2 Saving R Output Automatically
When working in the RStudio, R echoes commands, prints output, and returns error messages all in one place: the Console. However, the Console only buffers a limited amount of output, making it difficult to work with large quantities of output.
There are numerous methods of capturing printed output automatically. Here we will consider two basic methods that you might use when working within RStudio.
One option is to use the
sink() function. This redirects your
output to a file, while commands and error messages continue
to go to the console. This gives you clean (SAS-style) output,
and might be suitable for producing a simple report.
If you are running many similar commands with similar output, using this approach to create a single file quickly becomes difficult to read.
sink command to begin saving output, and another
empty (NULL) sink command to stop.
sink("outputfile.txt") t.test(rnorm(15, mean=2)) sink()
Which saves the following text in a file called “outputfile.txt”:
One Sample t-test data: rnorm(15, mean = 2) t = 9.4023, df = 14, p-value = 1.993e-07 alternative hypothesis: true mean is not equal to 0 95 percent confidence interval: 1.855096 2.951549 sample estimates: mean of x 2.403322
It is also possible to
sink() error messages. However,
this quickly gets complicated, and can be difficult to interpret.
If you want to save a large quantity of output that includes the
commands that produced it, you really want
You must first save your script. Then you process that file.
For example, save a file, testscript.R, with the following commands:
# testscript.R, used as an example t.test(mpg ~ am, data=mtcars, var.equal=TRUE)
Then issue this command in the Console:
tools::Rcmd("BATCH --no-save testscript.R")
In the Files pane you can find the output file and open it:
R version 4.0.2 (2020-06-22) -- "Taking Off Again" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # testscript.R, used as an example > > t.test(mpg ~ am, data=mtcars, var.equal=TRUE) Two Sample t-test data: mpg by am t = -4.1061, df = 30, p-value = 0.000285 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -10.84837 -3.64151 sample estimates: mean in group 0 mean in group 1 17.14737 24.39231 > > proc.time() user system elapsed 0.28 0.17 0.56
R CMD BATCH command has a lot of options you could
specify, mostly manipulating how your R session is configured.
For instance, the
--no-save option tells R not to save your
workspace at the end of this script.
2.3 Exercises - Saving Output
- Use the scripts you created in section 1.3.5, Exercises - Saving Files.
- Sink the results of the one-sample t-test.
- Batch process the two-sample t-test script.