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Move prior predictive section to avoid conflict with PR stan-dev#439
Placed the section after "Providing an interface" and before "References" so it doesn't conflict with the *_data() section that PR stan-dev#439 adds at line 315.
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vignettes/graphical-ppcs.Rmd

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@@ -314,45 +314,6 @@ See Figure 8 in [Gabry et al. (2019)](#gabry2019) for another example of using
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<br>
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## Using PPC plots for prior predictive checking
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Although this vignette focuses on *posterior* predictive checking, the same
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`ppc_*` functions can be used for **prior** predictive checking as well. The
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idea is the same: instead of passing draws from the posterior predictive
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distribution as `yrep`, you pass draws from the **prior** predictive
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distribution. This can be useful for understanding the implications of your
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priors before conditioning on the data (see Gabry et al. (2019) for more on
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when prior predictive checks are useful).
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For example, with **rstanarm** you can obtain prior predictive draws using
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`posterior_predict()` on a model fit with `prior_PD = TRUE`:
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```{r prior-pd, eval=FALSE}
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fit_prior <- stan_glm(
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y ~ roach100 + treatment + senior,
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offset = log(exposure2),
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family = poisson,
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data = roaches,
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prior_PD = TRUE # sample from prior predictive only
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)
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yrep_prior <- posterior_predict(fit_prior)
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# use the same ppc_ functions with prior predictive draws
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ppc_dens_overlay(y, yrep_prior[1:50, ])
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ppc_stat(y, yrep_prior, stat = "mean")
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```
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If you want to examine the prior predictive distribution *without* comparing to
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observed data, you can use the `ppd_*` functions (PPD = prior/posterior
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predictive distribution) instead:
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```{r ppd-example, eval=FALSE}
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ppd_dens_overlay(yrep_prior[1:50, ])
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ppd_stat(yrep_prior, stat = "mean")
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```
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<br>
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## Providing an interface to bayesplot PPCs from another package
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The **bayesplot** package provides the S3 generic function `pp_check`. Authors of
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and [**brms**](https://CRAN.R-project.org/package=brms) packages.
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<br>
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## Using PPC plots for prior predictive checking
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Although this vignette focuses on *posterior* predictive checking, the same
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`ppc_*` functions can be used for **prior** predictive checking as well. The
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idea is the same: instead of passing draws from the posterior predictive
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distribution as `yrep`, you pass draws from the **prior** predictive
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distribution. This can be useful for understanding the implications of your
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priors before conditioning on the data (see Gabry et al. (2019) for more on
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when prior predictive checks are useful).
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For example, with **rstanarm** you can obtain prior predictive draws using
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`posterior_predict()` on a model fit with `prior_PD = TRUE`:
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```{r prior-pd, eval=FALSE}
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fit_prior <- stan_glm(
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y ~ roach100 + treatment + senior,
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offset = log(exposure2),
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family = poisson,
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data = roaches,
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prior_PD = TRUE # sample from prior predictive only
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)
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yrep_prior <- posterior_predict(fit_prior)
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# use the same ppc_ functions with prior predictive draws
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ppc_dens_overlay(y, yrep_prior[1:50, ])
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ppc_stat(y, yrep_prior, stat = "mean")
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```
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If you want to examine the prior predictive distribution *without* comparing to
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observed data, you can use the `ppd_*` functions (PPD = prior/posterior
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predictive distribution) instead:
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```{r ppd-example, eval=FALSE}
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ppd_dens_overlay(yrep_prior[1:50, ])
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ppd_stat(yrep_prior, stat = "mean")
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```
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<br>
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## References

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