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Finding code for R functions

4 messages · Wolfrum, Ed, Bert Gunter, Duncan Murdoch +1 more

Original
Wolfrum, Ed
# 
Greetings,

I am trying to figure out how to find the source code for R functions. I
am specifically interested in finding the code for the "prcomp"
function. I know that typing the function name without parenthesis will
lead to the code (or to a .Internal or .FORTRAN or .C  call). However, I
don't really understand what is going on. For example, typing "mean"
gives a "UseMethod" response, while typing "mean.default" give the
actual code:
function (x, ...) 
UseMethod("mean")
<environment: namespace:base>
function (x, trim = 0, na.rm = FALSE, ...) 
---SNIP---
}
<environment: namespace:base>

Why is this? What does "mean.default" mean? I tried the same thing with
"prcomp". With the stats package loaded, I cannot get to the source code
for "prcomp".
[1] TRUE
function (x, ...) 
UseMethod("prcomp")
<environment: namespace:stats>
Error: object "prcomp.default" not found
 
How do I find the prcomp code? Are there general rules for finding the
source code for functions that I should know?

Thanks in Advance,

Edward J. Wolfrum, Ph.D.
National Renewable Energy Laboratory
Golden, Colorado
Bert Gunter
# 
See chapter 5 on object oriented programming in the R language definition
manual. Also the  ?UseMethod man page. These will explain R's (S3) method
dispatch procedures.

Finally, search on CRAN for the R New newsletter article on namespaces,
which is where you'll find info on why you can't "see" certain functions.
See ?getAnywhere to learn how to see code for functions in namespaces.

-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
 
"The business of the statistician is to catalyze the scientific learning
process."  - George E. P. Box
Duncan Murdoch
#
Wolfrum, Ed wrote:
That is the source for prcomp.  It's a one-liner, that says to call the 
prcomp method for whatever type of x you're passing in.  As Bert said, 
you need to read up on methods.
Notice that prcomp lives in "namespace:stats"?  That's the first place 
to look for prcomp methods.  Besides getAnywhere which Bert suggested, 
you can try

stats:::prcomp.default

to see the method.  (Methods aren't necessarily in the same namespace as 
the generic, but that's the most common place for them.)

Duncan Murdoch
Roger D. Peng
# 
If you're really interested in reading the source for functions and aren't 
interested in tracking down various methods (possibly hidden in namespaces) at 
the R prompt, I think it's much easier to download the R source code from CRAN 
and go through the original source files.

-roger
Wolfrum, Ed wrote: