add links to overview pages

mitzimorris · mitzimorris · commit 5b1563cd1573 · 2019-12-12T10:45:24.000-05:00
diff --git a/src/functions-reference/_bookdown.yml b/src/functions-reference/_bookdown.yml
@@ -1,4 +1,5 @@
-new_session: TRUE
+new_session: FALSE
+delete_merged_file: TRUE
 
 rmd_files: [
   "index.Rmd",
@@ -35,4 +36,3 @@ rmd_files: [
   "references.Rmd"
   ]
 
-delete_merged_file: TRUE
diff --git a/src/functions-reference/index.Rmd b/src/functions-reference/index.Rmd
@@ -5,6 +5,7 @@ subtitle: "`r paste('Version', Sys.getenv('STAN_DOCS_VERSION'))`"
 author: "Stan Development Team"
 description: "Reference for the functions defined in the Stan math library and available in the Stan programming language."
 site: bookdown::bookdown_site
+cover-image: img/logo_tm.png
 documentclass: book
 bibliography: [../bibtex/all.bib]
 biblio-style: apalike
@@ -13,11 +14,10 @@ fontsize: 10pt
 monofont: "Lucida Console"
 subparagraph: yes
 ---
-# <i style="font-size: 110%; padding:1.5em 0 0 0; color:#990017;">Overview</i> {-}
 
-<img style="float:right; margin: -2em 0em 4em 4em" src="img/logo_tm.png" width="225" alt="Stan logo" />
+# <i style="font-size: 110%; padding:1.5em 0 0 0; color:#990017;">Overview</i> {-}
 
-#### About {-}
+<img style="float:right; margin: -2em 0em 4em 4em" src="https://mc-stan.org/images/stan_logo.png" width="225" alt="Stan logo" />
 
 This is the reference for the functions defined in the Stan math
 library and available in the Stan programming language.
@@ -28,16 +28,29 @@ probability library, algorithms for Bayesian posterior inference and
 posterior analysis, along with interfaces and analysis tools in all of
 the popular data analysis languages.
 
+In addition to this reference manual, there is a user's guide and
+a language reference manual for the Stan language and algorithms.
+The [*Stan User's Guide*](https://mc-stan.org/docs/stan-users-guide/index.html)
+provides example models and programming
+techniques for coding statistical models in Stan.
+The [*Stan Reference Manual*](https://mc-stan.org/docs/reference-manual/index.html)
+specifies the Stan programming language
+and inference algorithms.
+
+There is also a separate installation and getting started guide for
+each of the Stan interfaces (R, Python, Julia, Stata, MATLAB, 
+Mathematica, and command line).
 
 #### Interfaces and Platforms {-}
 
 Stan runs under Windows, Mac OS X, and Linux.
 
 Stan uses a domain-specific programming language that is portable
-across data anlsysi languages.  Stan has interfaces for R, Python,
+across data analysis languages.  Stan has interfaces for R, Python,
 Julia, MATLAB, Mathematica, Stata, and the command line, as well
-as an alternative language interface in Scala.  See the web
-site (link below) for links and getting started instructions.
+as an alternative language interface in Scala.  See the web site
+[https://mc-stan.org](https://mc-stan.org) for interface-specific
+links and getting started instructions 
 
 #### Web Site {-}
 
diff --git a/src/reference-manual/index.Rmd b/src/reference-manual/index.Rmd
@@ -17,17 +17,19 @@ subparagraph: yes
 
 # <i style="font-size: 110%; padding:1.5em 0 0 0; color:#990017;">Overview</i> {-}
 
-<img style="float:right; margin: -2em 0em 4em 4em" src="img/logo_tm.png" width="225" alt="Stan logo" />
+<img style="float:right; margin: -2em 0em 4em 4em" src="https://mc-stan.org/images/stan_logo.png" width="225" alt="Stan logo" />
 
 This is the official reference manual for Stan's *programming
 language* for coding probability models, *inference algorithms* for
 fitting models and making predictions, and *posterior analysis* tools
 for evaluating the results.  This manual applies to all Stan
-inteferfaces.
+interfaces.
 
-There are two additional interface-neutral manuals, a *Functions
-Reference* listing all the built-in functions and their signatures,
-and a *User's Guide* providing examples and programming techniques.
+There are two additional interface-neutral manuals, the
+[*Stan Functions Reference*]((https://mc-stan.org/docs/functions-reference/index.html)
+listing all the built-in functions and their signatures,
+and the [*Stan User's Guide*]((https://mc-stan.org/docs/stan-users-guide/index.html)
+providing examples and programming techniques.
 There is also a separate installation and getting started guide for
 each interface.
 
diff --git a/src/stan-users-guide/index.Rmd b/src/stan-users-guide/index.Rmd
@@ -16,41 +16,39 @@ monofont: "Lucida Console"
 subparagraph: yes
 ---
 
-# About this Book {-}
+# <i style="font-size: 110%; padding:1.5em 0 0 0; color:#990017;">Overview</i> {-}
 
 <img style="float:right; margin: -2em 0em 4em 4em" src="img/logo-tm.png" width="225" alt="Stan logo" />
 
-This book is the official user's guide for Stan.  It provides example
-models and programming techniques for coding statistical models in Stan.
+#### About this user's guide {-}
 
-#### How to use this book {-}
+This is the official user's guide for Stan.  It provides example
+models and programming techniques for coding statistical models in Stan.
 
-Part 1 gives Stan code and discussions for several important classes
+- Part 1 gives Stan code and discussions for several important classes
 of models.
 
-Part 2 discusses various general Stan programming techniques that are
+- Part 2 discusses various general Stan programming techniques that are
 not tied to any particular model.
 
-The appendices provide a style guide and advice for users of BUGS and JAGS.
-
-We recommend working through this book using the textbooks _Bayesian
-Data Analysis_ and _Statistical Rethinking: A Bayesian Course with
-Examples in R and Stan_ as references on the concepts, and using the
-Stan Reference Manual when necessary to clarify programming issues.
-Further resources are given at the end of the introductory chapter.
-
-#### Additional Stan manuals and guides {-}
+- The appendices provide a style guide and advice for users of BUGS and JAGS.
 
 In addition to this user's guide, there are two reference manuals for
-the Stan language and algorithms.  The *Stan Reference Manual*
+the Stan language and algorithms.  The [*Stan Reference Manual*](https://mc-stan.org/docs/reference-manual/index.html)
 specifies the Stan programming language and inference algorithms. The
-*Stan Functions Reference* specifies the functions built into the Stan
-programming language.
+[*Stan Functions Reference*](https://mc-stan.org/docs/functions-reference/index.html)
+specifies the functions built into the Stan programming language.
 
 There is also a separate installation and getting started guide for
 each of the Stan interfaces (R, Python, Julia, Stata, MATLAB, 
 Mathematica, and command line).
 
+We recommend working through this guide using the textbooks _Bayesian
+Data Analysis_ and _Statistical Rethinking: A Bayesian Course with
+Examples in R and Stan_ as references on the concepts, and using the
+[*Stan Reference Manual*](https://mc-stan.org/docs/reference-manual/index.html)
+when necessary to clarify programming issues.
+
 #### Web resources {-}
 
 Stan is an open-source software project, resources for which are

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`		`-new_session: TRUE`
	`1`	`+new_session: FALSE`
	`2`	`+delete_merged_file: TRUE`
`2`	`3`
`3`	`4`	`rmd_files: [`
`4`	`5`	`"index.Rmd",`
`@@ -35,4 +36,3 @@ rmd_files: [`
`35`	`36`	`"references.Rmd"`
`36`	`37`	`]`
`37`	`38`
`38`		`-delete_merged_file: TRUE`