Using `list.files()` for bibliography field in Rmd YAML

Question

I need some help to automatically list all *.bib files in ../bib directory for bibliography field in Rmd YAML using list.files() function.

I have three bib files ("a.bib", "b.bib", "c.bib") in ../bib directory. Without having to manually type in every file name in bibliography field of YAML, I would like to automatically parse each bib file name with its relative path for the field so that I just simply add more bib files in the "bib" directory whenever I need more references. I have tried some possible code like below; however, it failed. Any help would be greatly appreciated.

---
title: "Test Document"
output: pdf_document
bibliography: ['`r paste0("bib/", list.files("bib", pattern = "(*.bib)$"))`']
---


# Intro

This is test.

I would like to have the bibliography field in YAML is filled with the existing *.bib file name list (with their relative path) as follows:

bibliography: ["bib/a.bib", "bib/b.bib", "bib/c.bib"]

twb10 twb10 · Accepted Answer · 2019-01-20T17:22:41

You seem to be on track with using single quotes to indicate executable R code in your YAML header, but nothing I have tried seems to work. This might not be possible...

Rather than trying to execute an expression that references each .bib file in your YAML header, why not create a new, merged bibliography.

To create a merged bibliography, you can use the bib2df package.

Try the following code:

# Load the bib2df library.
library(bib2df)

# Set path to .bib files. 
bib_path <- paste0(getwd(),"/bib")

# Create vector of all .bib files. 
bib_refs <- list.files(path=bib_path,pattern = ".bib")

# Create an empty list for storing bib data frames. 
bibs_list <- list()

# Loop through bib_refs and store as df in bibs_list
for (i in 1:length(bib_refs)){
  ref_path <- paste0(bib_path,"/",bib_refs[i])
  bibs_list[[i]] <- bib2df(ref_path)
  }

# bind dfs in list.
bibs_df <- do.call(rbind,bibs_list)

# Create new merged bibliography
df2bib(bibs_df, file = paste0(bib_path,"/","bibliography.bib"))

Now you will probably need to specify a path to your .bib files that differs from your working directory, where you are rendering the .R or .Rmd file. To do this, I changed my YAML header to look like this:

bibliography: D:\\Documents\\R\\StackOverflow\\bib\\bibliography.bib

Using `list.files()` for bibliography field in Rmd YAML

1 Answers