This is because the default LaTeX template redefines \paragraph. To disable this behaviour, you can use the subparagraph variable in pandoc. You could supply this at the command-line: pandoc –variable subparagraph -o file.pdf file.md Or you could embed it in the document’s YAML metadata, with any non-null value: — subparagraph: yes — From man pandoc … Read more
Go into RStudio and find the system environment variable for RSTUDIO_PANDOC Sys.getenv(“RSTUDIO_PANDOC”) Then put that in your R script prior to calling the render command. Sys.setenv(RSTUDIO_PANDOC=”— insert directory here —“) This worked for me after I’d been struggling to find how rmarkdown finds pandoc. I had to check github to look at the source.