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2020-12-06
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/*    Author :    Daniel tulps liu  */
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[ 1 ]   require package

复制代码



> library(rstan)
> library(ggplot2)
> library(foreign)
>
> sesame <- read.dta("sesame.dta")
> attach(sesame)
>
> ## Rename variables of interest
> watched <- regular
> encouraged <- encour
> y <- postlet
>
> ## Instrumental variables estimate (sesame_one_pred_a.stan)
> ## lm (watched ~ encouraged)
>
> dataList.1 <- list(N=length(watched), watched=watched,encouraged=encouraged)
> sesame_one_pred_a.sf1 <- stan(file='sesame_one_pred_a.stan', data=dataList.1,
+                               iter=1000, chains=4)

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.001 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 10 seconds.
Chain 1: Adjust your expectations accordingly!
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 2).
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 3).
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 4).
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Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
> print(sesame_one_pred_a.sf1)
Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

          mean se_mean   sd   2.5%    25%    50%    75%  97.5% n_eff Rhat
beta[1]   0.55    0.00 0.04   0.47   0.52   0.55   0.57   0.62   782    1
beta[2]   0.36    0.00 0.05   0.27   0.33   0.36   0.39   0.45   819    1
sigma     0.38    0.00 0.02   0.35   0.37   0.38   0.40   0.42  1300    1
lp__    110.19    0.04 1.20 106.95 109.65 110.48 111.08 111.59   909    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:18:11 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
>
> beta.post <- extract(sesame_one_pred_a.sf1, "beta")$beta
> beta.mean1 <- colMeans(beta.post)
>
> ## (sesame_one_pred_b.stan)
> ## lm (y ~ encouraged)
>
> dataList.2 <- list(N=length(y), watched=y,encouraged=encouraged)

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2020-12-6 09:22:11
> sesame_one_pred_b.sf1 <- stan(file='sesame_one_pred_a.stan', data=dataList.2,
+                               iter=1000, chains=4)

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1:  Elapsed Time: 0.081 seconds (Warm-up)
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Chain 1:

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 2).
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Chain 2: Adjust your expectations accordingly!
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Chain 2:

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 3).
Chain 3:
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 4).
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Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
> print(sesame_one_pred_b.sf1)
Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

           mean se_mean   sd    2.5%     25%     50%     75%   97.5% n_eff Rhat
beta[1]   24.89    0.05 1.38   22.19   23.98   24.91   25.76   27.71   897    1
beta[2]    2.92    0.06 1.77   -0.55    1.78    2.95    4.12    6.32   967    1
sigma     13.41    0.02 0.64   12.22   12.96   13.37   13.83   14.76  1111    1
lp__    -739.55    0.04 1.24 -742.69 -740.15 -739.21 -738.64 -738.14   840    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:18:16 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
>
> beta.post <- extract(sesame_one_pred_b.sf1, "beta")$beta
> beta.mean2 <- colMeans(beta.post)
>
>
> iv.est.1 <- beta.mean2[2] / beta.mean1[2]
> print(iv.est.1)
[1] 8.077231
> library(rstan)
> library(ggplot2)
>
> source("10.5_CasualEffectsUsingIV.R") # where data was cleaned
The following objects are masked from sesame (pos = 3):

    _Isite_2, _Isite_3, _Isite_4, _Isite_5, age, agecat, encour, id, peabody, postbody,
    postclasf, postform, postlet, postnumb, postrelat, prebody, preclasf, preform,
    prelet, prenumb, prerelat, regular, rownames, setting, sex, site, viewcat, viewenc


SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
Chain 1: Adjust your expectations accordingly!
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 2).
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 3).
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 4).
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Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

          mean se_mean   sd   2.5%    25%    50%    75%  97.5% n_eff Rhat
beta[1]   0.54    0.00 0.04   0.47   0.52   0.54   0.57   0.63   931    1
beta[2]   0.36    0.00 0.05   0.27   0.33   0.36   0.40   0.46   854    1
sigma     0.38    0.00 0.02   0.35   0.37   0.38   0.39   0.42  1440    1
lp__    110.21    0.04 1.18 107.38 109.61 110.54 111.10 111.59   754    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:18:48 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
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2020-12-6 09:22:50
SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
Chain 1:
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Chain 1: Adjust your expectations accordingly!
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 2).
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SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 3).
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Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

           mean se_mean   sd    2.5%     25%     50%     75%   97.5% n_eff Rhat
beta[1]   24.90    0.06 1.40   22.24   23.97   24.87   25.81   27.69   643    1
beta[2]    2.92    0.07 1.78   -0.57    1.70    2.94    4.17    6.28   692    1
sigma     13.39    0.02 0.61   12.31   12.96   13.35   13.79   14.66  1203    1
lp__    -739.48    0.04 1.15 -742.23 -740.00 -739.21 -738.63 -738.13   851    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:18:53 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
[1] 8.002048
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2020-12-6 09:23:57
> pretest <- prelet
>
> ## 2 stage least squares (sesame_one_pred_a.stan)
> ## lm (watched ~ encouraged)
>
> dataList.1 <- list(N=length(watched), watched=watched,encouraged=encouraged)
> sesame_one_pred_2a.sf1 <- stan(file='sesame_one_pred_a.stan', data=dataList.1,
+                                iter=1000, chains=4)

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
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Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
> print(sesame_one_pred_2a.sf1)
Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

          mean se_mean   sd   2.5%    25%    50%    75%  97.5% n_eff Rhat
beta[1]   0.55    0.00 0.04   0.47   0.52   0.55   0.57   0.63   947    1
beta[2]   0.36    0.00 0.05   0.26   0.33   0.36   0.40   0.46   981    1
sigma     0.38    0.00 0.02   0.35   0.37   0.38   0.39   0.42  1380    1
lp__    110.14    0.05 1.29 106.88 109.56 110.51 111.08 111.58   786    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:18:58 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
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2020-12-6 09:24:33
> beta.post <- extract(sesame_one_pred_2a.sf1, "beta")$beta
> beta.mean2a <- colMeans(beta.post)
>
> watched.hat <- beta.mean2a[1] + beta.mean2a[2] * encouraged
>
> ## (sesame_one_pred_2b.stan)
> ## lm (y ~ watched.hat)
>
> dataList.2 <- list(N=length(y), watched=y,encouraged=watched.hat)
> sesame_one_pred_2b.sf1 <- stan(file='sesame_one_pred_a.stan', data=dataList.2,
+                                iter=1000, chains=4)

SAMPLING FOR MODEL 'sesame_one_pred_a' NOW (CHAIN 1).
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2020-12-6 09:25:05
> print(sesame_one_pred_2b.sf1)
Inference for Stan model: sesame_one_pred_a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

           mean se_mean   sd    2.5%     25%     50%     75%   97.5% n_eff Rhat
beta[1]   20.66    0.16 3.98   12.53   17.96   20.80   23.37   28.33   600 1.01
beta[2]    7.89    0.20 4.99   -2.41    4.55    7.68   11.26   18.15   607 1.01
sigma     13.42    0.02 0.62   12.28   12.99   13.40   13.84   14.68   823 1.00
lp__    -739.56    0.05 1.25 -742.81 -740.13 -739.22 -738.66 -738.15   608 1.00

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:19:03 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
>
> ## Adjusting for covariates in a IV framework (sesame_multi_preds_3a.stan)
> ## lm (watched ~ encouraged + pretest + as.factor(site) + setting)
>
> dataList.3 <- list(N=length(watched), watched=watched,encouraged=encouraged,pretest=pretest, site=site,setting=setting)
> sesame_multi_pred_3a.sf1 <- stan(file='sesame_multi_preds_3a.stan',
+                                  data=dataList.3,
+                                  iter=1000, chains=4)

SAMPLING FOR MODEL 'sesame_multi_preds_3a' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0 seconds
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Chain 1: Adjust your expectations accordingly!
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SAMPLING FOR MODEL 'sesame_multi_preds_3a' NOW (CHAIN 2).
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SAMPLING FOR MODEL 'sesame_multi_preds_3a' NOW (CHAIN 3).
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Warning message:
In system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) :
  'C:/rtools40/usr/mingw_/bin/g++' not found
> print(sesame_multi_pred_3a.sf1)
Inference for Stan model: sesame_multi_preds_3a.
4 chains, each with iter=1000; warmup=500; thin=1;
post-warmup draws per chain=500, total post-warmup draws=2000.

          mean se_mean   sd   2.5%    25%    50%    75%  97.5% n_eff Rhat
beta[1]   0.66    0.00 0.11   0.45   0.58   0.66   0.73   0.88  1010    1
beta[2]   0.34    0.00 0.05   0.24   0.31   0.34   0.38   0.45  1507    1
beta[3]   0.01    0.00 0.00   0.00   0.00   0.00   0.01   0.01  2915    1
beta[4]   0.03    0.00 0.07  -0.11  -0.02   0.03   0.08   0.17  1147    1
beta[5]  -0.11    0.00 0.07  -0.24  -0.16  -0.12  -0.07   0.02  1133    1
beta[6]  -0.34    0.00 0.07  -0.49  -0.39  -0.34  -0.29  -0.21  1250    1
beta[7]  -0.29    0.00 0.11  -0.51  -0.36  -0.29  -0.22  -0.09  1313    1
beta[8]  -0.05    0.00 0.05  -0.15  -0.09  -0.06  -0.02   0.05  1336    1
sigma     0.36    0.00 0.02   0.32   0.34   0.35   0.37   0.39  1682    1
lp__    127.78    0.07 2.16 122.77 126.48 128.09 129.41 131.02   980    1

Samples were drawn using NUTS(diag_e) at Sun Dec 06 09:19:50 2020.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at
convergence, Rhat=1).
>
> beta.post <- extract(sesame_multi_pred_3a.sf1, "beta")$beta
> beta.mean3a <- colMeans(beta.post)
>
> watched.hat <- beta.mean3a[1] + beta.mean3a[2] * encouraged + beta.mean3a[3] * pretest + beta.mean3a[4] * (site==2) + beta.mean3a[5] * (site==3) + beta.mean3a[6] * (site==4) + beta.mean3a[7] * (site==5) + beta.mean3a[8] * setting
>
> ## (sesame_multi_preds_3b.stan)
> ## lm (y ~ watched.hat + pretest + as.factor(site) + setting)
> dataList.4 <- list(N=length(watched.hat), watched=y,encouraged=watched.hat,pretest=pretest, site=site,setting=setting)
> sesame_multi_pred_3b.sf1 <- stan(file='sesame_multi_preds_3b.stan',
+                                  data=dataList.4,
+                                  iter=1000, chains=4)
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