I’ve written a post about rendering IPA symbols properly regardless of the output format of the R Markdown document. I implemented the ideas into an R package, linguisticsdown.
linguisticsdown provides a Shiny interface to facilitate inserting IPA symbols in R Markdown. See a quick demo of the current feature of linguisticsdown in the gif at the end of the post.
A live demo is hosted on shinyapps.io. For more details, visit linguisticsdown.