R Style Guide -- Was Post-hoc tests in MASS using glm.nb

On Wed, May 18, 2011 at 6:28 PM, David Scott<d.scott at auckland.ac.nz>  wrote:

  Another style guide is at:
http://www1.maths.lth.se/help/R/RCC/

Listed as a first draft and dated 2005, but still worth a read. Has some
references also.

That URL obsolete (I need to have it removed) - a more recent/stable
URL is [5] below.

LIST OF CONVENTIONS/STYLES FOR R:

[1] R coding standards in the R Internals manual
   http://www.cran.r-project.org/doc/manuals/R-ints.html#R-coding-standards

[2] Bioconductor coding standards
   http://wiki.fhcrc.org/bioc/Coding_Standards

[3] Google R style
[http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html]

[4] R style guide by Hadley Wickham (based on [3])
   http://had.co.nz/stat405/resources/r-style-guide.html

[5] R Coding Conventions (RCC) - a draft by Henrik Bengtsson
   http://aroma-project.org/developers/RCC

[6] The Aroma R Coding Conventions (Aroma RCC) by Henrik Bengtsson
(based on [5])
   http://aroma-project.org/developers/AromaRCC

Note that there are often different objectives driving the different
coding styles, which is why it makes little sense to debate certain
items. As an example, one convention may favor portability to another
language limiting it to not use S4 (just an example).

/Henrik

I think I recall Hadley having a style guide which he requested his students
followed, but I didn't like it too much (sorry Hadley) .

I am with Bill that style guides should be consulted and their
recommendations considered, but it is personal preference as to which rules
one accepts. I don't find it objectionable if someone has written in a style
I don't particularly like, but it is objectionable if no thought has been
given to programming style.

David Scott


On 19/05/11 10:26, Bill.Venables at csiro.au wrote:

Hi Bert,

I think people should know about the Google Sytle Guide for R because, as
I said, it represents a thoughtful contribution to the debate.  Most of its
advice is very good (meaning I agree with it!) but some is a bit too much
(for example, the blanket advice never to use S4 classes and methods -
that's just resisting progress, in my view).  The advice on using<- for the
(normal) assingment operator rather than = is also good advice, (according
to me), but people who have to program in both C and R about equally often
may find it a bit tedious.  We can argue over that one.

I suggest it has a place in the R FAQ but with a suitable warning that
this is just one view, albeit a thougtful one.  I don't think it need be
included in the posting guide, though.  It would take away some of the fun.
  :-)

Bill Venables.

-----Original Message-----
From: Bert Gunter [mailto:gunter.berton at gene.com]
Sent: Wednesday, 18 May 2011 11:47 PM
To: Venables, Bill (CMIS, Dutton Park)
Cc: r-help at r-project.org
Subject: R Style Guide -- Was Post-hoc tests in MASS using glm.nb

Thanks Bill. Do you and others think that a link to this guide (or
another)should be included in the Posting Guide and/or R FAQ?

-- Bert

On Tue, May 17, 2011 at 4:07 PM,<Bill.Venables at csiro.au>    wrote:

Amen to all of that, Bert.  Nicely put.  The google style guide (not
perfect, but a thoughtful contribution on these kinds of issues, has
avoiding attach() as its very first line.  See
http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html)

I would add, though, that not enough people seem yet to be aware of
within(...), a companion of with(...) in a way, but used for modifying data
frames or other kinds of list objects.  It should be seen as a more flexible
replacement for transform() (well, almost).

The difference between with() and within() is as follows:

with(data, expr, ...)

allows you to evaluate 'expr' with 'data' providing the primary source
for variables, and returns *the evaluated expression* as the result.  By
contrast

within(data, expr, ...)

again uses 'data' as the primary source for variables when evaluating
'expr', but now 'expr' is used to modify the varibles in 'data' and returns
*the modified data set* as the result.

I use this a lot in the data preparation phase of a project, especially,
which is usually the longest, trickiest, most important, but least discussed
aspect of any data analysis project.

Here is a simple example using within() for something you cannot do in
one step with transform():

polyData<- within(data.frame(x = runif(500)), {
  x2<- x^2
  x3<- x*x2
  b<- runif(4)
  eta<- cbind(1,x,x2,x3) %*% b
  y<- eta + rnorm(x, sd = 0.5)
  rm(b)
})

check:

str(polyData)

'data.frame':   500 obs. of  5 variables:
  $ x  : num  0.5185 0.185 0.5566 0.2467 0.0178 ...
  $ y  : num [1:500, 1] 1.343 0.888 0.583 0.187 0.855 ...
  $ eta: num [1:500, 1] 1.258 0.788 1.331 0.856 0.63 ...
  $ x3 : num  1.39e-01 6.33e-03 1.72e-01 1.50e-02 5.60e-06 ...
  $ x2 : num  0.268811 0.034224 0.309802 0.060844 0.000315 ...
Bill Venables.

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Bert Gunter
Sent: Wednesday, 18 May 2011 12:08 AM
To: Peter Ehlers
Cc: R list
Subject: Re: [R] Post-hoc tests in MASS using glm.nb

Folks:

Only if the user hasn't yet been introduced to the with() function,
which is linked to on the ?attach page.

Note also this sentence from the ?attach page:
  ".... attach can lead to confusion."

I can't remember the last time I needed attach().

Peter Ehlers

Yes. But perhaps it might be useful to flesh this out with a bit of
commentary. To this end, I invite others to correct or clarify the
following.

The potential "confusion" comes from requiring R to search for the
data. There is a rigorous process by which this is done, of course,
but it requires that the runtime environment be consistent with that
process, and the programmer who wrote the code may not have control
over that environment. The usual example is that one has an object
named,say,  "a" in the formula and in the attached data and another
"a" also in the global environment. Then the wrong "a" would be found.
The same thing can happen if another data set gets attached in a
position before the one of interest. (Like Peter, I haven't used
attach() in so long that I don't know whether any warning messages are
issued in such cases).

Using the "data = " argument when available or the with() function
when not avoids this potential confusion and tightly couples the data
to be analyzed with the analysis.

I hope this clarifies the previous posters' comments.

Cheers,
Bert

[... non-germane material snipped ...]

--
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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