sink()to send the output to a file, you will have to enclose some commands in
print()to get the same output as on the command line. To run a script, let's say one with the name:
you may either use:
on the command line of R OR
R CMD BATCH /home/jim/psych/adoldrug/partyuse1.R
Let's pause to note a little historical bifurcation that has caused almost as much strife as the question of exactly what the <Delete> key should do. The convention that the slash (/) character is used as a separator in the notation for a filesystem path is not universal. PC-DOS, for example, used the backslash (\). Like Fords vs Chevrolets, French vs English, and whether you crack the egg at the big or small end, it doesn't really matter a rat's behind which one you use as long as it works. To make it work in R, however, where the *NIX convention of using the backslash as an escape character is respected, you will have to double backslashes in paths for them to be read properly. Thus if the filename above was:
I would have to refer to it as:
in an R script.
First, choose your directory. This will be the place where all of your R scripts will be stored. You can either change to this directory before starting R or use the method described in Starting Up. Let's examine the beginning and end of a typical script written for this purpose:
# store the current directory initial.dir<-getwd() # change to the new directory setwd("/home/jim/psych/risk/adol") # load the necessary libraries library(nlme) # set the output file sink("adolrisk03.out") # load the dataset ... # close the output file sink() # unload the libraries detach("package:nlme") # change back to the original directory setwd(initial.dir)
First notice that the script stores the initial directory and changes to the directory where the data is, and where output will be generated. The libraries necessary for the analysis are then loaded. Finally, the output of the script is directed to a text file, producing a record of the analysis. Then comes the action. After the analysis has been completed, the output file is closed, the libraries are unloaded, and the directory is changed back to where the scripts reside. At this point, you may want to start another script or shut down R.
cat("\nMean risk-taking scores for all groups\n\n") brkdn(risk~group,adolrisk03.df)
cat() is used to label a breakdown of means, leaving a blank
line above and two below the label. Spacing the
output with meaningful labels improves the appearance and comprehensibility.
... par(ask=TRUE) xpos<-barplot(loaeval[1,],ylim=c(0,5),main="Lecture evaluation scores", names.arg=eval.names) error.bars(xpos,loaeval) dev.copy2eps("loaeval.ps",width=6,height=6) ... par(ask=FALSE)
par(ask=TRUE) requires you to hit <Return> before each
plot is displayed. If you want such a prompt after display you can
readline("Press <Enter> to continue")
Remember that the little message will show up in the command window and the user
will have to switch to that window to restart the action by pressing
<Enter>. If you want a little window to pop up with a flashing message
that will alert the near-unconscious, get into the Tcl-Tk interface. It's amazing.
The example then uses
dev.copy2eps() to copy the display to a
Postscript file so that the plot may be printed or inserted into a document.
For more information, see An Introduction to R: Device Drivers.
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