How do I get all the output from script I am running in RStudio

Question

I want to see the output of a script that has 149 lines. All the way through the script there are tables that I want to see. I am using RStudio IDE. In the past I have used Tinn-R. I would run the whole script and the lines of code and the printed objects would be visible in the console.

For instance, here is an excerpt

attach(uniquehuman.race.eth)
partA.eth <-table(Ethnicity, Sex,useNA="ifany")
partA.eth
margin.table(partA.eth,1)#row totals
margin.table(partA.eth,2)#column totals
nrow(uniquehuman.race.eth)#total logged in

The above code would give a text output of the tables and the numbers I needed. I could then save the console or copy and paste the whole thing in a text file.

How can I do that in RStudio? The closest I come to it is hitting CTRL-ENTER on each line, but I do not want to do that 149 times. If I hit CTRL-SHIFT-ENTER for "run all", then R processes all the data and puts the objects into memory, but I do not see the output.

Please tell me how I can see all the output and/or send the output to a text file.

Answer 1

I'm one of the RStudio developers. Thanks for the feedback--I'll log a bug.

In the meantime, one workaround is to do source(filename, echo=T) from the console.

Answer 2

You can simply select the code you want to run and press CTRL+ENTER to do what you want in RStudio. This works for multiple lines, exactly like in Tinn-R. If you want to run everything at once in a verbose way, you press CTRL-A CTRL-ENTER.

As another option for saving to a text file, you can check ?sink :

sink(file='path/to/somefile.ext')
... # the code generating output
sink()

sink() redirects all output of the console to a connection, in this case some file. Mind you, this is only the standard output, not the warnings or errors. This command also come in handy to create output files in analyses, in combination with print(), cat(), sprintf() etc.

If you use "run all" in RStudio, you have to explicitly use any of the mentioned functions to generate the output to the file. In principle, RStudio runs silently if you run the whole script.

Answer 3

Use options(verbose=TRUE) to print all output verbosely throughout the script or session.