Generate R script using user imported data

Question

I am currently developping a Shiny app that lets a user import a data set, performs analysis on it and then displays the results. I would like the user to be able to download the R script used to perform the calculations, for reproductibility purposes. In order to do this, I would like to print the imported data set directly into the script, and here's how I was thinking to do it:

library(shiny)

df <- data.frame("time" = c(0,1,2,3), "conc" = c(0,0.1,0.2,0.3))

ui <- fixedPage(
    
    fixedRow(
        downloadButton("download_button", label = "Download")
    )
)

server <- function(input, output, session){
    
    output$download_button <- downloadHandler(
        filename = function(){
            paste0("script_", Sys.Date(), ".R")
        },
        content = function(file) {
            writeLines(paste("df <- ", df), file)
        
        }
    )
}

shinyApp(ui,server)

The issue is that the result file looks like this:

df <-  c(0, 1, 2, 3)
df <-  c(0, 0.1, 0.2, 0.3)

And I want it to look like this (or at least something similar):

df <- data.frame("time" = c(0,1,2,3), "conc" = c(0,0.1,0.2,0.3))

Is it even possible?

Thank you for your time.

Perhaps you might want to use dput() in your writeLines statement for a more descriptive look at df? Instead of just df try dput(df)? — Ben
– Ben, Commented Jan 19, 2020 at 14:04
Thanks for the answer. The dput()works on its own, but as soon as I add the Paste() / Paste0() , the output goes back to it's previous state. — Go.0
– Go.0, Commented Jan 19, 2020 at 14:37
Sorry, you would need capture.output in your paste(). When you use dput the result is actually a data.frame --- you need to have this as a string when you use paste() — Ben
– Ben, Commented Jan 19, 2020 at 14:48

Timsy Suri · Accepted Answer · 2020-01-19 14:33:51Z

3

Use the capture.ouput(dput(df)) in the writelines function

  writeLines(paste("df <- ", capture.output(dput(df))), file, sep = "\n")

It will produce this in the Rscript

df <- structure(list(time = c(0, 1, 2, 3), conc = c(0, 0.1, 0.2, 0.3 df <- )), class = "data.frame", row.names = c(NA, -4L))

answered Jan 19, 2020 at 14:33

Timsy Suri

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1 Comment

Timsy Suri Over a year ago

capture.output function captures the output that is sent to the console so it can be stored in a variable or stored in a text file. This could be useful if a void function like str, dput prints to the console but returns no object to be stored.

Roman Luštrik · Accepted Answer · 2020-01-19 14:25:09Z

One solution would be to create a .Rmd rmarkdown script with a header that includes data which would be used in the analysis. This is a small example:

---
title: "title"
output: html_document
date: "`r Sys.Date()`"
params:
  input1: NA
  input2: NA
---

In the script, you would call the parameters using syntax params$input1.

On the server side, you would offer the download like so (example adapter from here):

output$report <- downloadHandler(
  filename = "report.html",
  content = function(file) {
    tempReport <- file.path(tempdir(), "report.Rmd")
    file.copy("report.Rmd", tempReport, overwrite = TRUE)

    rmarkdown::render(tempReport, output_file = file,
      params = list(input1 = mydata1(), input2 = mydata2()),
      envir = new.env(parent = globalenv())
    )
  }
)

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