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I have an R code my_code.R which takes in an argument a file test.txt. I can use:
Rscript -e my_code.R test.txt
and run the script, but i want to use stitch() from knitR to generate the report of the script in pdf/tex.
I have trolled around stack overflow and used following suggestions, but didn't get any results:
Rscript -e "library(knitr);knit('my_code.R "-args arg1=test.txt" ')"
Rscript -e "knitr::stitch('my_code.R "-args arg1=test.txt"')"
Here is another similar discussion on what i want (link), but with option for adding argument(s).
622
Running R from the Command LineTo open up the command prompt, just press the windows key and search for cmd. When R is installed, it comes with a utility called Rscript. This allows you to run R commands from the command line.
Use commandArgs(trailingOnly = TRUE) to obtain a vector of the command-line arguments that a program was run with.
Use Rscript to run R from bash You can run it using Rscript test. r . And even better, if you add an initial shebang line #!/usr/bin/env Rscript in the script above and make it executable with chmod +x test. r , you can directly launch your R script with ./test.
I do not see why this is not possible. Here is my_code.R:
commandArgs(TRUE)
And I simply run
Rscript -e "library(knitr); stitch('my_code.R')" --args foo bar whatever=blabla
I get the output
It seems you did not use double quotes correctly in your original attempt. It should be
Rscript -e "library(knitr); stitch('my_code.R')" --args arg1=test.txt
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