Bert Gunter
2011-May-18 13:47 UTC
[R] 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. >-- "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 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml
Steve_Friedman at nps.gov
2011-May-18 14:06 UTC
[R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb
This is the first time I've seen an R Style Guide. I will admit that I
haven't looked for one previously, but nevertheless I still haven't seen
one. My code style simply evolved (perhaps, chugged along) by reading posts
from other users who post to the r-help community.
I regularly program with a colleague who is a Java software development
specialist, hacking together code that we both develop. Since his coding
style differs substantially from mine and the conventions described for R
we end up modifying my code to follows his convention. For example, he
typically likes to name variables in this form: "variable_" , which
the
guide frowns on.
I think this guide will be very helpful. First for me to become more
proficient and conventional following R stylistics. Secondly, he will see
why R users do things the way R. The guide should be helpful.
I appreciate you posting the link to the guide. Much appreciated.
Steve
Steve Friedman Ph. D.
Ecologist / Spatial Statistical Analyst
Everglades and Dry Tortugas National Park
950 N Krome Ave (3rd Floor)
Homestead, Florida 33034
Steve_Friedman at nps.gov
Office (305) 224 - 4282
Fax (305) 224 - 4147
Bert Gunter
<gunter.berton at ge
ne.com> To
Sent by: Bill.Venables at csiro.au
r-help-bounces at r- cc
project.org r-help at r-project.org
Subject
[R] R Style Guide -- Was Post-hoc
05/18/2011 09:47 tests in MASS using glm.nb
AM
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.
>
--
"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
467-7374
http://devo.gene.com/groups/devo/depts/ncb/home.shtml
______________________________________________
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.
Bill.Venables at csiro.au
2011-May-18 22:26 UTC
[R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb
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. >-- "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 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml
Martin Maechler
2011-May-19 10:26 UTC
[R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb
BertG> Thanks Bill. Do you and others think that a link to
BertG> this guide (or another)should be included in the
BertG> Posting Guide and/or R FAQ?
Hmm, that guide is Google's work, and is probably quite good if
you have a group of R programmers in the same company,
but e.g., has not been published in collaboration with the R core team,
and actually somewhat differs from our own .. much less formal
and not officially laid down styles
{yes: "s".. but we still have a few parts we agree on...}
2nd problem with any style guide: "Base R" already comes
with several thousand of functions, classes and other objects, which
have grown from more than 20 years of S, S+ and then R history,
and most things cannot feasibly be changed now (or could, say 5
years ago), for back compatibility reasons.
Further,... more philosophically:
For many of us, programming (R or otherwise) is considered
a creative activity to quite some extent, and creativity can be
crushed by too rigid rules. I'd state that cultural history
shows that human culture implicitly follows many rules, but it
is (almost) only interesting because the are enough exceptions
to those rules.
Martin Maechler
@ ETH Zurich and R Core Team since its inception
but speaking entirely for myself ..
BertG> On Tue, May 17, 2011 at 4:07 PM,
BertG> <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.
[ .... very nice reasoning and example add why
people should use within() in many cases ... ]