Run selected chunks from one Rmd in another

Question

I've run my analyses in a source Rmd file and would like to knit a clean version from a final Rmd file using only a few of the chunks from the source. I've seen a few answers with regard to pulling all of the chunks from a source Rmd in Source code from Rmd file within another Rmd and How to source R Markdown file like `source('myfile.r')`?. I share the concern with these posts in that I don't want to port out a separate .R file, which seems to be the only way that read_chunk works.

I think I'm at the point where I can import the source Rmd, but now I'm not sure how to call specific chunks from it in the final Rmd. Here's a reproducible example:

SourceCode.Rmd

---
title: "Source Code"
output:
  pdf_document:
    latex_engine: xelatex
---

```{r}
# Load libraries
library(knitr) # Create tables
library(kableExtra) # Table formatting
# Create a dataframe
df <- data.frame(x = 1:10,
                 y = 11:20,
                 z = 21:30)
```

Some explanatory text

```{r table1}
# Potentially big block of stuff I don't want to have to copy/paste
# But I want it in the final document
kable(df, booktabs=TRUE,
      caption="Big long title for whatever") %>%
  kable_styling(latex_options=c("striped","HOLD_position")) %>%
  column_spec(1, width="5cm") %>%
  column_spec(2, width="2cm") %>%
  column_spec(3, width="3cm")
```

[Some other text, plus a bunch of other chunks I don't need for anyone to see in the clean version.]

```{r}
save(df, file="Source.Rdata")
```

FinalDoc.Rmd

---
title: "Final Doc"
output:
  pdf_document:
    latex_engine: xelatex
---

```{r setup, include=FALSE}
# Load libraries and data
library(knitr) # Create tables
library(kableExtra) # Table formatting
opts_chunk$set(echo = FALSE)
load("Source.Rdata")
```

As far as I can tell, this is likely the best way to load up SourceCode.Rmd (from the first linked source above):

```{r}
options(knitr.duplicate.label = 'allow')
source_rmd2 <- function(file, local = FALSE, ...){
  options(knitr.duplicate.label = 'allow')

  tempR <- tempfile(tmpdir = ".", fileext = ".R")
  on.exit(unlink(tempR))
  knitr::purl(file, output=tempR, quiet = TRUE)

  envir <- globalenv()
  source(tempR, local = envir, ...)
}

source_rmd2("SourceCode.Rmd")
```

At this point, I'm at a loss as to how to call the specific chunk table1 from SourceCode.Rmd. I've tried the following as per instructions here with no success:

```{r table1}
```

```{r}
<<table1>>
```

The first seems to do nothing, and the second throws an unexpected input in "<<" error.

My suggestion would be the same as this answer, you can save the results(figures, tables etc) and load results & do the formatting in your report. — TC Zhang
@TCZhang, yeah if all I wanted to do was load specific objects, that would be fine. I actually want to bring in more complex chunks (kable tables, plots, etc) that I've already worked out in the source. I've made the example more complex to demonstrate what I'd like. — bcarothers
@TCZhang, ah, ok - upon further work, I just need to take it a step further and stick the formatted table into an object in the source, save it, then call that object in the final. That works - thanks! — bcarothers

Bryan Shalloway Bryan Shalloway · Accepted Answer · 2021-04-01T13:36:11

0

votes

I wrote a function source_rmd_chunks() that sources chunk(s) by label name. See gist.

Run selected chunks from one Rmd in another

1 Answers