rautomationr-markdowncommentsreproducible-research

How to write reproducible comment in rmarkdown


Can anyone help in how to write a reproducible comment in Rmarkdown?

For example, we have the data set as shown below:

age fnlwgt education_num
39 77516 13
50 83311 13
38 215646 9
53 234721 7

In Rmarkdown report comments are typed using # before the text within code chunk. I want to write a reproducible comment for mean age.

# The average age is 45

Is there any way to write the above comment as reproducible? In case I change the values for age variable, the average value should automatically updated in the comment...

I would be thankful for your kind support.

Regards, Farhan


Solution

  • Option 1

    One option could be generating the code chunk dynamically using chunk option results="asis".

    ---
    title: "Reproducible comments"
    output: html_document
    ---
    
    ```{r setup, include=FALSE}
    knitr::opts_chunk$set(echo = TRUE)
    ```
    
    ## R Markdown
    
    ```{r dt, echo=FALSE}
    df <- tibble::tribble(
      ~age, ~fnlwgt, ~education_num,
       39L,  77516L,            13L,
       50L,  83311L,            13L,
       38L, 215646L,             9L,
       53L, 234721L,             7L
      )
    
    ```
    
    
    ```{r results="asis", echo=FALSE}
    cmnt <- paste0(
    "```{r}\n",
    "df <- tibble::tribble(
      ~age, ~fnlwgt, ~education_num,
       39L,  77516L,            13L,
       50L,  83311L,            13L,
       38L, 215646L,             9L,
       53L, 234721L,             7L
      )\n\n",
    "# The average age is ", mean(df$age), "\n",
    "```\n"
    )
    
    cat(cmnt)
    ```
    

    comment created dynmically in code chunk


    Option 2

    Another option could be using knitr::knit_expand to dynamically expand the comments with {{}} in a template r-markdown file.

    Suppose this is the template r-markdown file,


    template.Rmd

    
    ```{r}
    mean_age <- mean(dat$age)
    # The mean age is {{age}}
    
    mean_educ <- mean(dat$education_num)
    # The mean education_num is {{educ}}
    ```
    

    Now to expand these comments in our main document, we use knitr::knit_expand and pass the variable to be expanded in the comments, and then we add the contents of template.Rmd using knitr::knit_child.

    ---
    title: "Reproducible comments"
    output: 
      html_document:
        keep_md: TRUE
    ---
    
    ```{r setup, include=FALSE}
    knitr::opts_chunk$set(echo = TRUE)
    ```
    
    ## R Markdown
    
    ```{r}
    dat <- tibble::tribble(
      ~age, ~fnlwgt, ~education_num,
       39L,  77516L,            13L,
       50L,  83311L,            13L,
       38L, 215646L,             9L,
       53L, 234721L,             7L
      )
    ```
    
    ## Comments reproduced dynamically
    
    ```{r, echo=FALSE, results='asis'}
    src = knitr::knit_expand(
      "template.Rmd", 
      age = mean(dat$age), 
      educ = mean(dat$education_num)
    )
    
    res = knitr::knit_child(text = src, quiet = TRUE)
    cat(res, sep = '\n')
    ```
    

    dynamically added comments