Make data for case study 2 directly available

Report/case_study_1.html

@@ -171,7 +171,7 @@
 
 <h1 class="title toc-ignore">Illustrative case study 1</h1>
 <h4 class="author">Thomas Debray</h4>
-<h4 class="date">This report was generated on 03 oktober, 2022</h4>
+<h4 class="date">This report was generated on 11 oktober, 2022</h4>
 
 </div>
 
@@ -604,23 +604,23 @@ <h1>Results</h1>
 <td align="left">-0.33</td>
 <td align="left">0.07</td>
 <td align="left">-0.46 ; -0.20</td>
-<td align="left">0.00</td>
+<td align="left">0.01</td>
 </tr>
 <tr class="even">
 <td align="left">DSR NNM</td>
 <td align="right">0</td>
 <td align="left">0.02</td>
 <td align="left">0.08</td>
 <td align="left">-0.14 ; 0.17</td>
-<td align="left">0.06</td>
+<td align="left">0.08</td>
 </tr>
 <tr class="odd">
 <td align="left">DSR OFM</td>
 <td align="right">0</td>
 <td align="left">0.07</td>
 <td align="left">0.06</td>
 <td align="left">-0.06 ; 0.19</td>
-<td align="left">2.62</td>
+<td align="left">2.78</td>
 </tr>
 <tr class="even">
 <td align="left">DSR IPW</td>
@@ -636,7 +636,7 @@ <h1>Results</h1>
 <td align="left">0.04</td>
 <td align="left">0.06</td>
 <td align="left">-0.08 ; 0.17</td>
-<td align="left">0.06</td>
+<td align="left">0.04</td>
 </tr>
 </tbody>
 </table>

Report/case_study_2.Rmd

@@ -20,14 +20,15 @@ library(ggplot2)
 library(rms)
 ```
 
-
+# Data source
 ```{r}
 ################################################################################
 # Prepare data
 ################################################################################
 
 # Fetch IST v2.0 from the web
-d <- read.csv("https://datashare.ed.ac.uk/bitstream/handle/10283/124/IST%20dataset%20supp1%20%281%29%20trials%202011.csv?sequence=4&isAllowed=y")
+#d <- read.csv("https://datashare.ed.ac.uk/bitstream/handle/10283/124/IST%20dataset%20supp1%20%281%29%20trials%202011.csv?sequence=4&isAllowed=y")
+load("../Data/dat_cs2.rda")
 
 dat <- data.frame(HOSPNUM = d$HOSPNUM,
                   OCCODE = d$OCCODE,

Report/case_study_2.html

@@ -171,11 +171,13 @@
 
 <h1 class="title toc-ignore">Illustrative case study 2</h1>
 <h4 class="author">Thomas Debray</h4>
-<h4 class="date">This report was generated on 29 september, 2022</h4>
+<h4 class="date">This report was generated on 11 oktober, 2022</h4>
 
 </div>
 
 
+<div id="data-source" class="section level1">
+<h1>Data source</h1>
 <p>The International Stroke Trial (IST) was a large, multi-center, randomized, placebo-controlled trial including 19435 stroke patients. Individual participant data are available from <a href="https://datashare.ed.ac.uk/handle/10283/124">Edinburgh DataShare</a>. The IST evaluated the effect of Aspirin on a primary composite outcome of death or dependency (i.e. absence of autonomy) at 6 months (binary outcome). In this illustrative case study, we focus on 9148 patients from IST database version 2 that were randomized to receive Aspirin.</p>
 <p>We excluded patients with</p>
 <ul>
@@ -578,6 +580,7 @@ <h4 class="date">This report was generated on 29 september, 2022</h4>
 </tbody>
 </table>
 </div>
+</div>
 <div id="estimation-of-the-treatment-effect" class="section level1">
 <h1>Estimation of the treatment effect</h1>
 <p>We consider the Expanded Disability Status Scale (EDSS) measured 36 weeks after baseline as the primary outcome. Subsequently, we estimate the ATT in the simulated observation study using five approaches:</p>
@@ -617,21 +620,21 @@ <h1>Results</h1>
 <td align="left">-0.01</td>
 <td align="left">0.01</td>
 <td align="left">-0.04 ; 0.01</td>
-<td align="left">1.07</td>
+<td align="left">1.19</td>
 </tr>
 <tr class="odd">
 <td align="left">DSR OFM</td>
 <td align="left">0.00</td>
 <td align="left">0.01</td>
 <td align="left">-0.02 ; 0.02</td>
-<td align="left">73.26</td>
+<td align="left">83.33</td>
 </tr>
 <tr class="even">
 <td align="left">DSR IPW</td>
 <td align="left">-0.01</td>
 <td align="left">0.01</td>
 <td align="left">-0.03 ; 0.01</td>
-<td align="left">0.08</td>
+<td align="left">0.10</td>
 </tr>
 <tr class="odd">
 <td align="left">DSR TDW</td>