[Rd] Incorrect formatted output after subtracting non-integer seconds from POSIXt origin
x-as.POSIXct(1970-1-1, tz=UTC)-.5 y-as.POSIXct(1970-1-1, tz=UTC)+.5 x==y [1] FALSE # of course but x and y appear to be the same when formatted, even with extra precision: format(x, format=%Y-%m-%d %H:%M:%OS2) [1] 1970-01-01 00:00:00.50 format(y, format=%Y-%m-%d %H:%M:%OS2) [1] 1970-01-01 00:00:00.50 Formatted output is fine for integral difference points ... x-as.POSIXct(1970-1-1, tz=UTC)-1 y-as.POSIXct(1970-1-1, tz=UTC)+1 format(x, format=%Y-%m-%d %H:%M:%OS2) [1] 1969-12-31 23:59:59.00 format(y, format=%Y-%m-%d %H:%M:%OS2) [1] 1970-01-01 00:00:01.00 ... but seems to be a second off for non-integers: format(as.POSIXct(1970-1-1, tz=UTC)-1.5, format=%Y-%m-%d %H:%M:%OS2) [1] 1969-12-31 23:59:59.50 # a second later than expected format(as.POSIXct(1970-1-1, tz=UTC)-86400, format=%Y-%m-%d %H:%M:%OS2) [1] 1969-12-31 00:00:00.00 # OK format(as.POSIXct(1970-1-1, tz=UTC)-86400.5, format=%Y-%m-%d %H:%M:%OS2) [1] 1969-12-31 00:00:00.50 # why after previous time? Bug, or user misunderstanding? R version 2.11.1 (2010-05-31) on Windows Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Incorrect formatted output after subtracting non-integer seconds from POSIXt origin
Thanks. Yes, negative POSIX time would correspond to dates prior to 1970-1-1, or to dates prior to a more recent origin that borrows functionality from the POSIXt class: as.POSIXct(-.5, origin=as.POSIXct(2011-1-1)). If negative POSIX time is supposed to work then it's a bug in as.POSIXlt(). Now fixed in R-devel (and patched). Cheers, Simon before: str(unclass(as.POSIXlt(as.POSIXct(1970-1-1, tz=UTC)-0.2))) List of 9 $ sec : num 0.8 $ min : int 0 $ hour : int 0 $ mday : int 1 $ mon : int 0 $ year : int 70 $ wday : int 4 $ yday : int 0 $ isdst: int 0 - attr(*, tzone)= chr UTC R-devel: str(unclass(as.POSIXlt(as.POSIXct(1970-1-1, tz=UTC)-0.2))) List of 9 $ sec : num 59.8 $ min : int 59 $ hour : int 23 $ mday : int 31 $ mon : int 11 $ year : int 69 $ wday : int 3 $ yday : int 364 $ isdst: int 0 - attr(*, tzone)= chr UTC R version 2.11.1 (2010-05-31) on Windows Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Extract callNextMethod array calls matrix?
Thanks, John. Enjoy Gaithersburg! On Wed, Jul 21, 2010 at 8:58 AM, John Chambers j...@r-project.org wrote: There does indeed seem to be a bug in the C code that implements callNextMethod, with the effect of adding a spurious index to calls to the primitive `[` code with more than 2 subscripts. The message incorrect number of dimensions is telling the truth, the primitive code gets 4 subscripts instead of 3 (note the x[i = i, j = j, NULL, ...] in the error message). Given the time of year, meetings, and the obscurity of this piece of code, the bug won't likely be fixed soon, so any workaround that avoids the use of callNextMethod on `[` with 3 or more subscripts is a good idea. On 7/20/10 1:41 PM, Daniel Murphy wrote: I have a class that extends array and my method for [ stops with an error: setClass(A, contains=array) [1] A setMethod([, A, function(x, i, j, ..., drop = TRUE) new(A, callNextMethod())) [1] [ a-new(A,array(1:12,c(4,3,1))) a An object of class A , , 1 [,1] [,2] [,3] [1,]159 [2,]26 10 [3,]37 11 [4,]48 12 a[1:2,2:3,1] Error in x[i = i, j = j, NULL, ...] : incorrect number of dimensions Error in callNextMethod() : error in evaluating a 'primitive' next method A similar error does not occur when extending a matrix: setClass(M, contains=matrix) [1] M setMethod([, M, function(x, i, j, ..., drop = TRUE) new(M, callNextMethod())) [1] [ a-new(M,matrix(1:12,4,3)) a[1:2,2:3] An object of class M [,1] [,2] [1,]59 [2,]6 10 Is there a problem with my method definition for the array-extending class? My work-around is as follows: setMethod([, A, function(x, i, j, ..., drop = TRUE) new(A, `[`(as(x,array), i=i, j=j, ..., drop=drop))) [1] [ a[1:2,2:3,1] An object of class A [,1] [,2] [1,]59 [2,]6 10 Cheers, Dan [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Extract callNextMethod array calls matrix?
I have a class that extends array and my method for [ stops with an error: setClass(A, contains=array) [1] A setMethod([, A, function(x, i, j, ..., drop = TRUE) new(A, callNextMethod())) [1] [ a-new(A,array(1:12,c(4,3,1))) a An object of class A , , 1 [,1] [,2] [,3] [1,]159 [2,]26 10 [3,]37 11 [4,]48 12 a[1:2,2:3,1] Error in x[i = i, j = j, NULL, ...] : incorrect number of dimensions Error in callNextMethod() : error in evaluating a 'primitive' next method A similar error does not occur when extending a matrix: setClass(M, contains=matrix) [1] M setMethod([, M, function(x, i, j, ..., drop = TRUE) new(M, callNextMethod())) [1] [ a-new(M,matrix(1:12,4,3)) a[1:2,2:3] An object of class M [,1] [,2] [1,]59 [2,]6 10 Is there a problem with my method definition for the array-extending class? My work-around is as follows: setMethod([, A, function(x, i, j, ..., drop = TRUE) new(A, `[`(as(x,array), i=i, j=j, ..., drop=drop))) [1] [ a[1:2,2:3,1] An object of class A [,1] [,2] [1,]59 [2,]6 10 Cheers, Dan [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 class extends data.frame, getDataPart sees list
Thank you. For getDataPart I was following (my interpretation of) advice from the documentation for Classes: The functions getDataParthttp://127.0.0.1:15455/library/methods/help/getDataPart and setDataPart http://127.0.0.1:15455/library/methods/help/setDataPart are a cleaner, but essentially equivalent way to deal with the data part. I interpreted cleaner to mean preferred. From your reply, John, it sounds like I should go back to the obj...@.data construct. -Dan On Tue, Jul 13, 2010 at 5:57 AM, John Chambers j...@r-project.org wrote: On 7/11/10 9:08 PM, Daniel Murphy wrote: R-Devel: When I get the data part of an S4 class that contains=data.frame, it gives me a list, even when the data.frame is the S4 version: d-data.frame(x=1:3) isS4(d) [1] FALSE # of course dS4-new(data.frame,d) isS4(dS4) [1] TRUE# ok class(dS4) [1] data.frame # good attr(,package) [1] methods setClass(A, representation(label=character), contains=data.frame) [1] A a-new(A,dS4, label=myFrame) getDataPart(a) [[1]] # oh? [1] 1 2 3 class(a...@.data) [1] list # hmm names(a) [1] x # sure, that makes sense a Object of class A x 1 1 2 2 3 3 Slot label: [1] myFrame Was I wrong to have expected the data part of 'a' to be a data.frame? Yes. Also, there is a clue in the documentation for getDataPart: rarely suitable to be called directly The data part, aka data slot, generally does not have a class (S4 or S3). You are probably looking for S3Part(): setClass(myFrame, contains = data.frame) [1] myFrame z = new(myFrame, data.frame(x=1:3)) z Object of class myFrame x 1 1 2 2 3 3 S3Part(z) Object of class data.frame x 1 1 2 2 3 3 S3Part(z, strictS3 = TRUE) x 1 1 2 2 3 3 Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 class extends data.frame, getDataPart sees list
OK, I see. Thanks. -Dan On Tue, Jul 13, 2010 at 9:11 AM, John Chambers j...@r-project.org wrote: On 7/13/10 8:43 AM, Daniel Murphy wrote: Thank you. For getDataPart I was following (my interpretation of) advice from the documentation for Classes: The functions |getDataPart http://127.0.0.1:15455/library/methods/help/getDataPart| and |setDataPart http://127.0.0.1:15455/library/methods/help/setDataPart| are a cleaner, but essentially equivalent way to deal with the data part. I interpreted cleaner to mean preferred. From your reply, John, it sounds like I should go back to the obj...@.data construct. No, that's not the distinction. Preferred for what, is the question. In order for a class to extend a basic type, it has to have that type. Then the .Data slot is a sort of fiction needed for the metadata. (Because of some features of R implementation, it's not quite that simple. Matrices act like a basic type, and some types, such as environment require a second kludge.) If you really want that slot, the advice holds, but only because there is no actual .Data slot (i.e., attribute). But you weren't talking about that at all. In fact (just to contradict my previous mail) you probably wanted to turn your object into a data.frame. If so, best to say so: as(z, data.frame) Object of class data.frame x 1 1 2 2 3 3 and, for that matter: as(z, list) [[1]] [1] 1 2 3 -Dan On Tue, Jul 13, 2010 at 5:57 AM, John Chambers j...@r-project.org mailto:j...@r-project.org wrote: On 7/11/10 9:08 PM, Daniel Murphy wrote: R-Devel: When I get the data part of an S4 class that contains=data.frame, it gives me a list, even when the data.frame is the S4 version: d-data.frame(x=1:3) isS4(d) [1] FALSE # of course dS4-new(data.frame,d) isS4(dS4) [1] TRUE# ok class(dS4) [1] data.frame # good attr(,package) [1] methods setClass(A, representation(label=character), contains=data.frame) [1] A a-new(A,dS4, label=myFrame) getDataPart(a) [[1]] # oh? [1] 1 2 3 class(a...@.data) [1] list # hmm names(a) [1] x # sure, that makes sense a Object of class A x 1 1 2 2 3 3 Slot label: [1] myFrame Was I wrong to have expected the data part of 'a' to be a data.frame? Yes. Also, there is a clue in the documentation for getDataPart: rarely suitable to be called directly The data part, aka data slot, generally does not have a class (S4 or S3). You are probably looking for S3Part(): setClass(myFrame, contains = data.frame) [1] myFrame z = new(myFrame, data.frame(x=1:3)) z Object of class myFrame x 1 1 2 2 3 3 S3Part(z) Object of class data.frame x 1 1 2 2 3 3 S3Part(z, strictS3 = TRUE) x 1 1 2 2 3 3 Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailto:R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 class extends data.frame, getDataPart sees list
R-Devel: When I get the data part of an S4 class that contains=data.frame, it gives me a list, even when the data.frame is the S4 version: d-data.frame(x=1:3) isS4(d) [1] FALSE # of course dS4-new(data.frame,d) isS4(dS4) [1] TRUE# ok class(dS4) [1] data.frame # good attr(,package) [1] methods setClass(A, representation(label=character), contains=data.frame) [1] A a-new(A,dS4, label=myFrame) getDataPart(a) [[1]] # oh? [1] 1 2 3 class(a...@.data) [1] list # hmm names(a) [1] x # sure, that makes sense a Object of class A x 1 1 2 2 3 3 Slot label: [1] myFrame Was I wrong to have expected the data part of 'a' to be a data.frame? Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Attributes of 1st argument in ...
I stand corrected. It is possible for the S4 cbind to know the symbol of
unnamed arguments, by cheating: colnames(base::cbind(...,deparse.level =
deparse.level)) -- which tells me that there ought to be a non-cheating way.
I note that the Rmpfr class union, Mnumber, means that the simple cbind(1:3)
must go through the S4 cbind. Now I know why your method, Martin, tests for
all is.atomic at the beginning (which will not work for mondates, which test
TRUE). This actually increases the price of an S4 cbind, a price increase
that I believe could be avoided if S4 dispatch on dots occurred based on the
first argument, which is back to my original post. I'm guessing that's too
difficult to implement.
Again, thanks to everyone for your time in schooling me on the issues. :-)
Dan
On Mon, Jul 5, 2010 at 10:35 PM, Daniel Murphy chiefmur...@gmail.comwrote:
I truly am grateful for all the help.
I never would have thought defining a class union for objects that can be
combined with cbind, as you do in Rmpfr. That does the trick.
Is it true that the only difference in behavior between the S4 cbind and
base::cbind is that, unlike base::cbind, the S4 cbind does not seem to know
the symbol of unnamed arguments? E.g.,
x-mpfr(0:7,100)
cbind(x,x)
If so, that seems a small price to pay for the S4 functionality.
Thanks again.
Cheers,
Dan
On Mon, Jul 5, 2010 at 2:47 AM, Martin Maechler
maech...@stat.math.ethz.ch wrote:
DM == Daniel Murphy chiefmur...@gmail.com
on Sun, 4 Jul 2010 11:11:43 -0700 writes:
DM Thank you, Professor, for drawing my attention to the nifty
tracemem
DM function. I'm using the ..1 syntax to check the properties of the
S4 class
DM at function call.
DM The Description at ?cBind tells me that I'm not alone in this
predicament.
DM Just as Matrix needs its own cBind function, my package will need
its own
DM cbindMondate function. Alas, subclasses of mondate will also need
their own
DM binding functions, thus defeating one of the purposes of the class
paradigm
DM (for binding, anyway).
I don't think you see the full picture:
Matrix::cBind() builds on methods::cbind2()
and cbind2 / rbind2 are there (in package methods) for you to
use setMethod() on them.
BTW: When Matrix::cBind() -- and cbind2 / rbind2 in package
methods were written,
R did not have the possibility yet to write methods for ...,
which it now does.
In the package Rmpfr (arbitrary-precision number [mpfr] computing),
where I also define methods for matrices of such mpfr numbers
(classes mpfrMatrix and mpfrArray),
I use the new feature of defining methods for ... :
setGeneric(cbind, signature = ...)
setMethod(cbind, Mnumber,
function(..., deparse.level = 1) {
args - list(...)
if(all(sapply(args, is.atomic)))
return( base::cbind(..., deparse.level = deparse.level) )
## else: at least one is mpfr(Matrix/Array)
if(any(sapply(args, is.character))) {
## result will be character matrix !
isM - sapply(args, is, class2 = mpfr)
args[isM] - lapply(args[isM], as, Class = character)
return(do.call(base::cbind,
c(args,
list(deparse.level=deparse.level
} else if(any(sapply(args, is.complex))) {
## result will be complex matrix;
## in the future complex_mpfr ???
stop(cbind(...) of 'complex' and 'mpfr' objects is not
implemented)
## give at least warning !!
}
## else
..
..
})
where I use a useful class union
setClassUnion(Mnumber,
members = c(array_or_vector, # *but* must be numeric-like
mpfr, mpfrArray, mpfrMatrix))
As always, I'd recommend to read the R source, rather than just
investigate the installed package.
You can get the *source* tarbal, i.e., the *.tar.gz file from
CRAN, or, as it's all on R-forge,
http://rmpfr.r-forge.r-project.org/
you can get the source tarball here,
https://r-forge.r-project.org/R/?group_id=386
or browse the source at
https://r-forge.r-project.org/scm/viewvc.php/pkg/?root=rmpfr
But if I were you I'd get it via
svn checkout svn://svn.r-forge.r-project.org/svnroot/rmpfr/pkg Rmpfr
DM As an aside, I wonder why, on around line 75, cBind uses 'rep.int
(,
DM ncol(r))' rather than the slightly faster 'character(ncol(r))'.
Well, I would not remember, but the first one is a more self-explaining,
... and I would guess strongly that time difference is
irrelevant in the context where it's used...
... but then thanks for your hint :-)
Martin
snip
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Re: [Rd] Attributes of 1st argument in ...
Thank you, Professor, for drawing my attention to the nifty tracemem function. I'm using the ..1 syntax to check the properties of the S4 class at function call. The Description at ?cBind tells me that I'm not alone in this predicament. Just as Matrix needs its own cBind function, my package will need its own cbindMondate function. Alas, subclasses of mondate will also need their own binding functions, thus defeating one of the purposes of the class paradigm (for binding, anyway). As an aside, I wonder why, on around line 75, cBind uses 'rep.int(, ncol(r))' rather than the slightly faster 'character(ncol(r))'. Thanks again, Dan On Sun, Jul 4, 2010 at 4:36 AM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: I think you have missed the use of ..1 etc: see e.g. cBind() in package Matrix. So x - attr(list(...)[[1L]], foo) can be x - attr(..1, foo) As for 'extra copying', it all depends on exactly what you are doing, but compare foo1 - function(...) length(..1) foo2 - function(...) length(list(...)[[1L]]) tracemem(x - runif(1000)) [1] 0x1b27800 foo1(x) [1] 1000 tracemem(x - runif(1000)) [1] 0x1b29800 foo2(x) tracemem[0x1b29800 - 0x10a2200]: foo2 [1] 1000 snip -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Attributes of 1st argument in ...
Hi Hadley,
My actual goal is to have a cbind method in the mondate package that behaves
just like the base cbind function: class and shape of the result, names,
etc. Perhaps it's due to the fact that 'cbind' uses its own internal
dispatching, but I have not found a way to implement a true S3-style cbind
method. (This is probably ancient news to the development team.) An S4 cbind
method will utilize callNextMethod with just setGeneric(cbind), which has
no 'x' in the formal arguments. With no 'x', there's no first argument on
which to dispatch a mondate method. I can make the cbind of mondates also
be a mondate with an all-encompassing setMethod(cbind,ANY, etc) method,
but that wrests dispatch control from cbind which makes no sense whatsoever.
So, to make a long story even longer, I settled for a cbindmondate
function that utilizes the speed of base::cbind and (with one exception)
gives me the hoped-for base cbind behavior.
I can send examples of my trial-and-error attempts under separate email if
you're interested.
Best regards,
Dan
On Sat, Jul 3, 2010 at 9:17 AM, Hadley Wickham had...@rice.edu wrote:
Hi Dan,
Is there a reason you can't change the function to
f - function(x, ...) {}
?
Hadley
On Fri, Jul 2, 2010 at 4:26 PM, Daniel Murphy chiefmur...@gmail.com
wrote:
R-Devel:
I am trying to get an attribute of the first argument in a call to a
function whose formal arguments consist of dots only and do something,
e.g.,
call 'cbind', based on the attribute
f- function(...) {get first attribute; maybe or maybe not call 'cbind'}
I thought of (ignoring deparse.level for the moment)
f-function(...) {x - attr(list(...)[[1L]], foo); if (x==bar)
cbind(...) else x}
but I feared my solution might do some extra copying, with a performance
penalty if the dotted objects in the actual call to f' are very large.
I thought the following alternative might avoid a potential performance
hit
by evaluating the attribute in the parent.frame (and therefore avoid
extra
copying?):
f-function(...)
{
L-match.call(expand.dots=FALSE)[[2L]]
x - eval(substitute(attr(x,foo), list(x=L[[1L]])))
if (x==bar) cbind(...) else x
}
system.time tests showed this second form to be only marginally faster.
Is my fear about extra copying unwarranted? If not, is there a better way
to
get the foo attribute of the first argument other than my two
alternatives?
Thanks,
Dan Murphy
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--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
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[Rd] Attributes of 1st argument in ...
R-Devel:
I am trying to get an attribute of the first argument in a call to a
function whose formal arguments consist of dots only and do something, e.g.,
call 'cbind', based on the attribute
f- function(...) {get first attribute; maybe or maybe not call 'cbind'}
I thought of (ignoring deparse.level for the moment)
f-function(...) {x - attr(list(...)[[1L]], foo); if (x==bar)
cbind(...) else x}
but I feared my solution might do some extra copying, with a performance
penalty if the dotted objects in the actual call to f' are very large.
I thought the following alternative might avoid a potential performance hit
by evaluating the attribute in the parent.frame (and therefore avoid extra
copying?):
f-function(...)
{
L-match.call(expand.dots=FALSE)[[2L]]
x - eval(substitute(attr(x,foo), list(x=L[[1L]])))
if (x==bar) cbind(...) else x
}
system.time tests showed this second form to be only marginally faster.
Is my fear about extra copying unwarranted? If not, is there a better way to
get the foo attribute of the first argument other than my two
alternatives?
Thanks,
Dan Murphy
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[Rd] format: different S4 behavior in a package
R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B - function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphy snipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] format: different S4 behavior in a package
Thank you, Martin. That worked. And fyi 'export(format)' alone was not sufficient. Best, Dan On Wed, Jun 23, 2010 at 5:15 AM, Martin Morgan mtmor...@fhcrc.org wrote: On 06/23/2010 12:16 AM, Daniel Murphy wrote: R-Devel-ers: I have an S4 method that simply formats an object: setGeneric(formatMe, function(x) standardGeneric(formatMe)) setMethod(formatMe, ANY, function(x) format(x)) If I issue the above in an R session, then define an S4 class with its own format method, I get the desired result: setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv [1] format a-new(A,1968) formatMe(a) [1] Hey Jude However, if I put the two formatMe definitions into a package (Test), I do not get the desired result. start new R session library(Test) setClass(A,contains=numeric) [1] A setMethod(format,A, function(x, ...) Hey Jude) Creating a new generic function for format in .GlobalEnv This is the clue -- you're creating a new S4 generic, so there's a base::format, and a .GlobalEnv::format. Test::formatMe respects its name space, and sees base::format. In the S3 case, base::format is already an S3 generic, and you're just adding a method, so there's only base::format for everyone to find. In Test, you could setGeneric(format) and then export(format). It might also be enough to just export(format); I'm not sure. Martin [1] format a-new(A,1968) formatMe(a) [1] 1968 The disconnect does not occur, however, if the S4 format method is an S3 incarnation: setClass(B,contains=numeric,S3methods=TRUE) [1] B format.B - function(x, ...) Don't make it bad b-new(B,1968) formatMe(b) [1] Don't make it bad Could the problem be in Test's NAMESPACE file? There is only one line: exportMethods(formatMe) Here is Test's DESCRIPTION file: Package: Test Type: Package Title: Testing format Version: 1.0 Date: 2010-06-22 Author: Dan Murphy Maintainer: Dan Murphy snipped Depends: methods Description: Does format in a package work with S4 format method? License: GPL (= 2) LazyLoad: yes (I would send the Help file, but I don't think that is the problem.) I am using version 2.11.1 on a Windows Vista machine. Any guidance would be appreciated. Thank you Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Extract/format/show for S4 objects (Johann Hibschman)
Johann, Following up on Gabor's reply, the mondate package (new on CRAN last week) will accomplish your needs. I'm trying to make an integer-backed quarter (as in fraction of year) class, but I can't quite it to work. I want integer-backed so I don't have to worry about floating-point effects when doing math, and so that I can use it as in data.table. mondate represents a date internally as a numeric, not an integer, but the integer part corresponds to months, not years, so a zero fractional part of a mondate corresponds to a complete month. Every third whole number, therefore, would correspond to a complete quarter. Arithmetic in months (or quarters by dividing by 3) returns a numeric with a timeunits attribute. mondate's can be stored in a data.frame. (A-mondate.ymd(2010,3*(1:4))) # display format is U.S., my location mondate: timeunits=months [1] 03/31/2010 06/30/2010 09/30/2010 12/31/2010 diff(A) # 3 months apart [1] 3 3 3 A-mondate(12/31/2009) # months since the end of last year; date input format also works for my location [1] 3 6 9 12 attr(,timeunits) [1] months c((A-mondate(12/31/2009))/3) # divide by 3 and remove the attribute and you have quarters [1] 1 2 3 4 data.frame(QtrEnd=A, Amount=rep(1000,4)) QtrEnd Amount 1 03/31/2010 1000 2 06/30/2010 1000 3 09/30/2010 1000 4 12/31/2010 1000 If the date you are subtracting off is somewhere in the fourth quarter of 2009 but you still want to treat it as being representative of the fourth quarter, the floor function will remove the fractional part of the difference in quarters (I will enter November 1st in non-US format): floor(c((A-mondate(2009-11-1))/3)) [1] 1 2 3 4 First of all, is there a good reference for this anywhere? All of the S4 tutorials that I've found have been too high-level, and I can't find any examples of implementing extract. In S3, I can use [.Date as my example, but I can't find the equivalent for S4. See the source code for an S4 [ method. I was unable to convert all S3 methods to S4, so you will see that some S3 methods remain (e.g., as.data.frame.mondate); S3methods=TRUE in the class definition as a result. I wrote this package to solve essentially your problem. If it falls short for you somehow, please me know. Thanks, - Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] pretty.Date(): new halfmonth time step
Felix, I see your point about the halfway point acting like the first day of the month in its relativity to the ending date of the month: they're both variable. I'm an actuary. Like accountants, actuaries tend to measure financial time in months because of how the books close. But in our mathematical models time takes on a continuous nature. So our problem is how to build a computer representation of time that reflects both its continuous nature as well as the varying-length, discrete nature of financial months. I've found that a fixed value for a halfway point complicates actuarial calculations. It could serve other purposes just fine, however. Best regards, Dan On Wed, May 19, 2010 at 7:48 PM, Felix Andrews fe...@nfrac.org wrote: On 20 May 2010 11:56, Daniel Murphy chiefmur...@gmail.com wrote: Much better to implement directly what this is trying to do: i.e. to have a halfmonth time step. This is just the union of two monthly sequences, one on the 1st of each month and another on the 15th of each month. For some applications that might be true. But not for others. For a month with 31 days, there are 14 days before the 15th of the month and 16 days after the 15th, so, for example, March 16th (specifically noon) rather than March 15th would be the halfway point if you define halfway in terms of the distances to the beginning and end of the month. For a month with 30 days -- like April -- the halfway point would be the instant between the 15th and the 16th of the month. Do you label that instant April 15 or April 16? (I prefer 15.) Don't get me started on February. Dan, you are correct: the midpoint of a 30 day month is the 16th at 00:00. That instant is called the 16th according to print.POSIXt. junstart - as.POSIXct(2000-06-01 00:00, tz=GMT) julstart - as.POSIXct(2000-07-01 00:00, tz=GMT) junstart + ((julstart - junstart) / 2) #[1] 2000-06-16 GMT How embarassing... So I think it would be better to use 16 rather than 15 for the halfmonth time step. Yes, months have variable lengths, but I think it is best to use a consistent date (the 16th) than to calculate exact midpoints, just as a normal monthly series has a consistent date (the 1st) and has variable lengths. Regards -Felix - Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Felix Andrews / å®ç¦ç« Postdoctoral Fellow Integrated Catchment Assessment and Management (iCAM) Centre Fenner School of Environment and Society [Bldg 48a] The Australian National University Canberra ACT 0200 Australia M: +61 410 400 963 T: + 61 2 6125 4670 E: felix.andr...@anu.edu.au CRICOS Provider No. 00120C -- http://www.neurofractal.org/felix/ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] pretty.Date(): new halfmonth time step
Yes. I looked at that feature of zoo. But it forced me to keep track of fractional months in the Date world. Square one. I ended up implementing a class under the paradigm of whole and fractional months. It allows me to do all my time arithmetic in ways that accountants expect. For example, accountants think of the close of business June 30th as being the halfway point of the year, but it's certainly not half the year as the crow flies. -Dan On Thu, May 20, 2010 at 4:01 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Note that in the zoo package that as.Date.yearmon has a frac= argument, e.g. library(zoo) ym - as.yearmon(2010-01) as.Date(ym, frac = 0.5) [1] 2010-01-16 On Wed, May 19, 2010 at 9:56 PM, Daniel Murphy chiefmur...@gmail.com wrote: Much better to implement directly what this is trying to do: i.e. to have a halfmonth time step. This is just the union of two monthly sequences, one on the 1st of each month and another on the 15th of each month. For some applications that might be true. But not for others. For a month with 31 days, there are 14 days before the 15th of the month and 16 days after the 15th, so, for example, March 16th (specifically noon) rather than March 15th would be the halfway point if you define halfway in terms of the distances to the beginning and end of the month. For a month with 30 days -- like April -- the halfway point would be the instant between the 15th and the 16th of the month. Do you label that instant April 15 or April 16? (I prefer 15.) Don't get me started on February. - Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] pretty.Date(): new halfmonth time step
Much better to implement directly what this is trying to do: i.e. to have a halfmonth time step. This is just the union of two monthly sequences, one on the 1st of each month and another on the 15th of each month. For some applications that might be true. But not for others. For a month with 31 days, there are 14 days before the 15th of the month and 16 days after the 15th, so, for example, March 16th (specifically noon) rather than March 15th would be the halfway point if you define halfway in terms of the distances to the beginning and end of the month. For a month with 30 days -- like April -- the halfway point would be the instant between the 15th and the 16th of the month. Do you label that instant April 15 or April 16? (I prefer 15.) Don't get me started on February. - Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] format.data.frame containing S4 class with format method
Hi again, I must be misunderstanding something fundamental about how an S4 class stored in a data.frame can be persuaded to print according to a desired format. The help page says: format.data.frame formats the data frame column by column, applying the appropriate method of format for each column. Here is my class: setClass(A,contains=character) [1] A a - new(A, aaa) a An object of class A [1] aaa I defined my format method to display in uppercase: setMethod(format,A, function(x, ...) toupper(x)) [1] format format(a) An object of class A [1] AAA I looked at the S4 class definition for data.frame (getClass(data.frame)) which prompted me to store the instance 'a' into a data.frame as follows: adf-new(data.frame,list(a), names=a, row.names=1) adf Object of class data.frame a 1 aaa ... not upper case. The str function clearly shows that the object was successfully stored in the data.frame: str(adf) 'data.frame': 1 obs. of 1 variable: 'data.frame': 1 obs. of 1 variable: Formal class 'data.frame' [package methods] with 4 slots ..@ .Data:List of 1 .. ..$ :Formal class 'A' [package .GlobalEnv] with 1 slots .. .. .. ..@ .Data: chr aaa ..@ names: chr a ..@ row.names: chr 1 ..@ .S3Class : chr data.frame Is there another step I should be taking so that A's format method is found and used? Thank you, Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Validity glitch when contains=matrix
Sirs: My validity function did not run when my class contains=matrix. But if I first define the class with contains=numeric, then define it again with contains=matrix, validity runs. Here's the session: f - function(object) BAD CLASS # force error to setClass(A, contains=matrix, validity=f) [1] A new(A,as.matrix(1)) # should generate a validity error, does not An object of class A [,1] [1,]1 setClass(B, contains=numeric, validity=f) [1] B new(B,1) # generates the error Error in validObject(.Object) : invalid class B object: BAD CLASS setClass(B, contains=matrix, validity=f) [1] B new(B,as.matrix(1)) # generates the error Error in validObject(.Object) : invalid class B object: BAD CLASS On the other hand, when I define the class with matrix in its representation, validity is called, no work-around necessary: setClass(C, representation(a=matrix), validity=f) [1] C new(C,a=as.matrix(1)) # error, as desired Error in validObject(.Object) : invalid class C object: BAD CLASS Should I 1) always put matrix into the setClass representation argument instead of the contains argument, or 2) use contains=numeric, put the matrix's dims and dimnames attributes into slots, and rely on a constructor to populate the instance? Option 2 seems most stable. Thanks, Dan Murphy Windows Vista, R version 2.11.0 (2010-04-22) [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 method execution time
Hello: I have written some an elementary S4 classes around a matrix to strengthen control of some key attributes. When I run a fairly elementary function (f) on the matrix outside the class it runs instantaneously (elapsed system.time = 0) but when I setMethod f on myClass -- returning an instance of myClass -- it runs perceptibly slower (elapsed system.time = .06). I suspect my initialization and/or validity functions are inefficiently written. I thought I read in this list of a function that will trace the execution time of each of the functions called during the evaluation of an R expression, but now I can't find that message. Is there such a function, or was I mistaken? Thank you. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] choose.files() latent highlighting in console
Greetings, When I call choose.files() from within a Windows (Vista or XP) Rgui.exe (2.10.0) session and double-click my choice, a large section of the text in the 'R Console' window appears as selected (highlighted in blue) when control returns to the console. The end point of the selected text is the mouse position at the time the 'Select files' window closes. Once a key is pressed in the R console, of course, the highlighted region vanishes. (Curiously, that highlighted section is not the actual selected region within the console, as hitting Ctrl-C ends up copying the text from the mouse position to the R prompt!) Is there a way to call choose.files() -- otherwise a work-around (sending a phantom, non-functioning keystroke?) -- so that this potentially confusing selection is not highlighted? Thanks, Dan [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Help in 2.10 lost its Find feature
Sirs: I understand that no one wanted to maintain the old Help, but one feature I used extensively -- as a newbie to R or to an unfamiliar package -- was the capability of searching for a word or phrase on the Help page itself. Ctrl-F/Command-F (Windows/mac) 'differently-phrased-capability' was a fast way to find out how to specify the arguments for a function call to accommodate a capability phrased differently than could be found in the author's designed argument list, especially for long and informative Help's. If new-Help could easily be enhanced to resurrect that feature, I believe many users would appreciate it. Thanks. Dan Murphy [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Help in 2.10 lost its Find feature
That did it. Was having trouble searching 'help' for how to optionally configure 'help'. Thanks. -Dan On Wed, Nov 11, 2009 at 8:57 AM, Henrik Bengtsson h...@stat.berkeley.eduwrote: For the text based help, there is no search feature on Windows, e.g. options(help_type=text); help(readLines); but if you use the HTML-based help, you can use the browser's search features as suggested/wanted: options(help_type=html); help(readLines); /Henrik On Wed, Nov 11, 2009 at 5:40 PM, hadley wickham h.wick...@gmail.com wrote: I understand that no one wanted to maintain the old Help, but one feature I used extensively -- as a newbie to R or to an unfamiliar package -- was the capability of searching for a word or phrase on the Help page itself. Ctrl-F/Command-F (Windows/mac) 'differently-phrased-capability' was a fast way to find out how to specify the arguments for a function call to accommodate a capability phrased differently than could be found in the author's designed argument list, especially for long and informative Help's. If new-Help could easily be enhanced to resurrect that feature, I believe many users would appreciate it. Thanks. Most browsers offer this feature - it certainly works in safari and firefox, and I'm sure in internet explorer too. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Match .3 in a sequence
I have a matrix whose columns were filled with values which were functions of cvseq-seq(.2,.3,by=.1) (and a row value of mode integer). To do a lookup for cv=.3 later, I wanted to match(.3,cvseq), which gave me NA, hence my question. I thought R would match .3 in cvseq within .Machine$double.eps, but I can understand it if .3 and the second element of cvseq would not have identical bits. Besides the helpful suggestions below, I also tried cvseqf - as.factor(cvseq) match(.3,cvseq) [1] 2 which worked. In general, would it be better to go the enumeration route via as.factor or the approximation route? Thanks for the help. -Dan On Mon, Mar 16, 2009 at 8:24 AM, Stavros Macrakis macra...@alum.mit.eduwrote: Well, first of all, seq(from=.2,to=.3) gives c(0.2), so I assume you really mean something like seq(from=.2,to=.3,by=.1), which gives c(0.2, 0.3). %in% tests for exact equality, which is almost never a good idea with floating-point numbers. You need to define what exactly you mean by in for floating-point numbers. What sort of tolerance are you willing to allow? Some possibilities would be for example: approxin - function(x,list,tol) any(abs(list-x)tol) # absolute tolerance rapproxin - function(x,list,tol) (x==0 0 %in% list) || any(abs((list-x)/x)=tol,na.rm=TRUE) # relative tolerance; only exact 0 will match 0 Hope this helps, -s On Mon, Mar 16, 2009 at 9:36 AM, Daniel Murphy chiefmur...@gmail.com wrote: Hello:I am trying to match the value 0.3 in the sequence seq(.2,.3). I get 0.3 %in% seq(from=.2,to=.3) [1] FALSE Yet 0.3 %in% c(.2,.3) [1] TRUE For arbitrary sequences, this invisible .3 has been problematic. What is the best way to work around this? [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Match .3 in a sequence
Got it. Thank you all. On Mon, Mar 16, 2009 at 4:39 PM, Stavros Macrakis macra...@alum.mit.eduwrote: The factor approach is horrifically ugly and dangerous. Even if it didn't have the extraordinarily poor behavior documented below, it simply isn't well-defined what it should do. The explicit approximation route is far far preferable in every way: more predictable, more controllable, and even (though it hardly matters usually) faster. Let's look at the extraordinarily poor behavior I was mentioning. Consider: nums - (.3 + 2e-16 * c(-2,-1,1,2)); nums [1] 0.3 0.3 0.3 0.3 Though they all print as .3 with the default precision (which is normal and expected), they are all different from .3: nums - .3 = -3.885781e-16 -2.220446e-16 2.220446e-16 3.885781e-16 When we convert nums to a factor, we get: fact - as.factor(nums); fact [1] 0.300 0.3 0.3 0.300 Levels: 0.300 0.3 0.3 0.300 Not clear what the difference between 0.300 and 0.3 is supposed to be, nor why some 0.300 are .3 and others are .3, but let's put that aside for the moment. Now let's look at the relations among the factor values: fact[1]==fact[2] [1] FALSE fact[1]==fact[4] [1] TRUE So though nums[1] nums[2] nums[3] nums[4], fact[1] compares *unequal* to fact[2] though it compares *equal* to fact[4]. Apparently R is comparing the *names* of the levels rather than the indexes in the factor. This would be weird even if it didn't lead to this very bad case. Hope this helps, -s On Mon, Mar 16, 2009 at 6:53 PM, Daniel Murphy chiefmur...@gmail.com wrote: I have a matrix whose columns were filled with values which were functions of cvseq-seq(.2,.3,by=.1) (and a row value of mode integer). To do a lookup for cv=.3 later, I wanted to match(.3,cvseq), which gave me NA, hence my question. I thought R would match .3 in cvseq within .Machine$double.eps, but I can understand it if .3 and the second element of cvseq would not have identical bits. Besides the helpful suggestions below, I also tried cvseqf - as.factor(cvseq) match(.3,cvseq) [1] 2 which worked. In general, would it be better to go the enumeration route via as.factor or the approximation route? Thanks for the help. -Dan On Mon, Mar 16, 2009 at 8:24 AM, Stavros Macrakis macra...@alum.mit.edu wrote: Well, first of all, seq(from=.2,to=.3) gives c(0.2), so I assume you really mean something like seq(from=.2,to=.3,by=.1), which gives c(0.2, 0.3). %in% tests for exact equality, which is almost never a good idea with floating-point numbers. You need to define what exactly you mean by in for floating-point numbers. What sort of tolerance are you willing to allow? Some possibilities would be for example: approxin - function(x,list,tol) any(abs(list-x)tol) # absolute tolerance rapproxin - function(x,list,tol) (x==0 0 %in% list) || any(abs((list-x)/x)=tol,na.rm=TRUE) # relative tolerance; only exact 0 will match 0 Hope this helps, -s On Mon, Mar 16, 2009 at 9:36 AM, Daniel Murphy chiefmur...@gmail.com wrote: Hello:I am trying to match the value 0.3 in the sequence seq(.2,.3). I get 0.3 %in% seq(from=.2,to=.3) [1] FALSE Yet 0.3 %in% c(.2,.3) [1] TRUE For arbitrary sequences, this invisible .3 has been problematic. What is the best way to work around this? [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
