diff --git a/data/fig1.dta b/data/fig1.dta
index b3d314d..27331e1 100644
Binary files a/data/fig1.dta and b/data/fig1.dta differ
diff --git a/data/fig2.dta b/data/fig2.dta
index 29e1290..ea50689 100644
Binary files a/data/fig2.dta and b/data/fig2.dta differ
diff --git a/data/fig3.dta b/data/fig3.dta
index 38983d8..333658a 100644
Binary files a/data/fig3.dta and b/data/fig3.dta differ
diff --git a/data/nhefs-formatted.dta b/data/nhefs-formatted.dta
index 37b8390..4059ec3 100644
Binary files a/data/nhefs-formatted.dta and b/data/nhefs-formatted.dta differ
diff --git a/data/nhefs-highprice.dta b/data/nhefs-highprice.dta
index 350481e..7172a6a 100644
Binary files a/data/nhefs-highprice.dta and b/data/nhefs-highprice.dta differ
diff --git a/data/nhefs-ps.dta b/data/nhefs-ps.dta
index 55d0009..a77609c 100644
Binary files a/data/nhefs-ps.dta and b/data/nhefs-ps.dta differ
diff --git a/data/nhefs-wcens.dta b/data/nhefs-wcens.dta
index 08e6e20..38165fc 100644
Binary files a/data/nhefs-wcens.dta and b/data/nhefs-wcens.dta differ
diff --git a/data/nhefs_std.dta b/data/nhefs_std.dta
index 445952d..7aab339 100644
Binary files a/data/nhefs_std.dta and b/data/nhefs_std.dta differ
diff --git a/data/nhefs_std1.dta b/data/nhefs_std1.dta
index 0372945..b0be18b 100644
Binary files a/data/nhefs_std1.dta and b/data/nhefs_std1.dta differ
diff --git a/data/nhefs_std2.dta b/data/nhefs_std2.dta
index 6fd3973..b7945d2 100644
Binary files a/data/nhefs_std2.dta and b/data/nhefs_std2.dta differ
diff --git a/data/nhefs_surv.dta b/data/nhefs_surv.dta
index bbbc509..bfbdc9d 100644
Binary files a/data/nhefs_surv.dta and b/data/nhefs_surv.dta differ
diff --git a/data/observe.mmat b/data/observe.mmat
index dcae375..df82810 100644
Binary files a/data/observe.mmat and b/data/observe.mmat differ
diff --git a/docs/11-why-model-r.md b/docs/11-why-model-r.md
index 171a12f..9a99fb8 100644
--- a/docs/11-why-model-r.md
+++ b/docs/11-why-model-r.md
@@ -18,7 +18,9 @@ Y <- c(200, 150, 220, 110, 50, 180, 90, 170, 170, 30,
plot(A, Y)
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{11-why-model-r_files/figure-latex/unnamed-chunk-1-1} \end{center}
``` r
summary(Y[A == 0])
@@ -35,7 +37,9 @@ Y2 <- c(110, 80, 50, 40, 170, 30, 70, 50, 110, 50, 180,
plot(A2, Y2)
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{11-why-model-r_files/figure-latex/unnamed-chunk-1-2} \end{center}
``` r
summary(Y2[A2 == 1])
@@ -69,7 +73,9 @@ Y3 <-
plot(Y3 ~ A3)
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{11-why-model-r_files/figure-latex/unnamed-chunk-2-1} \end{center}
``` r
diff --git a/docs/11-why-model-stata.md b/docs/11-why-model-stata.md
index d145dd4..2b83296 100644
--- a/docs/11-why-model-stata.md
+++ b/docs/11-why-model-stata.md
@@ -109,7 +109,8 @@ bysort A: sum Y
Y | 8 146.25 58.2942 50 220
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{figs/stata-fig-11-1} \end{center}
``` stata
@@ -197,7 +198,8 @@ bysort A: sum Y
Y | 4 195 31.09126 150 220
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{figs/stata-fig-11-2} \end{center}
``` stata
@@ -250,7 +252,8 @@ qui gr export figs/stata-fig-11-3.png, replace
17. end
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{figs/stata-fig-11-3} \end{center}
## Program 11.2
@@ -294,7 +297,8 @@ qui gr export figs/stata-fig-11-4.png, replace
------------------------------------------------------------------------------
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{figs/stata-fig-11-4} \end{center}
``` stata
@@ -361,4 +365,5 @@ qui gr export figs/stata-fig-11-5.png, replace
------------------------------------------------------------------------------
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{figs/stata-fig-11-5} \end{center}
diff --git a/docs/13-stand-gformula-r.md b/docs/13-stand-gformula-r.md
index cac0eb9..a8f07a2 100644
--- a/docs/13-stand-gformula-r.md
+++ b/docs/13-stand-gformula-r.md
@@ -87,11 +87,11 @@ nhefs[which(nhefs$seqn == 24770), c(
"active",
"wt71"
)]
-#> # A tibble: 1 × 11
+#> # A tibble: 1 x 11
#> predicted.meanY qsmk sex race age education smokeintensity smokeyrs
#>
#> 1 0.342 0 0 0 26 4 15 12
-#> # ℹ 3 more variables: exercise , active , wt71
+#> # i 3 more variables: exercise , active , wt71
summary(nhefs$predicted.meanY[nhefs$cens == 0])
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
@@ -344,14 +344,14 @@ bootstrap <-
ul
))
bootstrap
-#> V1 mean se ll
-#> 1 Observed 2.56188497106099 0.0549704676078034 2.45414483433637
-#> 2 No Treatment 1.65212306626744 0.143266399330196 1.37132608338552
-#> 3 Treatment 5.11474489549336 0.38239206319866 4.36527022365002
-#> 4 Treatment - No Treatment 3.46262182922592 0.508889999498158 2.46521575811692
+#> V1 mean se ll
+#> 1 Observed 2.56188497106099 0.120597104489459 2.32551898962183
+#> 2 No Treatment 1.65212306626744 0.106947069654509 1.4425106614925
+#> 3 Treatment 5.11474489549336 0.358814454471498 4.41148148759683
+#> 4 Treatment - No Treatment 3.46262182922592 0.392348048118945 2.6936337855082
#> ul
-#> 1 2.66962510778561
-#> 2 1.93292004914935
-#> 3 5.86421956733669
-#> 4 4.46002790033492
+#> 1 2.79825095250014
+#> 2 1.86173547104237
+#> 3 5.81800830338988
+#> 4 4.23160987294364
```
diff --git a/docs/15-prop-scores-r.md b/docs/15-prop-scores-r.md
index 579bf47..3264aaa 100644
--- a/docs/15-prop-scores-r.md
+++ b/docs/15-prop-scores-r.md
@@ -330,7 +330,9 @@ ggplot(nhefs, aes(x = ps, fill = qsmklabel, color = qsmklabel)) +
legend.title = element_blank())
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{15-prop-scores-r_files/figure-latex/unnamed-chunk-3-1} \end{center}
``` r
@@ -345,7 +347,9 @@ ggplot(nhefs, aes(x = ps, fill = as.factor(qsmk), color = as.factor(qsmk))) +
theme(legend.position = 'bottom', legend.direction = 'vertical')
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{15-prop-scores-r_files/figure-latex/unnamed-chunk-3-2} \end{center}
``` r
@@ -732,15 +736,15 @@ 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 0.238861089903915 2.16568695876514
-#> 2 No Treatment 1.71983636149845 0.197112530909323 1.33350290001464
-#> 3 Treatment 5.35072300362985 0.587017349690794 4.20019013993574
-#> 4 Treatment - No Treatment 3.6308866421314 0.592573338393775 2.46946424068094
+#> 1 Observed 2.63384609228479 0.279890742231742 2.0852703179044
+#> 2 No Treatment 1.71983636149845 0.275568960869064 1.17973112293796
+#> 3 Treatment 5.35072300362985 0.314161588160568 4.73497760550923
+#> 4 Treatment - No Treatment 3.6308866421314 0.451854865413406 2.74526737968193
#> ul
-#> 1 3.10200522580445
-#> 2 2.10616982298226
-#> 3 6.50125586732396
-#> 4 4.79230904358186
+#> 1 3.18242186666519
+#> 2 2.25994160005895
+#> 3 5.96646840175047
+#> 4 4.51650590458087
```
@@ -833,7 +837,7 @@ for(i in 1:nboot) {
}
}
#> 95% CI for the causal mean difference
-#> 2.679491 , 4.442331
+#> 2.714556 , 4.383686
```
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-stata.md b/docs/15-prop-scores-stata.md
index 7cc9898..a0ec602 100644
--- a/docs/15-prop-scores-stata.md
+++ b/docs/15-prop-scores-stata.md
@@ -345,7 +345,8 @@ Log likelihood = -838.44842 Pseudo R2 = 0.0611
file ./data/nhefs-ps.dta saved
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{./figs/stata-fig-15-2} \end{center}
## Program 15.3
diff --git a/docs/17-causal-surv-r.md b/docs/17-causal-surv-r.md
index b374235..8bea5cf 100644
--- a/docs/17-causal-surv-r.md
+++ b/docs/17-causal-surv-r.md
@@ -58,7 +58,9 @@ ggsurvplot(fit, data = nhefs, xlab="Months of follow-up",
fontsize = 3)
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{17-causal-surv-r_files/figure-latex/unnamed-chunk-2-1} \end{center}
## Program 17.2
@@ -137,7 +139,9 @@ ggplot(hazards.graph, aes(x=time, y=surv)) +
theme(legend.position="bottom")
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{17-causal-surv-r_files/figure-latex/unnamed-chunk-3-1} \end{center}
## Program 17.3
@@ -234,7 +238,9 @@ ggplot(ipw.graph, aes(x=time, y=surv)) +
theme(legend.position="bottom")
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{17-causal-surv-r_files/figure-latex/unnamed-chunk-4-1} \end{center}
## Program 17.4
@@ -350,7 +356,9 @@ ggplot(gf.graph, aes(x=time, y=surv)) +
theme(legend.position="bottom")
```
-
+
+
+\begin{center}\includegraphics[width=0.85\linewidth]{17-causal-surv-r_files/figure-latex/unnamed-chunk-5-1} \end{center}
## Program 17.5
diff --git a/docs/17-causal-surv-stata.md b/docs/17-causal-surv-stata.md
index e6642cc..e317d3c 100644
--- a/docs/17-causal-surv-stata.md
+++ b/docs/17-causal-surv-stata.md
@@ -78,7 +78,8 @@ Observed time interval: (0, survtime]
Analysis time _t: survtime
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{./figs/stata-fig-17-1} \end{center}
## Program 17.2
@@ -278,7 +279,8 @@ psurv0 float %9.0g psurv, interv == Original observat
psurv1 float %9.0g psurv, interv == Duplicated observation
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{./figs/stata-fig-17-2} \end{center}
## Program 17.3
@@ -620,7 +622,7 @@ psurv1 float %9.0g psurv, interv == Duplicated observ
26. drop if newseqn != 1 /* only need one pair */
27.
-r; t=0.00 6:43:12
+r; t=0.00 8:25:46
Command: bootipw_surv
PrY_a0: r(boot_0)
@@ -628,7 +630,7 @@ r; t=0.00 6:43:12
difference: r(boot_diff)
Simulations (10): .........10 done
-r; t=19.98 6:43:32
+r; t=20.55 8:26:06
@@ -646,7 +648,8 @@ Bootstrap results Number of obs = 1,629
------------------------------------------------------------------------------
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{./figs/stata-fig-17-3} \end{center}
## Program 17.4
@@ -866,7 +869,7 @@ file /Users/tom/Documents/GitHub/cibookex-r/figs/stata-fig-17-4.png saved as PNG
5. drop if time != 0
6. /*only predict on new version of data */
-r; t=0.00 6:43:39
+r; t=0.00 8:26:13
Command: bootstdz_surv
PrY_a0: r(boot_0)
@@ -874,7 +877,7 @@ r; t=0.00 6:43:39
difference: r(boot_diff)
Simulations (10): .........10 done
-r; t=23.62 6:44:03
+r; t=25.24 8:26:39
@@ -892,4 +895,5 @@ Bootstrap results Number of obs = 1,629
------------------------------------------------------------------------------
```
-
+
+\begin{center}\includegraphics[width=0.85\linewidth]{./figs/stata-fig-17-4} \end{center}
diff --git a/docs/18-session-info-r.md b/docs/18-session-info-r.md
index 93b9d91..dfff9d9 100644
--- a/docs/18-session-info-r.md
+++ b/docs/18-session-info-r.md
@@ -7,7 +7,7 @@ For reproducibility.
``` r
# install.packages("sessioninfo")
sessioninfo::session_info()
-#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> - Session info -------------------------------------------------------------------------------------------------------------------------------------------
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os macOS Sequoia 15.1
@@ -20,7 +20,7 @@ sessioninfo::session_info()
#> date 2024-11-13
#> pandoc 3.5 @ /opt/homebrew/bin/ (via rmarkdown)
#>
-#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> - Packages -----------------------------------------------------------------------------------------------------------------------------------------------
#> package * version date (UTC) lib source
#> bookdown 0.41 2024-10-16 [1] CRAN (R 4.4.1)
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
@@ -38,5 +38,5 @@ sessioninfo::session_info()
#> [1] /Users/tom/Library/R/arm64/4.4/library
#> [2] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#>
-#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> ----------------------------------------------------------------------------------------------------------------------------------------------------------
```
diff --git a/docs/18-session-info-stata.md b/docs/18-session-info-stata.md
index 36fa199..9007501 100644
--- a/docs/18-session-info-stata.md
+++ b/docs/18-session-info-stata.md
@@ -29,7 +29,7 @@ Serial number: 501809305331
``` r
# install.packages("sessioninfo")
sessioninfo::session_info()
-#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> - Session info -------------------------------------------------------------------------------------------------------------------------------------------
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os macOS Sequoia 15.1
@@ -42,7 +42,7 @@ sessioninfo::session_info()
#> date 2024-11-13
#> pandoc 3.5 @ /opt/homebrew/bin/ (via rmarkdown)
#>
-#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> - Packages -----------------------------------------------------------------------------------------------------------------------------------------------
#> package * version date (UTC) lib source
#> bookdown 0.41 2024-10-16 [1] CRAN (R 4.4.1)
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
@@ -61,5 +61,5 @@ sessioninfo::session_info()
#> [1] /Users/tom/Library/R/arm64/4.4/library
#> [2] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#>
-#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+#> ----------------------------------------------------------------------------------------------------------------------------------------------------------
```
diff --git a/docs/cibookex-r.pdf b/docs/cibookex-r.pdf
index 894ce3e..30df57d 100644
Binary files a/docs/cibookex-r.pdf and b/docs/cibookex-r.pdf differ
diff --git a/docs/cibookex-r.tex b/docs/cibookex-r.tex
index f6d5ad3..a6e333d 100644
--- a/docs/cibookex-r.tex
+++ b/docs/cibookex-r.tex
@@ -1743,15 +1743,15 @@ \section{Program 13.4}\label{program-13.4}
\NormalTok{ ))}
\NormalTok{bootstrap}
\CommentTok{\#\textgreater{} V1 mean se ll}
-\CommentTok{\#\textgreater{} 1 Observed 2.56188497106099 0.314019242951459 1.94641856442359}
-\CommentTok{\#\textgreater{} 2 No Treatment 1.65212306626744 0.303658428350452 1.05696348309852}
-\CommentTok{\#\textgreater{} 3 Treatment 5.11474489549336 0.438830011601556 4.25465387741901}
-\CommentTok{\#\textgreater{} 4 Treatment {-} No Treatment 3.46262182922592 0.288456715740051 2.89725705527671}
+\CommentTok{\#\textgreater{} 1 Observed 2.56188497106099 0.120597104489459 2.32551898962183}
+\CommentTok{\#\textgreater{} 2 No Treatment 1.65212306626744 0.106947069654509 1.4425106614925}
+\CommentTok{\#\textgreater{} 3 Treatment 5.11474489549336 0.358814454471498 4.41148148759683}
+\CommentTok{\#\textgreater{} 4 Treatment {-} No Treatment 3.46262182922592 0.392348048118945 2.6936337855082}
\CommentTok{\#\textgreater{} ul}
-\CommentTok{\#\textgreater{} 1 3.17735137769838}
-\CommentTok{\#\textgreater{} 2 2.24728264943636}
-\CommentTok{\#\textgreater{} 3 5.9748359135677}
-\CommentTok{\#\textgreater{} 4 4.02798660317513}
+\CommentTok{\#\textgreater{} 1 2.79825095250014}
+\CommentTok{\#\textgreater{} 2 1.86173547104237}
+\CommentTok{\#\textgreater{} 3 5.81800830338988}
+\CommentTok{\#\textgreater{} 4 4.23160987294364}
\end{Highlighting}
\end{Shaded}
@@ -2886,16 +2886,16 @@ \section{Program 15.4}\label{program-15.4}
\NormalTok{bootstrap }\OtherTok{\textless{}{-}} \FunctionTok{data.frame}\NormalTok{(}\FunctionTok{cbind}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"Observed"}\NormalTok{, }\StringTok{"No Treatment"}\NormalTok{, }\StringTok{"Treatment"}\NormalTok{,}
\StringTok{"Treatment {-} No Treatment"}\NormalTok{), mean, se, ll, ul))}
\NormalTok{bootstrap}
-\CommentTok{\#\textgreater{} V1 mean se ll}
-\CommentTok{\#\textgreater{} 1 Observed 2.63384609228479 0.128997515912632 2.3810156070009}
-\CommentTok{\#\textgreater{} 2 No Treatment 1.71983636149845 0.0944885980997972 1.53464211227317}
-\CommentTok{\#\textgreater{} 3 Treatment 5.35072300362985 0.369343979138947 4.6268221066108}
-\CommentTok{\#\textgreater{} 4 Treatment {-} No Treatment 3.6308866421314 0.396811917955185 2.85314957430297}
+\CommentTok{\#\textgreater{} V1 mean se ll}
+\CommentTok{\#\textgreater{} 1 Observed 2.63384609228479 0.279890742231742 2.0852703179044}
+\CommentTok{\#\textgreater{} 2 No Treatment 1.71983636149845 0.275568960869064 1.17973112293796}
+\CommentTok{\#\textgreater{} 3 Treatment 5.35072300362985 0.314161588160568 4.73497760550923}
+\CommentTok{\#\textgreater{} 4 Treatment {-} No Treatment 3.6308866421314 0.451854865413406 2.74526737968193}
\CommentTok{\#\textgreater{} ul}
-\CommentTok{\#\textgreater{} 1 2.88667657756869}
-\CommentTok{\#\textgreater{} 2 1.90503061072374}
-\CommentTok{\#\textgreater{} 3 6.0746239006489}
-\CommentTok{\#\textgreater{} 4 4.40862370995983}
+\CommentTok{\#\textgreater{} 1 3.18242186666519}
+\CommentTok{\#\textgreater{} 2 2.25994160005895}
+\CommentTok{\#\textgreater{} 3 5.96646840175047}
+\CommentTok{\#\textgreater{} 4 4.51650590458087}
\end{Highlighting}
\end{Shaded}
@@ -2989,7 +2989,7 @@ \section{Program 15.4}\label{program-15.4}
\NormalTok{ \}}
\NormalTok{\}}
\CommentTok{\#\textgreater{} 95\% CI for the causal mean difference}
-\CommentTok{\#\textgreater{} 2.700067 , 4.423406}
+\CommentTok{\#\textgreater{} 2.714556 , 4.383686}
\end{Highlighting}
\end{Shaded}
@@ -8961,7 +8961,7 @@ \section{Program 17.3}\label{program-17.3-1}
26. drop if newseqn != 1 /* only need one pair */
27.
-r; t=0.00 6:41:04
+r; t=0.00 8:25:46
Command: bootipw_surv
PrY_a0: r(boot_0)
@@ -8969,7 +8969,7 @@ \section{Program 17.3}\label{program-17.3-1}
difference: r(boot_diff)
Simulations (10): .........10 done
-r; t=21.01 6:41:25
+r; t=20.55 8:26:06
@@ -9215,7 +9215,7 @@ \section{Program 17.4}\label{program-17.4-1}
5. drop if time != 0
6. /*only predict on new version of data */
-r; t=0.00 6:41:32
+r; t=0.00 8:26:13
Command: bootstdz_surv
PrY_a0: r(boot_0)
@@ -9223,7 +9223,7 @@ \section{Program 17.4}\label{program-17.4-1}
difference: r(boot_diff)
Simulations (10): .........10 done
-r; t=23.90 6:41:56
+r; t=25.24 8:26:39
diff --git a/docs/index.md b/docs/index.md
index d2d8e86..0cde0d1 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -33,7 +33,8 @@ The Stata code is based on the code by Eleanor Murray and Roger Logan given [her
This repo is rendered at . Click the download button above for the pdf and eBook versions.
-
+
+\begin{center}\includegraphics[width=0.65\linewidth]{figs/download} \end{center}
## Downloading the code
@@ -42,12 +43,14 @@ The repo is available on GitHub [here](https://github.com/remlapmot/cibookex-r).
Either,
* click the green *Clone or download* button then choose to *Open in Desktop* or *Download ZIP*.
-
+
+ \begin{center}\includegraphics[width=0.65\linewidth]{figs/clone-or-download} \end{center}
The *Desktop* option means open in the [GitHub Desktop](https://desktop.github.com/) app (if you have that installed on your machine). The *ZIP* option will give you a zip archive of the repo, which you then unzip.
* or fork the repo into your own GitHub account and then clone or download your forked repo to your machine.
-
+
+ \begin{center}\includegraphics[width=0.65\linewidth]{figs/fork} \end{center}
## Installing dependency packages
It is easiest to open the repo in RStudio, as an RStudio project, by doubling click the `.Rproj` file. This makes sure that R's working directory is at the top level of the repo. If you don't want to open the repo as a project set the working directory to the top level of the repo directories using `setwd()`. Then run:
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
deleted file mode 100644
index fe3c72b..0000000
--- a/docs/reference-keys.txt
+++ /dev/null
@@ -1,68 +0,0 @@
-downloading-the-code
-installing-dependency-packages
-downloading-the-datasets
-program-11.1
-program-11.2
-program-11.3
-program-12.1
-program-12.2
-program-12.3
-program-12.4
-program-12.5
-program-12.6
-program-12.7
-program-13.1
-program-13.2
-program-13.3
-program-13.4
-program-14.1
-program-14.2
-g-estimation-checking-one-possible-value-of-psi
-g-estimation-checking-multiple-possible-values-of-psi
-program-14.3
-g-estimation-closed-form-estimator-linear-mean-models
-g-estimation-closed-form-estimator-for-2-parameter-model
-program-15.1
-program-15.2
-program-15.3
-program-15.4
-program-16.1
-program-16.2
-program-16.3
-program-16.4
-program-16.5
-program-17.1
-program-17.2
-program-17.3
-program-17.4
-program-17.5
-program-11.1-1
-program-11.2-1
-program-11.3-1
-program-12.1-1
-program-12.2-1
-program-12.3-1
-program-12.4-1
-program-12.5-1
-program-12.6-1
-program-12.7-1
-program-13.1-1
-program-13.2-1
-program-13.3-1
-program-13.4-1
-program-14.1-1
-program-14.2-1
-program-14.3-1
-program-15.1-1
-prorgam-15.2
-program-15.3-1
-program-15.4-1
-program-16.1-1
-program-16.2-1
-program-16.3-1
-program-16.4-1
-program-16.5-1
-program-17.1-1
-program-17.2-1
-program-17.3-1
-program-17.4-1