In jr-packages/efficientTutorial: Efficient R Programming

Start up

• This chapter deals with start up files

• It's quite easy to make an error and stop R working

• it's also very easy to fix, just delete the file

The .Rprofile file

When R starts up it will run

1. the site-wide R start up configuration file

2. .Rprofile in the current working directory (the directory where R is started on the command-line)

3. If that file doesn't exist, it will then check your home directory

The .Rprofile file

Determine your home area:

path.expand("~")

We can again test whether this file exists using

file.exists("~/.Rprofile")

Ten Minute Task

Ten Minute Task

• Use

    path.expand("~")

to determine your home directory and

    file.exists("~/.Rprofile")

to see if you have an .Rprofile

• Open .Rprofile and add the line

    message("Today is ", Sys.Date())

• Restart R.

Some Examples

Example .Rprofile settings

• options() is a list that contains a number of default options

• In my .Rprofile file, I have the line

options(prompt="R> ", # Exciting new R> prompt
        digits = 4, # No. of digits displayed
        show.signif.stars = FALSE, # I hate stars
        fix_width = 88, # Useful under Linux
        Ncpus = 6L, # Parallel package installation
        continue = " ", # Hide the `+`
        mc.cores = 6L) # Parallel (see later)

Setting the CRAN mirror

r = getOption("repos")             
r["CRAN"] = "https://cran.rstudio.com/"
options(repos = r)
rm(r)

Useful functions

• I also load a couple of useful functions.

• Be very careful about loading functions by default; code is no longer portable.

setnicepar = function(mar=c(3,3,2,1), mgp=c(2,0.4,0), 
    tck=-.01, cex.axis=0.9, las=1, mfrow=c(1,1), ...) {
     par(mar=mar, mgp=mgp, tck=tck,
       cex.axis=cex.axis, las=las, mfrow=mfrow, ...)
     }

Useful functions

• It is perfectly acceptable just to put your functions in your .Rprofile.

• Downside: clutters up your work space.

• If you run rm(list = ls()), your functions will be deleted.

Useful functions

• One neat trick is to combine hidden objects and environments.

• When an object name starts with ., by default it doesn't appear in the output of the ls() function

.obj = 1
ls()

Useful functions

This concept also works with environments. In our .Rprofile file we create a hidden environment

.env = new.env()

Then add our functions to the environment

.env$ht = function(d, n=6) rbind(head(d, n), tail(d,n))

At the end of the .Rprofile file, we use the attach()

attach(.env)

jr-packages/efficientTutorial documentation built on Feb. 16, 2020, 7:05 p.m.