A few edits

Author: bbbales2

knitr/planetary_motion/README.md

@@ -0,0 +1,3 @@
+Data for the plots in this case study are stored in RDS files in
+`saved_fit` because it takes a long time to generate it. To
+recreate the data, uncomment the appropriate code in `planetary_motion.rmd`.

knitr/planetary_motion/planetary_motion.rmd

@@ -43,12 +43,6 @@ In our presentation, we try to distinguish generalizable methods, problem-specif
 
 ### R setup {-#setup}
 
-```{r include=FALSE}
-# Adjust to your setting
-.libPaths("~/Rlib/")
-# setwd("~/Code/example-models/knitr/planetary_motion")
-```
-
 ```{r message = FALSE}
 library(cmdstanr)
 library(posterior)
@@ -66,11 +60,6 @@ bayesplot::color_scheme_set("viridisC")
 set.seed(1954)
 ```
 
-```{r include=FALSE}
-# Adjust to your setting
-set_cmdstan_path("~/Rlib/cmdstan/")
-```
-
 All the requisite code to run this notebook can be found online, in the [planetary motion github repository](https://github.com/stan-dev/example-models/tree/case-study/planet/knitr/planetary_motion).
 
 ## Building the model {-#sec2}
@@ -134,8 +123,7 @@ plot
 ```
 
 ## Fitting a simple model and diagnosing inference {-#sec3}
-
-A first attempt at fitting the complete model (`planetary_motion_star.stan`) fails spectacularly: the chains do not converge and take a long time to run.
+A first attempt at fitting the complete model ([planetary_motion_star.stan](https://github.com/stan-dev/example-models/blob/master/knitr/planetary_motion/model/planetary_motion_star.stan)) fails spectacularly: the chains do not converge and take a long time to run.
 This is an invitation to start with a simpler model.
 A useful simplification is more manageable but still exhibits the challenges we encounter with the complete model.
 The hope is that a fix in this simple context translates into a fix in a more sophisticated setting.

knitr/planetary_motion/ref.bib

@@ -56,5 +56,3 @@ @article{Yao:2018
               volume = {13},
               pages = {917 - 1003},
               year = {2018}}
-              
-