Re: [R] peering inside functions in a package?
On 17.05.2013 12:57, Duncan Murdoch wrote:
On 13-05-16 9:56 PM, Seth Myers wrote:
Let's say I would like to look inside the function corBrownian in library
(ape). When I type in the function name I get the following, which is
not
nearly the detail that goes into this function. I am wondering how to
begin cracking this function open (and others) so I can learn more
about it
and perhaps code my own corClass one day. Thanks.
corBrownian
function (value = 1, phy, form = ~1)
{
if (!inherits(phy, phylo))
stop(object \phy\ is not of class \phylo\)
attr(value, formula) - form
attr(value, fixed) - TRUE
attr(value, tree) - phy
class(value) - c(corBrownian, corPhyl, corStruct)
value
}
environment: namespace:ape
That's it. Why do you think something is missing?
I guess the OP is wondering about printed or plotted output and should
look into the corresponding print or plot methods, but then, we need
some more information to be able to help here.
Best,
Uwe Ligges
Duncan Murdoch
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Re: [R] peering inside functions in a package?
On Fri, May 17, 2013 at 2:56 AM, Seth Myers sjmyers3...@gmail.com wrote:
Let's say I would like to look inside the function corBrownian in library
(ape). When I type in the function name I get the following, which is not
nearly the detail that goes into this function. I am wondering how to
begin cracking this function open (and others) so I can learn more about it
and perhaps code my own corClass one day. Thanks.
corBrownian
function (value = 1, phy, form = ~1)
{
if (!inherits(phy, phylo))
stop(object \phy\ is not of class \phylo\)
attr(value, formula) - form
attr(value, fixed) - TRUE
attr(value, tree) - phy
class(value) - c(corBrownian, corPhyl, corStruct)
value
}
environment: namespace:ape
Your premise is wrong! This is exactly all that goes into the corBrownian
function. All that it does is create a thing with some values and most
importantly, a set of class attributes.
It's via that class attribute that your corBrownian objects get their
behaviour via _method_ functions. If you download the source code for ape
from CRAN and have a look in PGLS.R you will see a bunch of functions such
as Initialize.corPhyl and corMatrix.corBrownian which are methods for
Initialize and corMatrix for corPhyl classes and corBrownian classes
respectively.
So when you come to use one of these correlation structures, the calling
code doesn't care how the correlation structure computes its correlation
matrix, it just calls the corMatrix function and the object-oriented magic
calls the specific one for that specific class of model.
So in ape, all the phylogenetic correlation classes are initialised with
Initialize.corPhyl and the Brownian one has corMatrix.corBrownian as the
method for computing its correlation matrix. You can see the source code
for these methods by typing their names on the R command line. Sometimes
methods aren't exported and aren't so easily visible on the command line,
leading to frustration. Download the source package for complete
satisfaction.
The help for ?corClasses in the nlme package has a bit more help, but you
might do well to read the source code of how these methods are created in
the ape package, especially if you are going to be creating a variation on
these phylo-classes.
Good luck. I tried and failed to write a new corClass for nlme a few years
back.
corBlimey.
Barry
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] peering inside functions in a package?
On 13-05-16 9:56 PM, Seth Myers wrote:
Let's say I would like to look inside the function corBrownian in library
(ape). When I type in the function name I get the following, which is not
nearly the detail that goes into this function. I am wondering how to
begin cracking this function open (and others) so I can learn more about it
and perhaps code my own corClass one day. Thanks.
corBrownian
function (value = 1, phy, form = ~1)
{
if (!inherits(phy, phylo))
stop(object \phy\ is not of class \phylo\)
attr(value, formula) - form
attr(value, fixed) - TRUE
attr(value, tree) - phy
class(value) - c(corBrownian, corPhyl, corStruct)
value
}
environment: namespace:ape
That's it. Why do you think something is missing?
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
