Sending R output to disk files

Sometimes you want to get the results of an analysis from your R console to a word processor. Copy and paste does not work well unless you are prepared to use fixed width font in the target document. The trick is to send the output to a disk file using the sink() command first.

The sink() command allows you to send anything that would have gone to the console (your screen) to a disk file instead.

sink(file = NULL, append = FALSE, split = FALSE)

You need to supply the filename, setting file = NULL closes the connection and stops sink()ing. To add to an existing file use append = TRUE. If you set split = TRUE the output goes to the console and the file you specified.

When you issue the command a file is created, ready to accept the output. If you set append = FALSE and the file already exists, it will be overwritten. If you set file = TRUE a connection is opened and subsequent output goes to the file.

# Send output to screen and file
> sink(file = "Out1.txt", split = TRUE, append = FALSE)

> summary(lm(Fertility ~ . , data = swiss))

Call:
lm(formula = Fertility ~ ., data = swiss)
Residuals:
     Min       1Q   Median       3Q      Max
-15.2743  -5.2617   0.5032   4.1198  15.3213

Coefficients:
                 Estimate Std. Error t value Pr(>|t|)
(Intercept)      66.91518   10.70604   6.250 1.91e-07 ***
Agriculture      -0.17211    0.07030  -2.448  0.01873 *
Examination      -0.25801    0.25388  -1.016  0.31546
Education        -0.87094    0.18303  -4.758 2.43e-05 ***
Catholic          0.10412    0.03526   2.953  0.00519 **
Infant.Mortality  1.07705    0.38172   2.822  0.00734 **
—
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ‘ 1

Residual standard error: 7.165 on 41 degrees of freedom
Multiple R-squared:  0.7067,     Adjusted R-squared:  0.671
F-statistic: 19.76 on 5 and 41 DF,  p-value: 5.594e-10

# Stop sending output to file
> sink(file = NULL)

Note that even if you set append = FALSE subsequent output is appended to the file. Once you issue the command sink(file = NULL) output stops and you can see your file using any kind of text editor.

If you only want to send a single “result” to a disk file you can use the capture.output() command instead.

capture.output(..., file = NULL, append = FALSE)

You provide the commands that will produce the output and the filename. If you set append = TRUE and the target file exists, the output will be added to the file. If you set append = FALSE (the default) the file will be “blanked” and the output will therefore overwrite the original contents.

Note that there is no equivalent of the split argument, all output goes to the file and cannot be “mirrored” to the console. You can supply several commands, separated by commas.

> capture.output(ls(), search(), file = "Out1.txt")

This example sent the ls() command followed by search(), with the results being output to the disk file.

Once you have your output in a text file you can transfer it to your word processor with a little pre-processing via Excel.

You can also use Paste Special and select the RTF format option, which takes Excel cells and transfers them as table cells in Word.

If you have other elements to transfer, you can deal with them separately. This is not an ideal method but the amount of user intervention is fairly minimal. You might also try opening the file in Word to start with and replacing spaces with Tab characters. You want to keep single spaces as spaces so start by replacing 3-space with 2-space until there are no more double spaces left. Then replace 2-space with Tab (^t in the Word replace box). You’ll need to do some manual editing as this will not produce a perfect result but it will do most of the work automatically. Then save the file and use Excel again, setting the delimiter to Tab.