Reuse R child Rmd files - error: duplicate chunk labels

Question

I wrote an Rmd Markdown file main.Rmd which works on the basis of the data of a certain logfile (logfile1.Rda):

load("logfile1.Rda")

In this main.Rmd I refer to several child chunks:

{r child = 'child1.Rmd'}

and

{r child = 'child2.Rmd'}

and so on...

Now, I want to refer to a second logfile (logfile2.Rda):

load("logfile2.Rda")

and to reuse the child Rmd files again:

{r child = 'child1.Rmd'}

and

{r child = 'child2.Rmd'}

and so on...

But, as expected, there is the "duplicate chunk labels" warning.

Do you have an idea, how to reuse my child Rmd files which includes several chunks?

I already tried it, but nothing happened. **Where** do I have to add this? — , Feb 26 '21 at 11:32
Not sure, It should have worked, read it here : https://bookdown.org/yihui/rmarkdown-cookbook/duplicate-label.html — PKumar, Feb 26 '21 at 11:40
I cannot add it in my Rprofile, because I want others to reproduce my stuff. And adding it into the main.Rmd doesn't work — , Feb 26 '21 at 11:43
How about assigning numbers for chunks in your main.Rmd (i <- 1 for logfile 1 and after that i <- 2 for logfile 2) and then using them in the child as chunk name like ```{r chunk{{i}} ,eval = TRUE, results = "asis", echo=FALSE, warning=FALSE}` At least this worked for me when looping to create some plots with the same child.rmd You would need to use knit_expand in this case e.g. `knit_expand(text = readLines('child.rmd'), encoding = "UTF-8")` — kukuk1de, Feb 26 '21 at 13:34
Works! See: https://stackoverflow.com/questions/12095113/r-knitr-possible-to-programmatically-modify-chunk-labels — , Mar 01 '21 at 20:33

score 0 · Accepted Answer · answered Mar 17 '21 at 08:59

If found a solution:

load("logfile1.Rda")
z <- 1

src <- lapply(z, function(z) knitr::knit_expand(file = "child1.Rmd"))

r knitr::knit(text = unlist(src))

src <- lapply(z, function(z) knitr::knit_expand(file = "child2.Rmd"))

r knitr::knit(text = unlist(src))

load("logfile2.Rda")
z <- 1

src <- lapply(z, function(z) knitr::knit_expand(file = "child1.Rmd"))

r knitr::knit(text = unlist(src))

src <- lapply(z, function(z) knitr::knit_expand(file = "child2.Rmd"))

r knitr::knit(text = unlist(src))

Within the child-files I added {{z}} to each chunk label.

1 Answers1