep(2, nsim))))\n\nggplot(d, aes(x, color = grp)) +\n  geom_density() +\n  geom_vline(xintercept = sqrt(2) * s / sqrt(n)) +\n  scale_x_continuous(limits = c(-1, 1)) +\n  theme_bw() +\n  labs(title = paste0(\"Power = \", power))","id":1}];
+globalThis.qwebrCellDetails = [{"id":1,"options":{"results":"markup","out-width":"700px","autorun":"false","fig-height":5,"fig-width":7,"read-only":"false","editor-word-wrap":"true","label":"unnamed-chunk-1","classes":"","output":"true","warning":"true","editor-quick-suggestions":"false","fig-cap":"","context":"interactive","comment":"","editor-max-height":"","message":"true","editor-font-scale":"1","dpi":72,"out-height":""},"code":"set.seed(1000)\ninstall.packages(\"tidyverse\")\nlibrary(tidyverse)\nm1 <- 0\nm2 <- 0.2\ns <- 0.5\nn <- 10 # number of samples we observe in 1 expt (replicates)\nnsim <- 1000 # number of simulated expts\n\n# compute sampling distributions\nx1 <- replicate(nsim, mean(rnorm(n, m1, s)))\nx2 <- replicate(nsim, mean(rnorm(n, m2, s)))\n\ndr <- sqrt(n) * (x2 - x1) / (2 * s^2) > qnorm(0.95)\npower <- mean(dr)\n\nd <- tibble(x = c(x1, x2), grp = factor(c(rep(1, nsim), rep(2, nsim))))\n\nggplot(d, aes(x, color = grp)) +\n  geom_density() +\n  geom_vline(xintercept = sqrt(2) * s / sqrt(n)) +\n  scale_x_continuous(limits = c(-1, 1)) +\n  theme_bw() +\n  labs(title = paste0(\"Power = \", power))"}];
 
 </script><script type="module">
 // Declare startupMessageQWebR globally
@@ -1638,6 +1638,12 @@
   <a href="../chapters/week-05.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Survival analysis I</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chapters/week-06.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Survival analysis II</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 

chapters/week-03.html

@@ -213,6 +213,12 @@
   <a href="../chapters/week-05.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Survival analysis I</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chapters/week-06.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Survival analysis II</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
@@ -1015,7 +1021,7 @@ <h1 class="title"><span id="sec-week3" class="quarto-section-identifier"><span c
 </div>
 </div>
 <div class="no-row-height column-margin column-container"><div id="ref-hernan:2023" class="csl-entry" role="listitem">
-Hernan, Miguel A, and James M Robins. 2023. <span>“Causal Inference: What If.”</span>
+Hernan, Miguel A, and James M Robins. 2023. <span>“Causal Inference: What If.”</span> <a href="https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/">https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/</a>.
 </div><div id="ref-pearl:2018" class="csl-entry" role="listitem">
 Pearl, Judea, and Dana Mackenzie. 2018. <em>The Book of Why</em>. New York: Basic Books.
 </div></div><p>The idea behind this backdoor criterion is, if we condition on values of variables satisfing the backdoor criterion, then the spurious association generated by the confounder disappears. We can “deconfound” (<span class="citation" data-cites="pearl:2018">Pearl and Mackenzie (<a href="#ref-pearl:2018" role="doc-biblioref">2018</a>)</span>) the effect of the confounder by computing the effect of <em>X</em> on <em>Y</em> for every unique value of <em>Z</em> separately, and then take the weighted average of effects, with weights determined by the relative prevalence of different values of <em>Z</em>. To fix ideas, if we consider our earlier ibuprofen example and consider <em>Z</em> to be age groups, then we would compute the treatment effect within each age group, and then take the average treatment effect weighted by the number of people in each age group. One way to statistically approach this is through <em>adjustment</em> for the confounder in a regression model. This approach can be used in observational, non-randomized studies, but there is a more principled approach we will introduce in <a href="week-04.html" class="quarto-xref"><span>Chapter 4</span></a>.</p>

chapters/week-04.html

@@ -157,6 +157,12 @@
   <a href="../chapters/week-05.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Survival analysis I</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../chapters/week-06.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Survival analysis II</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container">