Complete participant setup: repo cloning (RStudio/Positron/Git/ZIP), Quarto note, fix stale chapter numbers

- index.qmd: new 'Getting the materials' subsection naming/linking the repo
  with four clone paths (RStudio, Positron, terminal, Download ZIP) and a
  Quarto-CLI note; drop phantom '(or .R)' (no .R chapter scripts exist)
- README.md: name RStudio or Positron; expand the bare clone step into the
  same four paths with inline URL + Quarto note; fix layout table to 01-16
- setup_check.R: correct stale chapter numbers throughout (MI-SOCP/SCIP is
  ch.11, DNLP/Uno+sparsediff is ch.14; were ch.6/ch.8 from the old layout)

Author: bnaras

README.md

@@ -13,8 +13,21 @@ and uses **CRAN solvers only**.
 
 ## For participants
 
-1. **Install R ≥ 4.3.0** and a recent [RStudio](https://posit.co/download/rstudio-desktop/).
-2. Clone or download this repository and open `cvxr-tutorial-2026.Rproj` in RStudio.
+1. **Install R ≥ 4.3.0** and a recent IDE ---
+   [RStudio](https://posit.co/download/rstudio-desktop/) or
+   [Positron](https://positron.posit.co).
+2. **Get the materials** (this repository):
+
+   - **RStudio:** *File → New Project → Version Control → Git*, paste
+     `https://github.com/bnaras/cvxr_tutorial.git`, then open `cvxr-tutorial-2026.Rproj`.
+   - **Positron:** Command Palette → *Git: Clone* → paste the same URL → open the folder.
+   - **Terminal:** `git clone https://github.com/bnaras/cvxr_tutorial.git`
+   - **No Git:** *Code → Download ZIP* on the repo page and unzip.
+
+   You also need the [Quarto CLI](https://quarto.org/docs/get-started/) (≥ 1.4) to
+   render chapters or the whole book. RStudio bundles Quarto; Positron and terminal
+   users install it once from that link. (Running individual code chunks needs no
+   render step.)
 3. Install the packages (CRAN only):
 
    ```r
@@ -53,7 +66,7 @@ needs no LaTeX. Rendered output goes to `_book/`.
 | Path | What |
 |------|------|
 | `index.qmd` | Preface |
-| `01-…`–`10-…qmd` | Chapters (see `_quarto.yml` for the structure) |
+| `01-…`–`16-…qmd` | Chapters (see `_quarto.yml` for the structure) |
 | `setup_check.R` | Pre-tutorial environment check |
 | `_check_status.R` | Helper sourced by example chunks |
 | `references.bib`, `cvxr.bib` | Bibliography |

index.qmd

@@ -27,9 +27,10 @@ that will interest experienced optimizers too; exercises marked with a star
 
 This is a **hands-on** book. You are meant to *run the code*, not just read it.
 
-- Open the accompanying **RStudio project** and work through each chapter's `.qmd`
-  (or `.R`) by **executing the code chunks** as you read. You do not need to type
-  anything --- click *Run* (or press `Ctrl/Cmd+Enter`) and watch what happens.
+- Open the accompanying **project** (see *Getting the materials* below) and work
+  through each chapter's `.qmd` by **executing the code chunks** as you read. You do
+  not need to type anything --- click *Run* (or press `Ctrl/Cmd+Enter`) and watch what
+  happens.
 - Each hands-on chapter ends with **exercises**. Try them, then click to reveal
   the solution:
 
@@ -39,6 +40,30 @@ Solutions look like this --- the code and its output are right here, hidden unti
 you want them.
 :::
 
+## Getting the materials
+
+All the materials --- chapter sources, data, and the `setup_check.R` script below ---
+live in one Git repository:
+[github.com/bnaras/cvxr_tutorial](https://github.com/bnaras/cvxr_tutorial). Get a copy
+in whichever way suits you:
+
+- **RStudio:** *File → New Project → Version Control → Git*, paste
+  `https://github.com/bnaras/cvxr_tutorial.git` as the repository URL, and click
+  *Create Project*. Then open `cvxr-tutorial-2026.Rproj`.
+- **Positron:** open the Command Palette (`Ctrl/Cmd+Shift+P`), run *Git: Clone*, paste
+  the same URL, and open the cloned folder.
+- **Terminal:** `git clone https://github.com/bnaras/cvxr_tutorial.git`, then open the
+  folder in your editor.
+- **No Git?** Use the green *Code → Download ZIP* button on the repository page and
+  unzip it.
+
+You will also need **[Quarto](https://quarto.org/docs/get-started/)** (≥ 1.4) to render
+the book or preview chapters. **RStudio bundles Quarto**, so there is nothing extra to
+install there. **Positron** and plain-terminal users should install the Quarto CLI
+once from the link above. You can still *run individual code chunks* without rendering
+anything --- Quarto is only required when you render a whole chapter or the full book
+(`quarto render`).
+
 ## Installation
 
 Everything in this tutorial runs on **CRAN packages only**. Two lines install all

setup_check.R

@@ -12,7 +12,7 @@
 ##
 ## Base R only -- no external dependencies -- so it runs even if a package
 ## failed to install. CORE = the four built-in solvers used by most chapters;
-## EXTRA = scip (ch.6, MI-SOCP) and Uno + sparsediff (ch.8, nonlinear) -- both
+## EXTRA = scip (ch.11, MI-SOCP) and Uno + sparsediff (ch.14, nonlinear) -- both
 ## are hands-on chapters, but if an EXTRA fails you can still do everything else.
 ## ---------------------------------------------------------------------------
 
@@ -21,7 +21,7 @@ line <- function(tag, label, detail = "") cat(sprintf("  [%s] %-28s %s\n", tag,
 hdr  <- function(x) cat(sprintf("\n== %s ==\n", x))
 
 core_ok  <- TRUE   # CVXR + four built-in solvers + helpers
-extra_ok <- TRUE   # scip (ch.6) and Uno + sparsediff (ch.8)
+extra_ok <- TRUE   # scip (ch.11) and Uno + sparsediff (ch.14)
 
 ## --- 1. R version --------------------------------------------------------
 hdr("R version")
@@ -48,10 +48,10 @@ core_ok <- check_pkg("highs", "1.14")  && core_ok   # CVXR requires highs >= 1.1
 ## Helper packages used by the example chapters (CRAN)
 for (h in c("ggplot2", "tidyr", "nnls", "glmnet", "boot", "png", "bench"))
   core_ok <- check_pkg(h) && core_ok
-## Extra solvers for chapters 6 and 8 (CRAN, in CVXR Enhances -> separate installs)
-extra_ok <- check_pkg("scip",       "1.10")  && extra_ok   # ch.6 MI-SOCP
-extra_ok <- check_pkg("Uno",        "2.7.3") && extra_ok   # ch.8 nonlinear (pulls rmumps)
-extra_ok <- check_pkg("sparsediff", "0.4.0") && extra_ok   # ch.8 autodiff
+## Extra solvers for chapters 11 and 14 (CRAN, in CVXR Enhances -> separate installs)
+extra_ok <- check_pkg("scip",       "1.10")  && extra_ok   # ch.11 MI-SOCP
+extra_ok <- check_pkg("Uno",        "2.7.3") && extra_ok   # ch.14 nonlinear (pulls rmumps)
+extra_ok <- check_pkg("sparsediff", "0.4.0") && extra_ok   # ch.14 autodiff
 
 ## --- 3. Functional solve test: the four core solvers ---------------------
 ## Tiny LP: minimize sum(x) s.t. x >= 1, x in R^2  ->  optimal value 2.
@@ -75,9 +75,9 @@ if (requireNamespace("CVXR", quietly = TRUE)) {
   core_ok <- FALSE
 }
 
-## --- 4. Chapter 6: SCIP integer solve (MI-SOCP-capable interface) --------
+## --- 4. Chapter 11: SCIP integer solve (MI-SOCP-capable interface) -------
 ## Tiny integer LP: minimize sum(x) s.t. x >= 1.5, integer -> value 4.
-hdr("Chapter 6 solver (SCIP integer solve, expect value 4)")
+hdr("Chapter 11 solver (SCIP integer solve, expect value 4)")
 if (requireNamespace("CVXR", quietly = TRUE) &&
     requireNamespace("scip", quietly = TRUE)) {
   xi <- Variable(2, integer = TRUE)
@@ -89,27 +89,27 @@ if (requireNamespace("CVXR", quietly = TRUE) &&
   line(mark(res$ok), "SCIP", res$detail)
   if (!isTRUE(res$ok)) extra_ok <- FALSE
 } else {
-  line("WARN", "SCIP", "scip not installed -- needed for chapter 6")
+  line("WARN", "SCIP", "scip not installed -- needed for chapter 11")
   extra_ok <- FALSE
 }
 
-## --- 5. Chapter 8: DNLP backends present ---------------------------------
-hdr("Chapter 8 backends (Uno + sparsediff)")
+## --- 5. Chapter 14: DNLP backends present --------------------------------
+hdr("Chapter 14 backends (Uno + sparsediff)")
 dnlp_ok <- requireNamespace("Uno", quietly = TRUE) &&
            requireNamespace("sparsediff", quietly = TRUE)
 line(if (dnlp_ok) "PASS" else "WARN", "Uno + sparsediff",
-     if (dnlp_ok) "loadable" else "missing -- needed for chapter 8 (ipopt NOT needed)")
+     if (dnlp_ok) "loadable" else "missing -- needed for chapter 14 (ipopt NOT needed)")
 if (!dnlp_ok) extra_ok <- FALSE
 
 ## --- Summary -------------------------------------------------------------
 hdr("Summary")
 cat(sprintf("  CORE   (most chapters)      : %s\n", if (core_ok)  "READY" else "NOT READY"))
-cat(sprintf("  EXTRAS (chapters 6 and 8)   : %s\n", if (extra_ok) "READY" else "incomplete"))
+cat(sprintf("  EXTRAS (chapters 11 and 14) : %s\n", if (extra_ok) "READY" else "incomplete"))
 if (!core_ok) {
   cat("\n  -> Fix CORE first:\n")
   cat("     install.packages(c(\"CVXR\",\"ggplot2\",\"tidyr\",\"nnls\",\"glmnet\",\"boot\",\"png\",\"bench\"))\n")
 } else if (!extra_ok) {
-  cat("\n  -> Core is ready (most chapters work). For chapters 6 and 8 also:\n")
+  cat("\n  -> Core is ready (most chapters work). For chapters 11 and 14 also:\n")
   cat("     install.packages(c(\"scip\", \"Uno\", \"sparsediff\"))\n")
 } else {
   cat("\n  All set -- every chapter is ready.\n")