R help system

An interesting feature of R is that it duiscarded tranditional Unix man format and created its own help system.

The material below is adapted from chapter The R environment  of  the Introduction to R by R Core Team

R does not use tranditional unix man format an provides its own built-in help facility. Hhelp is available in HTML format by running

> help.start()

which will launch a Web browser that allows the help pages to be browsed with hyperlinks. On UNIX, subsequent help requests are sent to the HTML-based help system. The ‘Search Engine and Keywords’ link in the page loaded by help.start()  is particularly useful as it is contains a high-level concept list which searches though available functions. It can be a great way to get your bearings quickly and to understand the breadth of what R has to offer.

Help on the Internet

There are many excellent resources on R on the Internet. Here are a few:

• The R Project’s manuals are available from the R home page, http://www.r-project.org/. Click Manuals.
• Several splecialised R search engines are listed on the R home page. One of them that deserve attention is RSeek search engine: http://www.rseek.org/.
• The sos  package offers highly sophisticated searching of R materials.
• You can post your R questions to r-help, the R list server. You can obtain information about this and other R list servers at http://www.r-project.org/mail.html. You can use various interfaces. I like Gmane (http://www.gmane.org/).

Because of its single-letter name, R is difficult to search for using general-purpose search engines such as Google. But there are tricks you can employ. One approach is to use Google’s filetype criterion. To search for R scripts (files having a .R suffix) pertaining to, say, permutations, enter this:

filetype:R permutations -rebol

The -rebol  asks Google to exclude pages with the word “rebol,” as the REBOL programming language uses the same suffix.

The Comprehensive R Archive Network (CRAN), at http://cran.r-project.org/, is a repository of user-contributed R code and thus makes for a good Google search term. Searching for “lm CRAN,” for instance, will help you find material on R’s lm()  function.

Access internal help system using command line help() function

To get information about particular function you can use help() function from the command line.

To get more information on any specific named function, for example solve, the command is

> help(solve)

A shorter alternative is

> ?solve

Similarly to get information on the seq()  function, you need to use:

> help(seq)

or

> ?seq

Special characters and some reserved words must be quoted when used with the help()  function.

You can enclose the argument iether in double or single quotes, making it a “character string”: This is a must for reserved words such as  if, for  and function. For example:

> ?"<"

> help("[[")

Either form of quote mark may be used to escape the other, as in the string "It's important". Our convention is to use double quote marks for preference.

The help.search  command (alternatively ??) allows searching for help in various ways. For example,

> ??solve

Try ?help.search  for details and more examples.

The examples on a help topic can normally be run by

> example(topic)

Windows versions of R have other optional help systems: for further details use

> ?help

The example() Function

Each of the help entries comes with examples. One really nice feature of R is that the example()  function will actually run those examples for you. Here’s an illustration:

> example(seq)

seq> seq(0, 1, length.out=11)
 [1] 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

seq> seq(stats::rnorm(20))
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20

seq> seq(1, 9, by = 2) # match
[1] 1 3 5 7 9

seq> seq(1, 9, by = pi)# stay below
[1] 1.000000 4.141593 7.283185

seq> seq(1, 6, by = 3)
[1] 1 4

seq> seq(1.575, 5.125, by=0.05)
 [1] 1.575 1.625 1.675 1.725 1.775 1.825 1.875 1.925 1.975 2.025 2.075 2.125
[13] 2.175 2.225 2.275 2.325 2.375 2.425 2.475 2.525 2.575 2.625 2.675 2.725
[25] 2.775 2.825 2.875 2.925 2.975 3.025 3.075 3.125 3.175 3.225 3.275 3.325
[37] 3.375 3.425 3.475 3.525 3.575 3.625 3.675 3.725 3.775 3.825 3.875 3.925
[49] 3.975 4.025 4.075 4.125 4.175 4.225 4.275 4.325 4.375 4.425 4.475 4.525
[61] 4.575 4.625 4.675 4.725 4.775 4.825 4.875 4.925 4.975 5.025 5.075 5.125

seq> seq(17) # same as 1:17
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17

The seq()  function generates various kinds of numeric sequences in arithmetic progression. Running example(seq)  resulted in R’s running some examples of seq()  before our very eyes.

Imagine how useful this can be for graphics! If you are interested in seeing what one of R’s excellent graphics functions does, the example()  function will give you a “graphic” illustration.

To see a quick and very nice example, try running the following command:

> example(persp)

This displays a series of sample graphs for the persp()  function. One of these is shown in Figure 1-2. Press enter in the R console when you are ready to go to the next one. Note that the code for each example is shown in the console, so you can experiment by tweaking the arguments.

If You Don’t Know Quite What You’re Looking For

You can use the function help.search()  to do a Google-style search through R’s documentation. For instance, say you need a function to generate random variates from multivariate normal distributions. To determine which function, if any, does this, you could try something like this:

> help.search("multivariate normal")

This produces a response containing this excerpt:

mvrnorm(MASS)           Simulate from a Multivariate Normal
                        Distribution

You can see that the function mvrnorm()  will do the job, and it is in the package MASS.

There is also a question-mark shortcut to help.search():

> ??"multivariate normal"

Help for Other Topics

R’s internal help files include more than just pages for specific functions. For example, the previous section mentioned that the function mvrnorm()  is in the package MASS. You can get information about the function by entering this:

> ?mvrnorm

And you can also learn about the entire package by typing this:

> help(package=MASS)

Help is available for general topics, too. For instance, if you’re interested in learning about files, type the following:

> ?files

This gives you information about a number of file-manipulation functions, such as file.create().

Here are some other topics:

Arithmetic
Comparison
Control
Dates
Extract
Math
Memory
NA
NULL
NumericaConstants
Paren
Quotes
Startup
Syntax

You may find it helpful to browse through these topics, even without a specific goal in mind.

Help for Batch Mode

Recall that R has batch commands that allow you to run a command directly from your operating system’s shell. To get help on a particular batch command, you can type:

R CMD command --help

For example, to learn all the options associated with the INSTALL  command (discussed in Appendix B), you can type this:

R CMD INSTALL --help

Etc

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Last modified: March, 12, 2019