CODEWITHSUNDEEP
rr-markdown
bretauv
bretauv

Reputation: 8577

Modify a .bib file from R Markdown

In the example below, I generate the bibliography for packages from a chunk of code. However, there is an error in the BibTeX entry for one package. I could modify this entry manually but my change will be overwritten next time I knit my file.

Therefore, I would like to know if it is possible to modify the line in the .bib file from a chunk in R Markdown, so that the entry is automatically corrected each time the file is knitted.

Example:

---
title: "Cite R packages"
author: ''
date: ""
output:
  pdf_document
bibliography: mistakeref.bib
---

```{r echo=FALSE}
# If not installed yet: 
# install.packages("cem")
```

This is a citation of a paper: @R-cem 

```{r cite-packages, echo=FALSE}
knitr::write_bib("cem", file = "mistakeref.bib", tweak = TRUE)
```

mistakeref.bib will be created by the code, but there is an error in the Bibtex entry for the package cem. I would like to replace:

author = {{Iacus} and Stefano M. and {King} and {Gary} and {Porro} and {Giuseppe}},

by:

author = {Stefano M. Iacus and Gary King and Giuseppe Porro},

Basically, it would be a sort of automatic "search and replace" from R. I have some trouble understanding this answer and I am not sure if it corresponds to what I would like to do.

Upvotes: 1

Views: 415

Answers (1)

jay.sf
jay.sf

Reputation: 73682

Read in the .bib file using readLines. Then use grep to identify the "bad" line (. is a special character, so we need to escape using \\.). Then just replace and save using cat. 

l <- readLines("mybib.bib")
l[grep("Stefano M\\.", l)] <- 
  "  author = {Stefano M. Iacus and Gary King and Giuseppe Porro},"
cat(l, sep="\n", file="mybib1.bib")

Just extend the grep regex until there is one single match.

Upvotes: 1

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