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diff --git a/data/fig1.dta b/data/fig1.dta
diff --git a/data/fig2.dta b/data/fig2.dta
diff --git a/data/fig3.dta b/data/fig3.dta
diff --git a/data/nhefs-formatted.dta b/data/nhefs-formatted.dta
diff --git a/data/nhefs-highprice.dta b/data/nhefs-highprice.dta
diff --git a/data/nhefs-ps.dta b/data/nhefs-ps.dta
diff --git a/data/nhefs-wcens.dta b/data/nhefs-wcens.dta
diff --git a/data/nhefs.csv b/data/nhefs.csv
diff --git a/data/nhefs_std.dta b/data/nhefs_std.dta
diff --git a/data/nhefs_std1.dta b/data/nhefs_std1.dta
diff --git a/data/nhefs_std2.dta b/data/nhefs_std2.dta
diff --git a/data/nhefs_surv.dta b/data/nhefs_surv.dta
diff --git a/data/observe.mmat b/data/observe.mmat
diff --git a/docs/11-why-model-r_files/figure-html/unnamed-chunk-1-1.png b/docs/11-why-model-r_files/figure-html/unnamed-chunk-1-1.png
diff --git a/docs/11-why-model-r_files/figure-html/unnamed-chunk-1-2.png b/docs/11-why-model-r_files/figure-html/unnamed-chunk-1-2.png
diff --git a/docs/11-why-model-r_files/figure-html/unnamed-chunk-2-1.png b/docs/11-why-model-r_files/figure-html/unnamed-chunk-2-1.png
diff --git a/docs/11-why-model-stata.md b/docs/11-why-model-stata.md
@@ -18,8 +18,6 @@ all files already exist and are up to date.
 
 checking tomata consistency and verifying not already installed...
 all files already exist and are up to date.
-
-end of do-file
 ```
 
 ```

diff --git a/docs/13-stand-gformula-r.md b/docs/13-stand-gformula-r.md
@@ -150,9 +150,9 @@ summary(glm.obj)
 ## Coefficients:
 ##               Estimate Std. Error t value Pr(>|t|)
 ## (Intercept)  2.500e-01  2.552e-01   0.980    0.342
-## A            2.602e-16  3.608e-01   0.000    1.000
+## A            3.957e-17  3.608e-01   0.000    1.000
 ## L            4.167e-01  3.898e-01   1.069    0.301
-## A:L         -3.237e-16  4.959e-01   0.000    1.000
+## A:L         -1.313e-16  4.959e-01   0.000    1.000
 ## 
 ## (Dispersion parameter for gaussian family taken to be 0.2604167)
 ## 
@@ -345,13 +345,13 @@ bootstrap <-
   ))
 bootstrap
 ##                         V1             mean                se               ll
-## 1                 Observed 2.56188497106103 0.111490524910664 2.34336755761866
-## 2             No Treatment 1.65212306626748 0.146316287347159 1.36534841271544
-## 3                Treatment  5.1147448954934 0.363908173238617 4.40149798226595
-## 4 Treatment - No Treatment 3.46262182922592 0.423315384649148 2.63293892121187
+## 1                 Observed 2.56188497106099   0.2624453491695 2.04750153877873
+## 2             No Treatment 1.65212306626744 0.280450871584822 1.10244945852832
+## 3                Treatment 5.11474489549336 0.219898563981165  4.6837516298382
+## 4 Treatment - No Treatment 3.46262182922592 0.210381517824761 3.05028163127652
 ##                 ul
-## 1  2.7804023845034
-## 2 1.93889771981953
-## 3 5.82799180872085
-## 4 4.29230473723997
+## 1 3.07626840334325
+## 2 2.20179667400655
+## 3 5.54573816114852
+## 4 3.87496202717532
 ```
diff --git a/docs/15-prop-scores-r.md b/docs/15-prop-scores-r.md
@@ -734,15 +734,15 @@ bootstrap <- data.frame(cbind(c("Observed", "No Treatment", "Treatment",
                                 "Treatment - No Treatment"), mean, se, ll, ul))
 bootstrap
 ##                         V1             mean                se               ll
-## 1                 Observed 2.63384609228479 0.250578351618104 2.14272154780789
-## 2             No Treatment 1.71983636149845 0.181128320605523  1.3648313765314
-## 3                Treatment 5.35072300362985 0.602689625221556 4.16947304433966
-## 4 Treatment - No Treatment  3.6308866421314 0.640841786137571 2.37485982151344
+## 1                 Observed 2.63384609228479 0.163790897037714 2.31282183309537
+## 2             No Treatment 1.71983636149845 0.093388447625048 1.53679836758125
+## 3                Treatment 5.35072300362985 0.482765980920664  4.4045190680642
+## 4 Treatment - No Treatment  3.6308866421314 0.468984551154229 2.71169381256343
 ##                 ul
-## 1 3.12497063676169
-## 2  2.0748413464655
-## 3 6.53197296292004
-## 4 4.88691346274936
+## 1 2.95487035147422
+## 2 1.90287435541565
+## 3 6.29692693919551
+## 4 4.55007947169937
 ```
 
 
@@ -835,7 +835,7 @@ for(i in 1:nboot) {
   }
 }
 ## 95% CI for the causal mean difference
-## 2.62305 , 4.458254
+## 2.54958 , 4.53291
 ```
 
 A more flexible and elegant way to do this is to write a function to perform the model fitting, prediction, bootstrapping, and reporting all at once.
diff --git a/docs/15-prop-scores-r_files/figure-html/unnamed-chunk-3-1.png b/docs/15-prop-scores-r_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/15-prop-scores-r_files/figure-html/unnamed-chunk-3-2.png b/docs/15-prop-scores-r_files/figure-html/unnamed-chunk-3-2.png
diff --git a/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-2-1.png b/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-2-1.png
diff --git a/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-3-1.png b/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-4-1.png b/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-5-1.png b/docs/17-causal-surv-r_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/17-causal-surv-stata.md b/docs/17-causal-surv-stata.md
@@ -620,7 +620,7 @@ psurv1          float   %9.0g                 psurv, interv == Duplicated observ
  26. drop if newseqn != 1  /* only need one pair */
  27.         
 
-r; t=0.00 10:11:06
+r; t=0.00 12:00:29
 
       Command: bootipw_surv
        PrY_a0: r(boot_0)
@@ -630,7 +630,7 @@ r; t=0.00 10:11:06
 Simulations (10)
 ----+--- 1 ---+--- 2 ---+--- 3 ---+--- 4 ---+--- 5 
 ..........
-r; t=18.94 10:11:25
+r; t=17.77 12:00:47
 
 
 
@@ -857,7 +857,8 @@ meanS_t1        float   %9.0g                 meanS_t, interv == Duplicated
                                                 observation
 
 
-file ./figs/stata-fig-17-4.png saved as PNG format
+file /Users/tom/Documents/GitHub/cibookex-r/figs/stata-fig-17-4.png saved as PNG
+    format
 
 (3,132 observations deleted)
 
@@ -867,7 +868,7 @@ file ./figs/stata-fig-17-4.png saved as PNG format
   5. drop if time != 0       
   6. /*only predict on new version of data */
 
-r; t=0.00 10:11:31
+r; t=0.00 12:00:54
 
       Command: bootstdz_surv
        PrY_a0: r(boot_0)
@@ -877,7 +878,7 @@ r; t=0.00 10:11:31
 Simulations (10)
 ----+--- 1 ---+--- 2 ---+--- 3 ---+--- 4 ---+--- 5 
 ..........
-r; t=21.11 10:11:52
+r; t=20.52 12:01:14
 
 
 

diff --git a/docs/18-session-info-r.md b/docs/18-session-info-r.md
@@ -9,35 +9,34 @@ For reproducibility.
 sessioninfo::session_info()
 ## ─ Session info ───────────────────────────────────────────────────────────────
 ##  setting  value
-##  version  R version 4.3.2 (2023-10-31 ucrt)
-##  os       Windows 11 x64 (build 22621)
-##  system   x86_64, mingw32
-##  ui       RTerm
+##  version  R version 4.3.2 (2023-10-31)
+##  os       macOS Sonoma 14.1.2
+##  system   aarch64, darwin20
+##  ui       X11
 ##  language (EN)
-##  collate  English_United Kingdom.utf8
-##  ctype    English_United Kingdom.utf8
+##  collate  en_US.UTF-8
+##  ctype    en_US.UTF-8
 ##  tz       Europe/London
-##  date     2023-11-01
-##  pandoc   3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
+##  date     2023-12-05
+##  pandoc   3.1.9 @ /opt/homebrew/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version date (UTC) lib source
-##  bookdown      0.36    2023-10-16 [1] CRAN (R 4.3.1)
+##  bookdown      0.37    2023-12-01 [1] CRAN (R 4.3.2)
 ##  cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
 ##  digest        0.6.33  2023-07-07 [1] CRAN (R 4.3.1)
-##  evaluate      0.22    2023-09-29 [1] CRAN (R 4.3.1)
+##  evaluate      0.23    2023-11-01 [1] CRAN (R 4.3.1)
 ##  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
-##  htmltools     0.5.6.1 2023-10-06 [1] CRAN (R 4.3.1)
+##  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.3.2)
 ##  knitr         1.45    2023-10-30 [1] CRAN (R 4.3.1)
-##  rlang         1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
+##  rlang         1.1.2   2023-11-04 [1] CRAN (R 4.3.2)
 ##  rmarkdown     2.25    2023-09-18 [1] CRAN (R 4.3.1)
 ##  rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.1)
 ##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
-##  xfun          0.40    2023-08-09 [1] CRAN (R 4.3.1)
+##  xfun          0.41    2023-11-01 [1] CRAN (R 4.3.1)
 ##  yaml          2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
 ## 
-##  [1] C:/Users/tom/AppData/Local/R/win-library/4.3
-##  [2] C:/Program Files/R/R-4.3.2/library
+##  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
 ## 
 ## ──────────────────────────────────────────────────────────────────────────────
 ```
diff --git a/docs/18-session-info-stata.md b/docs/18-session-info-stata.md
@@ -13,12 +13,11 @@ about
 ```
 
 ```
-Stata/MP 17.0 for Windows (64-bit x86-64)
-Revision 29 Aug 2023
+Stata/MP 17.0 for Mac (Apple Silicon)
+Revision 14 Nov 2023
 Copyright 1985-2021 StataCorp LLC
 
-Total physical memory:       32.00 GB
-Available physical memory:   20.19 GB
+Total physical memory: 8.01 GB
 
 Stata license: Unlimited-user 2-core network, expiring 21 Jan 2024
 Serial number: 501709378202
@@ -32,36 +31,35 @@ Serial number: 501709378202
 sessioninfo::session_info()
 ─ Session info ───────────────────────────────────────────────────────────────
  setting  value
- version  R version 4.3.2 (2023-10-31 ucrt)
- os       Windows 11 x64 (build 22621)
- system   x86_64, mingw32
- ui       RTerm
+ version  R version 4.3.2 (2023-10-31)
+ os       macOS Sonoma 14.1.2
+ system   aarch64, darwin20
+ ui       X11
  language (EN)
- collate  English_United Kingdom.utf8
- ctype    English_United Kingdom.utf8
+ collate  en_US.UTF-8
+ ctype    en_US.UTF-8
  tz       Europe/London
- date     2023-11-01
- pandoc   3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
+ date     2023-12-05
+ pandoc   3.1.9 @ /opt/homebrew/bin/ (via rmarkdown)
 
 ─ Packages ───────────────────────────────────────────────────────────────────
  package       * version date (UTC) lib source
- bookdown        0.36    2023-10-16 [1] CRAN (R 4.3.1)
+ bookdown        0.37    2023-12-01 [1] CRAN (R 4.3.2)
  cli             3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
  digest          0.6.33  2023-07-07 [1] CRAN (R 4.3.1)
- evaluate        0.22    2023-09-29 [1] CRAN (R 4.3.1)
+ evaluate        0.23    2023-11-01 [1] CRAN (R 4.3.1)
  fastmap         1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
- htmltools       0.5.6.1 2023-10-06 [1] CRAN (R 4.3.1)
+ htmltools       0.5.7   2023-11-03 [1] CRAN (R 4.3.2)
  knitr           1.45    2023-10-30 [1] CRAN (R 4.3.1)
- rlang           1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
+ rlang           1.1.2   2023-11-04 [1] CRAN (R 4.3.2)
  rmarkdown       2.25    2023-09-18 [1] CRAN (R 4.3.1)
  rstudioapi      0.15.0  2023-07-07 [1] CRAN (R 4.3.1)
  sessioninfo     1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
- Statamarkdown * 0.8.0   2023-06-01 [1] CRAN (R 4.3.1)
- xfun            0.40    2023-08-09 [1] CRAN (R 4.3.1)
+ Statamarkdown * 0.9.2   2023-12-04 [1] CRAN (R 4.3.1)
+ xfun            0.41    2023-11-01 [1] CRAN (R 4.3.1)
  yaml            2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
 
- [1] C:/Users/tom/AppData/Local/R/win-library/4.3
- [2] C:/Program Files/R/R-4.3.2/library
+ [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
 
 ──────────────────────────────────────────────────────────────────────────────
 ```
diff --git a/docs/404.html b/docs/404.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>Page not found | Causal Inference: What If. R and Stata code for Exercises</title>
   <meta name="description" content="Code examples from Causal Inference: What If by M. A. Hernán and J. M. Robins https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/" />
-  <meta name="generator" content="bookdown 0.36 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.37 and GitBook 2.6.7" />
 
   <meta property="og:title" content="Page not found | Causal Inference: What If. R and Stata code for Exercises" />
   <meta property="og:type" content="book" />
@@ -26,7 +26,7 @@
 <meta name="author" content="R Markdown code by Tom Palmer" />
 
 
-<meta name="date" content="2023-11-01" />
+<meta name="date" content="2023-12-05" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -59,7 +59,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -132,6 +132,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;

diff --git a/docs/causal-survival-analysis-stata.html b/docs/causal-survival-analysis-stata.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>17. Causal survival analysis: Stata | Causal Inference: What If. R and Stata code for Exercises</title>
   <meta name="description" content="Code examples from Causal Inference: What If by M. A. Hernán and J. M. Robins https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/" />
-  <meta name="generator" content="bookdown 0.36 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.37 and GitBook 2.6.7" />
 
   <meta property="og:title" content="17. Causal survival analysis: Stata | Causal Inference: What If. R and Stata code for Exercises" />
   <meta property="og:type" content="book" />
@@ -26,7 +26,7 @@
 <meta name="author" content="R Markdown code by Tom Palmer" />
 
 
-<meta name="date" content="2023-11-01" />
+<meta name="date" content="2023-12-05" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -59,7 +59,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -132,6 +132,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;
@@ -906,7 +907,7 @@ <h2>Program 17.3<a href="causal-survival-analysis-stata.html#program-17.3-1" cla
  26. drop if newseqn != 1  /* only need one pair */
  27.         
 
-r; t=0.00 10:04:50
+r; t=0.00 11:56:33
 
       Command: bootipw_surv
        PrY_a0: r(boot_0)
@@ -916,7 +917,7 @@ <h2>Program 17.3<a href="causal-survival-analysis-stata.html#program-17.3-1" cla
 Simulations (10)
 ----+--- 1 ---+--- 2 ---+--- 3 ---+--- 4 ---+--- 5 
 ..........
-r; t=18.38 10:05:08
+r; t=17.63 11:56:51
 
 
 
@@ -1137,7 +1138,8 @@ <h2>Program 17.4<a href="causal-survival-analysis-stata.html#program-17.4-1" cla
                                                 observation
 
 
-file ./figs/stata-fig-17-4.png saved as PNG format
+file /Users/tom/Documents/GitHub/cibookex-r/figs/stata-fig-17-4.png saved as PNG
+    format
 
 (3,132 observations deleted)
 
@@ -1147,7 +1149,7 @@ <h2>Program 17.4<a href="causal-survival-analysis-stata.html#program-17.4-1" cla
   5. drop if time != 0       
   6. /*only predict on new version of data */
 
-r; t=0.00 10:05:14
+r; t=0.00 11:56:58
 
       Command: bootstdz_surv
        PrY_a0: r(boot_0)
@@ -1157,7 +1159,7 @@ <h2>Program 17.4<a href="causal-survival-analysis-stata.html#program-17.4-1" cla
 Simulations (10)
 ----+--- 1 ---+--- 2 ---+--- 3 ---+--- 4 ---+--- 5 
 ..........
-r; t=22.29 10:05:37
+r; t=20.26 11:57:18
 
 
 

diff --git a/docs/causal-survival-analysis.html b/docs/causal-survival-analysis.html
@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>17. Causal survival analysis | Causal Inference: What If. R and Stata code for Exercises</title>
   <meta name="description" content="Code examples from Causal Inference: What If by M. A. Hernán and J. M. Robins https://www.hsph.harvard.edu/miguel-hernan/causal-inference-book/" />
-  <meta name="generator" content="bookdown 0.36 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.37 and GitBook 2.6.7" />
 
   <meta property="og:title" content="17. Causal survival analysis | Causal Inference: What If. R and Stata code for Exercises" />
   <meta property="og:type" content="book" />
@@ -26,7 +26,7 @@
 <meta name="author" content="R Markdown code by Tom Palmer" />
 
 
-<meta name="date" content="2023-11-01" />
+<meta name="date" content="2023-12-05" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -59,7 +59,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span { line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -132,6 +132,7 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
+  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;

diff --git a/docs/cibookex-r.epub b/docs/cibookex-r.epub
diff --git a/docs/cibookex-r.pdf b/docs/cibookex-r.pdf
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,8 +18,6 @@ all files already exist and are up to date. @@
     checking tomata consistency and verifying not already installed...
     all files already exist and are up to date.
-    end of do-file
     ```
     ```
@@ Expand Down @@