Bibliography not working when rendering a R Markdown document within an R Shiny App

Question

Problem

I am attempting to render an R Markdown document within a Shiny App, which I have achieved successfully using David's very helpful solution in this post (RMarkdown in Shiny Application). However, I have been unable to render the document with citations from a .bib file which is placed in the same directory as both the Shiny app and R Markdown document. Please find a minimum reproducible example below.

R Markdown Document

RMarkdownFile.rmd

---
title: "RMarkdownFile"
author: "Test Author"
date: "15/10/2020"
output: html_document
bibliography: bibliography.bib
link-citations: yes
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Statement

ggplot2 [@wickham2016ggplot2] is a great package!

## References

Bibliography

bibliography.bib

@book{wickham2016ggplot2,
  title={ggplot2: elegant graphics for data analysis},
  author={Wickham, Hadley},
  year={2016},
  publisher={springer}
}

Shiny App

app.R

library(shiny)
library(knitr)

rmdfiles <- c("RMarkdownFile.rmd")
sapply(rmdfiles, knit, quiet = T)

ui <- shinyUI(
    fluidPage(
        withMathJax(includeMarkdown("RMarkdownFile.md"))
  )
)
server <- function(input, output) { }

shinyApp(ui, server)

Result

Knitting the RMarkdownFile.rmd outside of the app works perfectly, producing the following output

RMarkdownFile
Test Author
15/10/2020
Statement
ggplot2 (Wickham 2016) is a great package!

References
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. springer.

However rendering RMarkdownFile.md within the Shiny app as above fails to generate the citations and references in the document from the bibliography.bib file, as below

Statement
ggplot2 [@wickham2016ggplot2] is a great package!

References

Update - Solution

After playing around with a few different methods, the simplest method ended up working. Below is the updated Shiny App which includes the html document rendered from R markdown document, with citations.

app.R

library(shiny)
library(knitr)

rmarkdown::render("RMarkdownFile.Rmd")

ui <- shinyUI(
    fluidPage(
        includeHTML("RMarkdownFile.html")
  )
)
server <- function(input, output) { }

shinyApp(ui, server)

Additional problem

However..... whilst this works with basic HTML documents produced from R markdown, when including "self_contained: false" in the YAML chunk of the RMarkdown document as follows

---
title: "RMarkdownFile"
author: "Test Author"
date: "15/10/2020"
output: 
    html_document:
        self_contained: false
bibliography: bibliography.bib
link-citations: yes
---

results in items that are placed in a supplementary folder, which in this case would be entitled "RMarkdownFile_files", failing to be found by the Shiny app. Inspecting the missing elements in Shiny via Rstudio devtools reveals the following error:

Failed to load resource: the server responded with a status of 404 (Not Found)

Conversely when including "self_contained: true" in the YAML chunk, the elements are no longer missing, but I lose access to multiple tabs in my non-reprex Shiny app which uses shinydashboard.

Edit: I have now documented this problem in an additional post Including a HTML file rendered from RMarkdown in R Shiny apps using shinydashboard is causing tabItems to break

Correct method

Edit: these problems have now been resolved using the code below, note that the RMarkdownFile.html file must be placed in the "www" folder in the Shiny app directory unless rendered there directly.

library(shiny)
library(knitr)

rmarkdown::render("RMarkdownFile.Rmd")

ui <- shinyUI(
    fluidPage(
        htmltools::tags$iframe(src = "RMarkdownFile.html", width = '100%',  height = 1000,  style = "border:none;"))
  )
)
server <- function(input, output) { }

shinyApp(ui, server)

Answer 1

As detailed in my updated post above, to include a HTML document in a Shiny app use the following code (obvious in hindsight!):

library(shiny)
library(knitr)

rmarkdown::render("RMarkdownFile.Rmd")

ui <- shinyUI(
    fluidPage(
        includeHTML("RMarkdownFile.html")
  )
)
server <- function(input, output) { }

shinyApp(ui, server)

This works for a very basic shiny app, however using shinydashboard produces additional problems detailed here, Including a HTML file rendered from RMarkdown in R Shiny apps using shinydashboard is causing tabItems to break

Edit: these problems have now been resolved using the code below, note that the RMarkdownFile.html file must be placed in the "www" folder in the Shiny app directory unless rendered there directly.

library(shiny)
library(knitr)

rmarkdown::render("RMarkdownFile.Rmd")

ui <- shinyUI(
    fluidPage(
        htmltools::tags$iframe(src = "RMarkdownFile.html", width = '100%',  height = 1000,  style = "border:none;"))
  )
)
server <- function(input, output) { }

shinyApp(ui, server)