data-raw/process_refs.R

In joelnitta/canaper: Categorical Analysis of Neo- And Paleo-Endemism

# Filter a list of references in YAML format to those cited in an RMD file
#
# The YAML list should be exported from Zotero
# like this: file -> "export library" -> "Better CSL YAML"

library(tidyverse)
library(yaml)
library(assertr)

filter_refs <- function(rmd, yaml_in, yaml_out) {

  # Set path to RMD file
  rmd_file <- here::here(rmd)

  # Parse RMD file and extract citation keys
  citations <-
    readr::read_lines(rmd_file) %>%
    stringr::str_split(" |;") %>%
    unlist() %>%
    magrittr::extract(., stringr::str_detect(., "@")) %>%
    stringr::str_remove_all("\\[|\\]|\\)|\\(|\\.$|,|\\{|\\}") %>%
    magrittr::extract(., stringr::str_detect(., "^@|^-@")) %>%
    stringr::str_remove_all("^@|^-@") %>%
    unique() %>%
    sort() %>%
    tibble(key = .)

  # Read in YAML including all references exported from Zotero
  ref_yaml <- yaml::read_yaml(yaml_in)

  # Extract citation keys from YAML, filter to only those in the RMD
  cite_keys <- map_chr(ref_yaml$references, "id") %>%
    tibble(
      key = .,
      order = 1:length(.)
    ) %>%
    inner_join(citations, by = "key") %>%
    # Stop if any keys are missing
    assert(not_na, everything())

  # Filter YAML to only those citation keys in the RMD
  list(references = ref_yaml$references[cite_keys$order]) %>%
    # Write out the YAML file
    yaml::write_yaml(file = yaml_out)
}

filter_refs(
  "vignettes/canape.Rmd",
  here::here("data-raw/main_library.yaml"),
  here::here("vignettes/references.yaml")
)

filter_refs(
  "vignettes/how-many-rand.Rmd",
  here::here("data-raw/main_library.yaml"),
  here::here("vignettes/nrand_references.yaml")
)