I have the following document, that I am trying to compile with Rstudio:
---
output:
word_document:
pandoc_args: [
"--biblio", "references.bib"
]
---
```{r}
library("knitcitations")
cleanbib()
```
This is a citation citet("10.1098/rspb.2013.1372"):
```{r}
citet("10.1098/rspb.2013.1372")
```
```{r}
write.bibtex(file="references.bib")
```
```{r}
summary(cars)
```
When I run knit, it compiles the .md file, but pandoc gives an error:
processing file: toy.Rmd
|...................... | 33%
ordinary text without R code
|............................. | 44%
label: unnamed-chunk-2
|.................................... | 56%
ordinary text without R code
|........................................... | 67%
label: unnamed-chunk-3
|................................................... | 78%
ordinary text without R code
|.......................................................... | 89%
label: unnamed-chunk-4
|.................................................................| 100%
ordinary text without R code
/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc toy.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output toy.docx --highlight-style tango --biblio references.bib
output file: toy.knit.md
pandoc: Error running filter pandoc-citeproc
pandoc-citeproc not found in path
Error: pandoc document conversion failed with error 83
Execution halted
The generated references file is references.bib:
@Article{Boettiger_2013,
doi = {10.1098/rspb.2013.1372},
url = {http://dx.doi.org/10.1098/rspb.2013.1372},
year = {2013},
month = {Jul},
publisher = {The Royal Society},
volume = {280},
number = {1766},
pages = {20131372-20131372},
author = {C. Boettiger and A. Hastings},
title = {No early warning signals for stochastic transitions: insights from large deviation theory},
journal = {Proceedings of the Royal Society B: Biological Sciences},
}
The error message is indicating that pandoc-citeproc is not found in your $PATH (i.e., /usr/bin/ etc.) One workaround is to create a link from pandoc-citeproc embedded in Rstudio and place it in the /usr/local/bin directory.
In the terminal:
pandoc result: