#17 from jhrcook/bookdown

Convert site to bookdown format

.gitignore

@@ -234,3 +234,6 @@ po/*~
 /*_files/
 
 # End of https://www.toptal.com/developers/gitignore/api/macos,python,r,jupyternotebooks
+
+_main.rds
+bookdown.rds

Makefile

@@ -6,14 +6,7 @@ SHELL=/bin/bash
 help:
 	@echo "available commands"
 	@echo " - help               : information about available commands"
-	@echo " - render             : render the distill website"
-	@echo " - notebooks          : run Notes and Assignment Rmd"
-	@echo " - build              : run all Rmd and render the site"
+	@echo " - book              : run all notebooks and build the gitbook"
 
-render:
-	Rscript -e "rmarkdown::render_site()" && rm -r docs/data
-
-notebooks:
-	Rscript run-all-notebooks.R
-
-build: notebooks render
+book:
+	Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'

_bookdown.yml

@@ -0,0 +1,67 @@
+title: "Notes for the Bayesian Data Analysis course"
+author: "Joshua Cook"
+description: "My notes and work for the Bayesian Data Analysis course taught by Aki Vehtari."
+book_filename: bookdown
+
+url: 'https://jhrcook.github.io/bayesian-data-analysis-course/'
+github-repo: 'hrcook/bayesian-data-analysis-course'
+twitter-handle: 'joshdoesa'
+
+date: "`r Sys.Date()`"
+
+documentclass: book
+new_session: yes
+delete_merged_file: true
+edit: https://github.com/jhrcook/bayesian-data-analysis-course/blob/master/%s
+view: https://github.com/jhrcook/bayesian-data-analysis-course/blob/master/%s
+
+before_chapter_script: ["src/globals.R"]
+
+output_dir: "docs"
+
+rmd_files: [
+  "index.Rmd",
+
+  "notes-intro.Rmd",
+  "notes-01_introduction_bda3-01.Rmd",
+  "notes-02_basics-of-Bayesian-inference_bda3-02.Rmd",
+  "notes-03_multidimensional-posterior_bda3-03.Rmd",
+  "notes-04_monte-carlo_bda3-10.Rmd",
+  "notes-05_mcmc_bda3-11.Rmd",
+  "notes-06_hmc-nuts-stan_bda3-12.Rmd",
+  "notes-07_hierarchical-models_bda3-5.Rmd",
+  "notes-08_model-checking-and-cv_bda3-6-7.Rmd",
+  "notes-09_model-selection_bda3-7.Rmd",
+  "notes-10_decision-analysis_bda3-9.Rmd",
+  "notes-11_normal-approx-freq-properties_bda3-04.Rmd",
+  "notes-12_extended-topics.Rmd",
+  "notes-13_intro-to-regression-models_bda3-14.Rmd",
+  "notes-14_hierarchical-linear-models_bda3-15.Rmd",
+  "notes-17_parametric-nonlinear-models_bda3-19.Rmd",
+  "notes-18_basis-function-models_bda3-20.Rmd",
+  "notes-19_gaussian-processes_bda3-21.Rmd",
+  "notes-20_finite-mixture-models_bda3-22.Rmd",
+  "notes-21_Dirichlet-process-models_bda3-23.Rmd",
+
+  "assignment_intro.Rmd",
+  "assignment-01.Rmd",
+  "assignment-02.Rmd",
+  "assignment-03.Rmd",
+  "assignment-04.Rmd",
+  "assignment-05.Rmd",
+  "assignment-06.Rmd",
+  "assignment-07.Rmd",
+  "assignment-08.Rmd",
+  "assignment-09.Rmd",
+
+  "exercises_intro.Rmd",
+  "exercises-01.Rmd",
+  "exercises-02.Rmd",
+  "exercises-07.Rmd",
+  "exercises-19.Rmd",
+
+  "stan_models.Rmd",
+
+  "about.Rmd",
+  "references.Rmd"
+]

_generate_models_notebook.R

@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript
+
+library(glue)
+
+# ---- Configuration ----
+
+# Directory contains the Stan models.
+MODELS_DIR <- file.path("models")
+# Name of the notebook to generate.
+OUTPUT_RMD_FILE <- file.path("stan_models.Rmd")
+
+# ----
+
+stan_model_files <- list.files(
+  MODELS_DIR,
+  pattern = "stan$",
+  full.names = TRUE,
+  recursive = FALSE,
+  ignore.case = TRUE
+)
+stan_model_files <- sort(stan_model_files)
+cat(glue("number Stan models: {length(stan_model_files)}"), "\n")
+
+stan_model_to_markdown <- function(model_file) {
+  model_txt <- readLines(model_file)
+  model_txt <- paste(model_txt, collapse = "\n")
+  md_txt <- "
+  ## Model: `{basename(model_file)}`
+
+  ```stan
+  {model_txt}
+  ```
+
+  "
+  return(glue(md_txt))
+}
+
+rmd_text <- "# (PART) Models {-}
+
+# Stan models
+
+Below are the Stan models built as a part of this course.
+The original files are available in the GitHub repo in the \"models\" directory.
+
+"
+
+for (mdl_file in stan_model_files) {
+  model_md <- stan_model_to_markdown(mdl_file)
+  rmd_text <- paste(rmd_text, model_md, sep = "\n")
+}
+
+rmd_text <- paste(rmd_text, "\n")
+writeLines(rmd_text, OUTPUT_RMD_FILE)
+cat(glue("output: {OUTPUT_RMD_FILE}"), "\n")

_output.yml

@@ -0,0 +1,17 @@
+bookdown::gitbook:
+  config:
+    toc:
+      collapse: section
+      before: |
+        <li><strong><a href="./">Notes for BDA3</a></strong></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="_blank">Published with bookdown</a></li>
+    search:
+      engine: fuse
+    edit:
+      link: https://github.com/hadley/r4ds/edit/master/%s
+      text: "Edit"
+    sharing:
+      github: true
+      twitter: true
+      facebook: false

about.Rmd

@@ -1,18 +1,18 @@
----
-title: "About"
-description: |
-  Some additional details about this website and it's author.
----
+# (PART) Misc {-}
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = FALSE)
-```
+# About {-}
 
 ## The website
 
-This site is built with ['distill'](https://rstudio.github.io/distill/) and deployed on GitHub pages.
-The main point of the website is to display my course notes in a easy to read and search format.
-It isn't perfect nor optimal, but there is a good balance of functionality and simplicity.
+The purpose of this website is to serve as a resource for using my notes and work for this course in the future.
+Originally, I built it using ['distill'](https://rstudio.github.io/distill/) and deployed it as a simple static website on GitHub.
+This worked well and was quick to build because the notebooks did not need to be re-run each time.
+Though it is a very flexible platform, it had some limitations and I didn't like the styling of the notebooks in HTML.
+I'm sure this could have been endlessly adjusted in CSS, but I realized firs that the ['bookdown'](https://pkgs.rstudio.com/bookdown/) format may be more appropriate for my needs.
+
+I transformed this site into a 'bookdown' book after completing the course.
+It took a bit of rearrangement, but I think the product is more logical and easier to use.
+It has replaced the 'distill' website completely and is deployed on GitHub.
 
 ## About me
 

assignments/jhcook-assignment-01.Rmd → assignment-01.Rmd

@@ -1,18 +1,14 @@
----
-title: "Assignment 1"
-date: "2021-08-19"
-output: distill::distill_article
----
+# Assignment 1
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, comment = "#>", dpi = 300)
-```
+2021-08-19
 
-**[Assignment 1](assignment-01.pdf)**
+**[Assignment 1](`r paste0(CM_URL, "assignment-01.pdf")`)**
 
 ## Setup
 
-```{r}
+```{r setup, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE, comment = "#>", dpi = 300)
+
 library(glue)
 ```
 
@@ -238,3 +234,9 @@ stopifnot(round(p_identical_twin(1 / 100, 1 / 500), 7) == 0.2857143)
 
 p_identical_twin(fraternal_prob = 1 / 150, identical_prob = 1 / 400)
 ```
+
+---
+
+```{r}
+sessionInfo()
+```

docs/assignments/jhcook-assignment-02.Rmd → assignment-02.Rmd

@@ -1,18 +1,14 @@
----
-title: "Assignment 2"
-date: "2021-08-30"
-output: distill::distill_article
----
+# Assignment 2
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, comment = "#>", dpi = 300)
-```
+2021-08-30
 
-**[Assignment 2](assignment-02.pdf)**
+**[Assignment 2](`r paste0(CM_URL, "assignment-02.pdf")`)**
 
 ## Setup
 
-```{r, warning=FALSE, message=FALSE}
+```{r setup, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = TRUE, comment = "#>", dpi = 300)
+
 for (f in list.files(here::here("src"), pattern = "R$", full.names = TRUE)) {
   source(f)
 }
@@ -173,3 +169,9 @@ posteriors %>%
 
 The posterior is not very sensitive to the prior save for the exception of an overly-confident prior of $\text{Beta}(20, 100)$.
 This is likely due to the large amount of data, meaning that the likelihood dominated the posterior.
+
+---
+
+```{r}
+sessionInfo()
+```