[R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb
Spencer Graves
spencer.graves at structuremonitoring.com
Thu May 19 17:11:33 CEST 2011
Is a list like Henrik's (below) available someplace on r-project.org or
on your local CRAN mirror? If no, where do you think it might most
conveniently fit? What about "www.r-project.org/other-docs.html"?
Perhaps add a bullet right under the link to "DevCheatSheet has a
collection of R Reference Cards" something like "For a list of R
Programming Style Guides, see ...", with a link to a page giving
Henrick's list. Or make it a CRAN Task View on "R Programming Style
Guides"?
Spencer
On 5/18/2011 7:17 PM, Henrik Bengtsson wrote:
> 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 ...]
>>>>>
>>>>> ______________________________________________
>>>>> R-help at 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.
>>>>>
>>>>
>>>> --
>>>> "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
>>>>
>>>> ______________________________________________
>>>> R-help at 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.
>>>>
>>>
>>
>> --
>> _________________________________________________________________
>> David Scott Department of Statistics
>> The University of Auckland, PB 92019
>> Auckland 1142, NEW ZEALAND
>> Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
>> Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
>>
>> ______________________________________________
>> R-help at 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.
>>
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
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