Accumulating R package references in a Quarto book

bib-at-end.Rmd

# Accumulating R package references in a Quarto book

In writing a book using Quarto, I was looking for a way to automatically
accumulate the packages used in each chapter and write them out to a `pkgs.bib`
file at the end.  (I posted this as a Posit Community question, 
https://community.rstudio.com/t/how-to-accumulate-packages-bib-used-in-a-quarto-book/167619 )

I can easily do this with a `knitr` vignette, where the essence
is to include a chunk at the end,

```
pkgs <- c(.to.cite, .packages()) |> unique()
knitr::write_bib(pkgs, file = "bib/pkgs.bib")
```

But Quarto processes each chapter ceparately, so this cannot work.  A solution involves

* use `.packages()` to get the packages used in each chapter, and append their names
to a text file.

* in the final (References) chapter, read the text file and call `knitr::write_bib()`

The following functions are included in a file, `common.R` which is `source()`ed at the start of every
chapter

```
# write list of packages used at end of every chapter
.pkg_file <- here::here("bib", "pkgs.txt")
write_pkgs <- function() {
  pkgs <- .packages() |> sort() |> unique()
  np <- length(pkgs)
  cat(np, " packages used here:\n", paste(pkgs, collapse = ", ")  )
  if(np > 0) cat(pkgs, file = .pkg_file, append=TRUE, sep = "\n")
}

# read in the list of packages, convert to a vector
read_pkgs <- function() {
  pkgs <- read.csv(.pkg_file, header = FALSE)
  pkgs <- pkgs[, 1] |> as.vector() |> sort() |> unique()
  np <- length(pkgs)
  pkgs
}

# use this in Chapter 1 to start with a clean slate.
clean_pkgs <- function() {
  if (file.exists(.pkg_file)) {
    #Delete file if it exists
    file.remove(.pkg_file)
  }
}

# packages to be cited here, but not actually loaded. 
.to.cite <- c(
  "rgl",
  "nnet", 
	"equatiomatic", 
  "geomtextpath")

```

Then, in the final chapter, I have the following chunk to write out
the `.bib` entries:


```{r}
if(!exists(".to.cite")) .to.cite <- NULL
pkgs <- read_pkgs()
pkgs <- c(.to.cite, pkgs) |> unique()
knitr::write_bib(pkgs, file = "bib/pkgs.bib")
```

Voila!