[Rd] "Panel Data Unit Root tests"
I could not find a package to run panel data unit root tests in R (there's a STATA module, though - PANELUNIT- and routines for Sarno and Taylor's MADF test, Levin-Lin-Chu's test, Im-Pesaran-Shin's Test, etc, to do this). Hence, I am toying with the idea of having a go at writing up one for R, but would like to know whether anyone is already working on this. José Mr José Luis Iparraguirre Senior Research Economist Economic Research Institute of Northern Ireland 2 -14 East Bridge Street Belfast BT1 3NQ Northern Ireland United Kingdom Tel: +44 (0)28 9072 7365 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] length of POSIXlt object (PR#13482)
'The R Inferno' page 93 and page 99.
Patrick Burns
patr...@burns-stat.com
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of "The R Inferno" and "A Guide for the Unwilling S User")
twoutop...@gmail.com wrote:
The length() of a POSIXlt object is given as 9 regardless of the actual
length. For example:
make.date.time
function (year=c(2006,2006),month=c(8,8),day=2:5,hour=13,minute=45)
{# convert year, etc., into POSIXlt object
#
d=as.character(make.date(year,month,day))
t=paste(hour,minute,sep=":")
as.POSIXlt(paste(d,t))
}
t=make.date.time()
t
[1] "2006-08-02 13:45:00" "2006-08-03 13:45:00" "2006-08-04 13:45:00"
[4] "2006-08-05 13:45:00"
length(t)
[1] 9
t[1]
[1] "2006-08-02 13:45:00"
length(t[1])
[1] 9
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[Rd] Methods not loaded in R-Devel vs 2.8.1
Dear list-member,
I am currently developing a package with S4 classes. The NAMESPACE and
DESCRIPTION is printed below. Within this package I have set a method
"residuals" for two classes. In version 2.8.1 these two are reported whereas in
R-Devel (2009-01-28 r47766). What have I missed? What has changed and how can I
rectify the issue? Your help and pointers are welcome.
For 2.8.1:
**
> library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
Warning message:
package 'gogarch' was built under R version 2.9.0
> showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
object="Goestml"
object="GoGARCH"
> getMethod("residuals", "GoGARCH")
Method Definition:
function (object, ...)
{
.local <- function (object, standardize = FALSE)
{
m <- ncol(obj...@x)
n <- nrow(obj...@x)
resl <- lapply(obj...@models, residuals, standardize = standardize)
resm <- matrix(c(unlist(resl)), ncol = m, nrow = n)
ynames <- paste("y", 1:2, sep = "")
colnames(resm) <- ynames
rownames(resm) <- rownames(obj...@x)
return(resm)
}
.local(object, ...)
}
Signatures:
object
target "GoGARCH"
defined "GoGARCH"
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets utils grDevices methods base
other attached packages:
[1] gogarch_0.2-8 fGarch_280.75 fBasics_280.74MASS_7.2-44
[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
>
For R-Devel:
> library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
> showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
> getMethod("residuals", "GoGARCH")
Error in getMethod("residuals", "GoGARCH") :
No method found for function "residuals" and signature GoGARCH
> sessionInfo()
R version 2.9.0 Under development (unstable) (2009-01-28 r47766)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] gogarch_0.2-8 fGarch_280.75 fBasics_280.74MASS_7.2-44
[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
loaded via a namespace (and not attached):
[1] grid_2.9.0 lattice_0.17-17 nlme_3.1-89 urca_1.2-2
[5] vars_1.4-4
>
DESCRIPTION:
Package: gogarch
Version: 0.2-8
Type: Package
Title: Generalized Orthogonal GARCH (GO-GARCH) models
Date: 2009-01-30
Author: Bernhard Pfaff
Maintainer: Bernhard Pfaff
Depends: R (>= 2.7.0), stats, methods, fGarch
Suggests: vars
Description: Implementation of the GO-GARCH model class.
License: GPL (>= 2)
LazyLoad: yes
LazyLoad: yes
NAMESPACE:
**
## Import packages
import(methods)
## Import functions
importFrom(stats, coef, logLik, residuals)
## Classes
exportClasses(Goestml, GoGARCH, Goinit, Orthom)
## Methods
exportMethods(angles, cvar, ccor, ccov, coef, converged, goest, logLik, M,
print, show, t, residuals)
## Functions
export(gogarch, goinit, gollh, gotheta, Rd2, UprodR, unvech, validOrthomObject,
validGoinitObject)
Dr. Bernhard Pfaff
Director
Invesco Quantitative Strategies International
Invesco Asset Management Deutschland GmbH
Bleichstrasse 60-62
D-60313 Frankfurt am Main
Tel: +49 (0)69 29807 230
Fax: +49 (0)69 29807 178
www.institutional.invesco.com
Email: bernhard_pf...@fra.invesco.com
Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
Alexander Lehmann, Christian Puschmann
Handelsregister: Frankfurt am Main, HRB 28469
Sitz der Gesellschaft: Frankfurt am Main
*
Confidentiality Note: The information contained in this ...{{dropped:10}}
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Re: [Rd] Methods not loaded in R-Devel vs 2.8.1
Sorry for bothering the list one more time. When I run the code with RGui.exe
the methods are shown in both versions of R and everything is fine. However,
there is a difference whence the showMethods("residuals") is invoked via
Rterm.exe. Here, neither under 2.8.1 nor R-Devel are the methods reported for
"GoGARCH" and "Goestml". I have the following in my .emacs:
(setq inferior-R-program-name "Q:/Shared/Applications/R/R-2.8.1/bin/Rterm.exe")
(setq inferior-R-args "--internet2")
(setq ess-ask-for-ess-directory nil)
and the result is the same:
> library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
Warning message:
package 'gogarch' was built under R version 2.9.0
> showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets utils grDevices methods base
other attached packages:
[1] gogarch_0.2-9 fGarch_280.75 fBasics_280.74MASS_7.2-44
[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-17 nlme_3.1-89 urca_1.2-2
[5] vars_1.4-4
> getMethod("residuals", "GoGARCH")
Error in getMethod("residuals", "GoGARCH") :
No method found for function "residuals" and signature GoGARCH
>
So now my question is rather about the difference between RGui.exe and
Rterm.exe with respect to the method map.
Best,
Bernhard
Dr. Bernhard Pfaff
Director
Invesco Quantitative Strategies International
Invesco Asset Management Deutschland GmbH
Bleichstrasse 60-62
D-60313 Frankfurt am Main
Tel: +49 (0)69 29807 230
Fax: +49 (0)69 29807 178
www.institutional.invesco.com
Email: bernhard_pf...@fra.invesco.com
Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
Alexander Lehmann, Christian Puschmann
Handelsregister: Frankfurt am Main, HRB 28469
Sitz der Gesellschaft: Frankfurt am Main
>-Ursprüngliche Nachricht-
>Von: r-devel-boun...@r-project.org
>[mailto:r-devel-boun...@r-project.org] Im Auftrag von Pfaff,
>Bernhard Dr.
>Gesendet: Freitag, 30. Januar 2009 12:13
>An: r-devel@r-project.org
>Betreff: [Rd] Methods not loaded in R-Devel vs 2.8.1
>
>Dear list-member,
>
>I am currently developing a package with S4 classes. The
>NAMESPACE and DESCRIPTION is printed below. Within this
>package I have set a method "residuals" for two classes. In
>version 2.8.1 these two are reported whereas in R-Devel
>(2009-01-28 r47766). What have I missed? What has changed and
>how can I rectify the issue? Your help and pointers are welcome.
>
>
>For 2.8.1:
>**
>
>> library(gogarch)
>Loading required package: fGarch
>Loading required package: timeDate
>Loading required package: timeSeries
>Loading required package: fBasics
>Loading required package: MASS
>Warning message:
>package 'gogarch' was built under R version 2.9.0
>> showMethods("residuals")
>Function: residuals (package stats)
>object="ANY"
>object="fGARCH"
>object="Goestml"
>object="GoGARCH"
>
>> getMethod("residuals", "GoGARCH")
>Method Definition:
>
>function (object, ...)
>{
>.local <- function (object, standardize = FALSE)
>{
>m <- ncol(obj...@x)
>n <- nrow(obj...@x)
>resl <- lapply(obj...@models, residuals, standardize =
>standardize)
>resm <- matrix(c(unlist(resl)), ncol = m, nrow = n)
>ynames <- paste("y", 1:2, sep = "")
>colnames(resm) <- ynames
>rownames(resm) <- rownames(obj...@x)
>return(resm)
>}
>.local(object, ...)
>}
>
>
>Signatures:
>object
>target "GoGARCH"
>defined "GoGARCH"
>> sessionInfo()
>R version 2.8.1 (2008-12-22)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
>MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
>attached base packages:
>[1] stats graphics datasets utils grDevices methods
> base
>
>other attached packages:
>[1] gogarch_0.2-8 fGarch_280.75 fBasics_280.74
>MASS_7.2-44
>[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
>>
>
>
>For R-Devel:
>
>> library(gogarch)
>Loading required package: fGarch
>Loading required package: timeDate
>Loading required package: timeSeries
>Loading required package: fBasics
>Loading required package: MASS
>> showMethods("residuals")
>Function: residuals (package stats)
>object="ANY"
>object="fGARCH"
>
>> getMethod("residuals", "GoGARCH")
>Error in getMethod("residuals", "GoGARCH") :
> No method found for function "residuals" and signature GoGARCH
>> sessionInfo()
>R version 2.9.0 Under development (unstable) (2009-01
Re: [Rd] Methods not loaded in R-Devel vs 2.8.1
I don't believe this is Rgui vs Rterm either. More likely it is in
the startup files for the two sessions, e.g. the library search paths.
Try using --vanilla.
On Fri, 30 Jan 2009, Pfaff, Bernhard Dr. wrote:
Sorry for bothering the list one more time. When I run the code with RGui.exe the methods are shown in both
versions of R and everything is fine. However, there is a difference whence the
showMethods("residuals") is invoked via Rterm.exe. Here, neither under 2.8.1 nor R-Devel are the
methods reported for "GoGARCH" and "Goestml". I have the following in my .emacs:
(setq inferior-R-program-name "Q:/Shared/Applications/R/R-2.8.1/bin/Rterm.exe")
(setq inferior-R-args "--internet2")
(setq ess-ask-for-ess-directory nil)
and the result is the same:
library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
Warning message:
package 'gogarch' was built under R version 2.9.0
showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets utils grDevices methods base
other attached packages:
[1] gogarch_0.2-9 fGarch_280.75 fBasics_280.74MASS_7.2-44
[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-17 nlme_3.1-89 urca_1.2-2
[5] vars_1.4-4
getMethod("residuals", "GoGARCH")
Error in getMethod("residuals", "GoGARCH") :
No method found for function "residuals" and signature GoGARCH
So now my question is rather about the difference between RGui.exe
and Rterm.exe with respect to the method map.
Best,
Bernhard
Dr. Bernhard Pfaff
Director
Invesco Quantitative Strategies International
Invesco Asset Management Deutschland GmbH
Bleichstrasse 60-62
D-60313 Frankfurt am Main
Tel: +49 (0)69 29807 230
Fax: +49 (0)69 29807 178
www.institutional.invesco.com
Email: bernhard_pf...@fra.invesco.com
Geschäftsführer: Karl Georg Bayer, Bernhard Langer, Dr. Jens Langewand,
Alexander Lehmann, Christian Puschmann
Handelsregister: Frankfurt am Main, HRB 28469
Sitz der Gesellschaft: Frankfurt am Main
-Ursprüngliche Nachricht-
Von: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] Im Auftrag von Pfaff,
Bernhard Dr.
Gesendet: Freitag, 30. Januar 2009 12:13
An: r-devel@r-project.org
Betreff: [Rd] Methods not loaded in R-Devel vs 2.8.1
Dear list-member,
I am currently developing a package with S4 classes. The
NAMESPACE and DESCRIPTION is printed below. Within this
package I have set a method "residuals" for two classes. In
version 2.8.1 these two are reported whereas in R-Devel
(2009-01-28 r47766). What have I missed? What has changed and
how can I rectify the issue? Your help and pointers are welcome.
For 2.8.1:
**
library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
Warning message:
package 'gogarch' was built under R version 2.9.0
showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
object="Goestml"
object="GoGARCH"
getMethod("residuals", "GoGARCH")
Method Definition:
function (object, ...)
{
.local <- function (object, standardize = FALSE)
{
m <- ncol(obj...@x)
n <- nrow(obj...@x)
resl <- lapply(obj...@models, residuals, standardize =
standardize)
resm <- matrix(c(unlist(resl)), ncol = m, nrow = n)
ynames <- paste("y", 1:2, sep = "")
colnames(resm) <- ynames
rownames(resm) <- rownames(obj...@x)
return(resm)
}
.local(object, ...)
}
Signatures:
object
target "GoGARCH"
defined "GoGARCH"
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_
MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics datasets utils grDevices methods
base
other attached packages:
[1] gogarch_0.2-8 fGarch_280.75 fBasics_280.74
MASS_7.2-44
[5] timeSeries_290.79 timeDate_290.81 fortunes_1.3-6
For R-Devel:
library(gogarch)
Loading required package: fGarch
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics
Loading required package: MASS
showMethods("residuals")
Function: residuals (package stats)
object="ANY"
object="fGARCH"
getMethod("residuals", "GoGARCH")
Error in getMethod("residuals", "GoGARCH") :
No method found for function "residuals" and signature GoGARCH
sessionInfo()
R version 2.9.0 Unde
Re: [Rd] "Panel Data Unit Root tests"
Jose, this is not the list for asking questions like this. You should ask on R-help or (alternatively!) R-SIG-Finance would be a good place to ask. I could not find a package to run panel data unit root tests in R (there's a STATA module, though - PANELUNIT- and routines for Sarno and Taylor's MADF test, Levin-Lin-Chu's test, Im-Pesaran-Shin's Test, etc, to do this). Hence, I am toying with the idea of having a go at writing up one for R, but would like to know whether anyone is already working on this. I think that there's currently no package for this on CRAN but I might be wrong. But there's a chance that someone on the SIG has code for this... Best, Z __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] (PR#13487) Segfault when mistakenly calling [.data.frame
On Thu, Jan 29, 2009 at 4:44 PM, Prof Brian Ripley wrote:
> What did your actual application do? This seems a very strange thing to
> do, and the segfault is in trying to construct the traceback.
>
> Only by using do.call on the object (and not even by name) do I get this
> error. E.g.
>
> `[.data.frame`(1:10, 3)
>>
> Error in NextMethod("[") : object not specified
>
>> do.call("[.data.frame", list(1:10, 3))
>>
> Error in NextMethod("[") : object not specified
>
> are fine.
>
> Obviously it would be nice to fix this, but I'd like to understand the
> actual circumstances: there is more to it than the subject line.
Yes, there is more. For reporting the problem, we tried to pare it down to
a concise, self-contained test case.
My boss was debugging an issue in our R code. We have our own "["
functions, because stock R drops names when subscripting. To bypass our
now-suspect functions and get the "real" subscripting method, he used "get"
from package:base. He was examining a large object, and believing it was a
data frame, chose "[.data.frame". As it turns out, that object was not a
data frame, and he got an unexpected segfault. I think it was a matrix.
But it doesn't matter -- a vector as in the test case will give the same.
We have since fixed the bug in our replacement subscripting function, so the
issue might not affect us any more.
Thanks,
/Christian
> On Thu, 29 Jan 2009, brechbueh...@gmail.com wrote:
>
> Full_Name: Christian Brechbuehler
>> Version: 2.7.2, 2.8.1
>> OS: linux-gnu
>>
>> If we mistakenly believe the object is a data frame (as we did in a much
>> more
>> complicated real situation), this happens:
>>
>> > do.call(get("[.data.frame",pos="package:base"),list(1:10,3))
>> Error in NextMethod("[") :
>>no calling generic was found: was a method called directly?
>>
>> *** caught segfault ***
>> address (nil), cause 'unknown'
>>
>> Process R:2 segmentation fault (core dumped) at Thu Jan 29 09:26:29 2009
>>
>> The Error message is appropriate. But the segmentation fault is
>> unexpected.
>>
>
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Re: [Rd] (PR#13487) Segfault when mistakenly calling [.data.frame
On Jan 30, 2009, at 10:30 , Christian Brechbühler wrote:
On Thu, Jan 29, 2009 at 4:44 PM, Prof Brian Ripley >wrote:
What did your actual application do? This seems a very strange
thing to
do, and the segfault is in trying to construct the traceback.
Only by using do.call on the object (and not even by name) do I get
this
error. E.g.
`[.data.frame`(1:10, 3)
Error in NextMethod("[") : object not specified
do.call("[.data.frame", list(1:10, 3))
Error in NextMethod("[") : object not specified
are fine.
Obviously it would be nice to fix this, but I'd like to understand
the
actual circumstances: there is more to it than the subject line.
Yes, there is more. For reporting the problem, we tried to pare it
down to
a concise, self-contained test case.
My boss was debugging an issue in our R code. We have our own "["
functions, because stock R drops names when subscripting.
... if you tell it to do so, yes. If you tell it to not do that, it
won't ... ever tried drop=FALSE ?
Cheers,
S
To bypass our
now-suspect functions and get the "real" subscripting method, he
used "get"
from package:base. He was examining a large object, and believing
it was a
data frame, chose "[.data.frame". As it turns out, that object was
not a
data frame, and he got an unexpected segfault. I think it was a
matrix.
But it doesn't matter -- a vector as in the test case will give the
same.
We have since fixed the bug in our replacement subscripting
function, so the
issue might not affect us any more.
Thanks,
/Christian
On Thu, 29 Jan 2009, brechbueh...@gmail.com wrote:
Full_Name: Christian Brechbuehler
Version: 2.7.2, 2.8.1
OS: linux-gnu
If we mistakenly believe the object is a data frame (as we did in
a much
more
complicated real situation), this happens:
do.call(get("[.data.frame",pos="package:base"),list(1:10,3))
Error in NextMethod("[") :
no calling generic was found: was a method called directly?
*** caught segfault ***
address (nil), cause 'unknown'
Process R:2 segmentation fault (core dumped) at Thu Jan 29
09:26:29 2009
The Error message is appropriate. But the segmentation fault is
unexpected.
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Re: [Rd] (PR#13487) Segfault when mistakenly calling [.data.frame
Simon Urbanek wrote:
On Jan 30, 2009, at 10:30 , Christian Brechbühler wrote:
On Thu, Jan 29, 2009 at 4:44 PM, Prof Brian Ripley
wrote:
What did your actual application do? This seems a very strange
thing to
do, and the segfault is in trying to construct the traceback.
Only by using do.call on the object (and not even by name) do I get
this
error. E.g.
`[.data.frame`(1:10, 3)
Error in NextMethod("[") : object not specified
do.call("[.data.frame", list(1:10, 3))
Error in NextMethod("[") : object not specified
are fine.
Obviously it would be nice to fix this, but I'd like to understand the
actual circumstances: there is more to it than the subject line.
Yes, there is more. For reporting the problem, we tried to pare it
down to
a concise, self-contained test case.
My boss was debugging an issue in our R code. We have our own "["
functions, because stock R drops names when subscripting.
... if you tell it to do so, yes. If you tell it to not do that, it
won't ... ever tried drop=FALSE ?
The common situation I have (which might be the same as the OP's) is
wanting to get a vector from a data frame, and having the rownames of
the dataframe become the names on the vector.
With matrix, the behavior I want is the default behavior, e.g.,
> x <- cbind(a=c(x=1,y=2,z=3),b=4:6)
> x
a b
x 1 4
y 2 5
z 3 6
> x[,1]
x y z
1 2 3
But with a data frame, subscripting returns a vector with no names:
> xd <- as.data.frame(x)
> xd[,1]
[1] 1 2 3
One can use drop=FALSE, but then you've still got a data frame, not a
vector:
> (xd1 <- xd[,1,drop=FALSE])
a
x 1
y 2
z 3
The simplest way I know to get a named vector is to use as.matrix on the
one-column dataframe:
> as.matrix(xd1)[,1]
x y z
1 2 3
>
(Which works fine except in the case where xd1 has only one row...)
And BTW, am I missing something, or does the behavior of drop() not
conform to the description in ?drop:
> Value:
> If 'x' is an object with a 'dim' attribute (e.g., a matrix or
> 'array'), then 'drop' returns an object like 'x', but with any
> extents of length one removed. Any accompanying 'dimnames'
> attribute is adjusted and returned with 'x': if the result is a
> vector the 'names' are taken from the 'dimnames' (if any). If the
> result is a length-one vector, the names are taken from the first
> dimension with a dimname.
How is this last sentence consistent with the following behavior?
> dimnames(x[1,1,drop=F])
[[1]]
[1] "x"
[[2]]
[1] "a"
> drop(x[1,1,drop=F])
[1] 1
>
From the description in "Value:" in ?drop, I would have expected above
result to have the name "x" (the name from the first dimension with a
dimname).
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
>
-- Tony Plate
Cheers,
S
To bypass our
now-suspect functions and get the "real" subscripting method, he used
"get"
from package:base. He was examining a large object, and believing it
was a
data frame, chose "[.data.frame". As it turns out, that object was
not a
data frame, and he got an unexpected segfault. I think it was a matrix.
But it doesn't matter -- a vector as in the test case will give the
same.
We have since fixed the bug in our replacement subscripting function,
so the
issue might not affect us any more.
Thanks,
/Christian
On Thu, 29 Jan 2009, brechbueh...@gmail.com wrote:
Full_Name: Christian Brechbuehler
Version: 2.7.2, 2.8.1
OS: linux-gnu
If we mistakenly believe the object is a data frame (as we did in a
much
more
complicated real situation), this happens:
do.call(get("[.data.frame",pos="package:base"),list(1:10,3))
Error in NextMethod("[") :
no calling generic was found: was a method called directly?
*** caught segfault ***
address (nil), cause 'unknown'
Process R:2 segmentation fault (core dumped) at Thu Jan 29 09:26:29
2009
The Error message is appropriate. But the segmentation fault is
unexpected.
[[alternative HTML version deleted]]
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Re: [Rd] In Rd: \describe \itemize and \item
Duncan Murdoch wrote on 01/29/2009 07:14:11 PM:
> On 29/01/2009 5:22 PM, Nicholas L Crookston wrote:
> > I rebuilt a test version of my yaImpute package using Uwe Ligges'
windows
> > build service.
> > I got this reply: Check result: OK
> > R version 2.9.0 Under development (unstable) (2009-01-27 r47756)
> >
> > Here is the issue: I have the following construct in help files (this
> > example relates to "data"):
> >
> > \format{
> > A data frame with 847 rows and 29 columns: \cr\cr
> > Ground based measurements of trees (Y-variables):
> > \itemize{
> > \item{TopHt}{Height of tallest trees (ft)}
> > \item{LnVolL}{Log of the volume \eqn{(ft^3/acre)} of western
larch}
> > .. many lines deleted ..
> > \item{LnVolPP}{Log of the volume \eqn{(ft^3/acre)} of ponderosa
pine}
> > \item{CCover}{Canopy cover (percent)}
> > }
> > Geographic Location, Slope, and Aspect (X-variables):
> > \itemize{
> > \item{utmx}{UTM easting at plot center}
> > \item{utmy}{UTM northing at plot center}
> > .. many lines deleted ..
> > \item{elevm}{Mean elevation (ft) above sea level over plot}
> > \item{slpsinaspm}{Mean of slope (proportion) times the sine of
aspect}
> > }
> > .. many lines deleted ..
> > }
> >
> > What I get in the help file is:
> > =
> > Format
> > A data frame with 847 rows and 29 columns:
> >
> > Ground based measurements of trees (Y-variables):
> >
> >TopHt
> > Height of tallest trees (ft)
> >LnVolL
> > Log of the volume (ft^3/acre) of western larch
> > = ..and so on
> > [I've inserted 3 spaces to mimic tabs in this illustration]
> >
> > I would expect (and I used to get) something like this:
> > =
> > Ground based measurements of trees (Y-variables):
> >
> >TopHt Height of tallest trees (ft)
> >LnVolL Log of the volume (ft^3/acre) of western larch
> > =
> >
> I think we need more info to comment on. Is this file one of the ones
> in the yaImpute package on CRAN, or is it unreleased? Is the Rd file
> available for us to look at? Does the man page look different in 2.8.1
> from what you expect (there haven't been serious changes there), or only
> in R-devel (2.9.0)? 2.6.2 is pretty old, but I don't think any of the
> requested changes should be incompatible with it.
> Duncan Murdoch
The problem is in an unreleased version built in the development
environment.
The entire unreleased package can be found at this temporary location:
http://forest.moscowfsl.wsu.edu/gems/yaImpute_1.0-8.tar.gz
The original is on CRAN (version 1.0-7). It worked under the old parser,
but
not using parser 2 (the warnings on CRAN point to the problem).
You can see the difference by looking at TallyLake.Rd
in the two versions. I would be happy to send you just these files if
you'd
like me to.
Note that text version of the help file builds as I expect it to.
The problem is in the htlm version.
PS: I tried two versions of \items
\item{utmx}{UTM easting at plot center}
and
\item{utmx }{UTM easting at plot center}
(note added spaces, added for readability of the Rd file
this difference does not seem to matter.)
Thanks, Nick
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Re: [Rd] In Rd: \describe \itemize and \item
On 1/30/2009 2:22 PM, Nicholas L Crookston wrote:
Duncan Murdoch wrote on 01/29/2009 07:14:11 PM:
On 29/01/2009 5:22 PM, Nicholas L Crookston wrote:
> I rebuilt a test version of my yaImpute package using Uwe Ligges'
windows
> build service.
> I got this reply: Check result: OK
> R version 2.9.0 Under development (unstable) (2009-01-27 r47756)
>
> Here is the issue: I have the following construct in help files (this
> example relates to "data"):
>
> \format{
> A data frame with 847 rows and 29 columns: \cr\cr
> Ground based measurements of trees (Y-variables):
> \itemize{
> \item{TopHt}{Height of tallest trees (ft)}
> \item{LnVolL}{Log of the volume \eqn{(ft^3/acre)} of western
larch}
> .. many lines deleted ..
> \item{LnVolPP}{Log of the volume \eqn{(ft^3/acre)} of ponderosa
pine}
> \item{CCover}{Canopy cover (percent)}
> }
> Geographic Location, Slope, and Aspect (X-variables):
> \itemize{
> \item{utmx}{UTM easting at plot center}
> \item{utmy}{UTM northing at plot center}
> .. many lines deleted ..
> \item{elevm}{Mean elevation (ft) above sea level over plot}
> \item{slpsinaspm}{Mean of slope (proportion) times the sine of
aspect}
> }
> .. many lines deleted ..
> }
>
> What I get in the help file is:
> =
> Format
> A data frame with 847 rows and 29 columns:
>
> Ground based measurements of trees (Y-variables):
>
>TopHt
> Height of tallest trees (ft)
>LnVolL
> Log of the volume (ft^3/acre) of western larch
> = ..and so on
> [I've inserted 3 spaces to mimic tabs in this illustration]
>
> I would expect (and I used to get) something like this:
> =
> Ground based measurements of trees (Y-variables):
>
>TopHt Height of tallest trees (ft)
>LnVolL Log of the volume (ft^3/acre) of western larch
> =
>
I think we need more info to comment on. Is this file one of the ones
in the yaImpute package on CRAN, or is it unreleased? Is the Rd file
available for us to look at? Does the man page look different in 2.8.1
from what you expect (there haven't been serious changes there), or only
in R-devel (2.9.0)? 2.6.2 is pretty old, but I don't think any of the
requested changes should be incompatible with it.
Duncan Murdoch
The problem is in an unreleased version built in the development
environment.
The entire unreleased package can be found at this temporary location:
http://forest.moscowfsl.wsu.edu/gems/yaImpute_1.0-8.tar.gz
The original is on CRAN (version 1.0-7). It worked under the old parser,
but
not using parser 2 (the warnings on CRAN point to the problem).
You can see the difference by looking at TallyLake.Rd
in the two versions. I would be happy to send you just these files if
you'd
like me to.
Note that text version of the help file builds as I expect it to.
The problem is in the htlm version.
PS: I tried two versions of \items
\item{utmx}{UTM easting at plot center}
and
\item{utmx }{UTM easting at plot center}
(note added spaces, added for readability of the Rd file
this difference does not seem to matter.)
Okay, I think I see now. I installed your package version 1.0-8 in
R-devel (to be 2.9.0), and the ?TallyLake man page looks fine to me in
text mode, looks slightly funny in HTML (with the labels one line above
the thing they're describing). But to me it looks better in the new
HTML than version 1.0-7 looked in 2.8.1: in that version, there was no
attempt to line up the descriptions to a common left margin, so they
tended to be confused with the thing they were describing.
So I'm not sure what you'd really like to see in the output. Can you
describe it again?
Duncan Murdoch
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Re: [Rd] In Rd: \describe \itemize and \item
Duncan Murdoch wrote on 01/30/2009 12:04:56 PM: > > Okay, I think I see now. I installed your package version 1.0-8 in > R-devel (to be 2.9.0), and the ?TallyLake man page looks fine to me in > text mode, looks slightly funny in HTML (with the labels one line above > the thing they're describing). But to me it looks better in the new > HTML than version 1.0-7 looked in 2.8.1: in that version, there was no > attempt to line up the descriptions to a common left margin, so they > tended to be confused with the thing they were describing. > So I'm not sure what you'd really like to see in the output. Can you > describe it again? Reading from the R-exts.pdf, section 2.4: "The \itemize and \enumerate commands take a single argument, within which there may be one or more \item commands. The text following each \item is formatted as one or more paragraphs, suitably indented and with the first paragraph marked with a bullet point (\itemize) or a number (\enumerate)." I'm using \itemize so I expect to see a bullet point making the first paragraph of each item. What I'm getting is what you would expect with the \describe command, as described here: "The \describe command is similar to \itemize but allows initial labels to be specified. The \items take two arguments, the label and the body of the item, in exactly the same way as argument and value \items. \describe commands are mapped to lists in HTML and \description lists in LATEX." > Duncan Murdoch Nick Crookston __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Side-effects of require() vs library() on x86_64 aka amd64
On 28 January 2009 at 22:26, Dirk Eddelbuettel wrote: | | RDieHarder fails its regression tests on x86_64 (aka "amd64") at CRAN (using | Debian), and I see the same on Ubuntu 8.10 in 64 bit. No issues on 32bit. | | One odd thing is that the program behaves well if run via | | R --no-save < tests/RDieHarder.R | | but NOT when started using | | R --slave < tests/RDieHarder.R | | as R CMD check does. Turns out, as so often, that there was a regular bug lurking which is now fixed in RDieHarder 0.1.1. But I still would like to understand exactly what is different so that --slave was able to trigger it when --vanilla, --no-save, ... did not. [ The library() vs require() issue may have been a red herring. ] Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
