99-references.Rmd

`r if (knitr:::is_html_output()) '# References {-}'`

```{r}
#| label: refs-package-list
#| include: FALSE
# generate a BibTeX database automatically for some R packages
library(targets)
library(visdat)
library(readxl)
library(httr2)
library(jsonlite)
library(tidycensus)
library(pak)


our_write_bib <- function (x = .packages(), file = "", tweak = TRUE, width = NULL, 
          prefix = getOption("knitr.bib.prefix", "R-"), lib.loc = NULL) 
{
  .this.year = sprintf('  year = {%s},', format(Sys.Date(), '%Y'))
  system.file = function(...) base::system.file(..., lib.loc = lib.loc)
  citation = function(...) utils::citation(..., lib.loc = lib.loc)
  x = x[nzchar(x)]
  idx = mapply(system.file, package = x) == ""
  if (any(idx)) {
    warning("package(s) ", paste(x[idx], collapse = ", "), 
            " not found")
    x = x[!idx]
  }
  x = setdiff(x, setdiff(xfun::base_pkgs(), "base"))
  x = sort(x)
  bib = sapply(x, function(pkg) {
    cite = citation(pkg, auto = if (pkg != "base") {
      meta = packageDescription(pkg, lib.loc = lib.loc)
      if (identical(meta$Repository, "CRAN") && !is.null(meta$URL)) {
        if (!grepl("[, ]", meta$URL)) 
          meta$Repository = NULL
      }
      meta
    })
    
    
    if (tweak) {
      cite$title = gsub(sprintf("^(%s: )(\\1)", pkg), 
                        "\\1", cite$title)
      cite$title = gsub(pkg, paste0("{", pkg, "}"), cite$title)
      cite$title = gsub("\\b(R)\\b", "{R}", cite$title)
      cite$title = gsub("\\b(ggplot2)\\b", "{ggplot2}", cite$title)
      cite$title = gsub("\\b(dplyr)\\b", "{dplyr}", cite$title)
      cite$title = gsub("\\b(tidyverse)\\b", "{tidyverse}", cite$title)
      cite$title = gsub("\\b(sf)\\b", "{sf}", cite$title)
      cite$title = gsub(" & ", " \\\\& ", cite$title)
    }
    entry = toBibtex(cite)
    entry[1] = sub("\\{,$", sprintf("{%s%s,", prefix, pkg), 
                   entry[1])
    entry
  }, simplify = FALSE)
  if (tweak) {
    for (i in intersect(names(knitr:::.tweak.bib), x)) {
      message("tweaking ", i)
      bib[[i]] = merge_list(bib[[i]], knitr:::.tweak.bib[[i]])
    }
    bib = lapply(bib, function(b) {
      b["author"] = sub("Duncan Temple Lang", "Duncan {Temple Lang}", 
                        b["author"])
      # b["title"] = gsub("(^|\\W)'([^']+)'(\\W|$)", "\\1\\2\\3", 
      #                   b["title"])
      if (!is.na(b["note"])) 
        b["note"] = gsub("(^.*?https?://.*?),\\s+https?://.*?(},\\s*)$", 
                         "\\1\\2", b["note"])
      if (!("year" %in% names(b))) 
        b["year"] = .this.year
      b
    })
  }
  bib2 = lapply(x, function(pkg) {
    if (pkg == "base") 
      return()
    if (system.file("CITATION", package = pkg) == "") 
      return()
    cites = citation(pkg, auto = FALSE)
    cites = Filter(x = cites, function(cite) {
      !isTRUE(grepl("R package version", cite$note))
    })
    s = knitr:::make_unique(unlist(lapply(cites, function(cite) {
      if (is.null(cite$year)) 
        format(Sys.Date(), "%Y")
      else cite$year
    })))
    mapply(cites, s, FUN = function(cite, suffix) {
      if (isTRUE(grepl("R package version", cite$note))) 
        return()
      entry = toBibtex(cite)
      entry[1] = sub("\\{,$", sprintf("{%s%s,", pkg, suffix), 
                     entry[1])
      entry
    }, SIMPLIFY = FALSE)
  })
  bib = c(bib, unlist(bib2, recursive = FALSE))
  bib = lapply(bib, function(b) {
    idx = which(names(b) == "")
    if (!is.null(width)) 
      b[-idx] = str_wrap(b[-idx], width, 2, 4)
    structure(c(b[idx[1L]], b[-idx], b[idx[2L]], ""), class = "Bibtex")
  })
  if (!is.null(file) && length(x)) 
    xfun::write_utf8(unlist(bib), file)
  invisible(bib)
}



our_write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown', 'renv', 'here'
), 'packages.bib')
```