Re: [Rd] Re: [R] Problem going back to a viewport with gridBase
On 6/2/05, Paul Murrell [EMAIL PROTECTED] wrote:
Hi
Thanks. I have mucked around in vpTree structures and discovered its
actually quite easy to specify children so I have changed my example
so that instead of naming the children of 'layout' and then remembering
coordinates linked to the names of the children of 'layout' in
the 'coords' structure (which really just duplicates state information
already available in grid) it simply follows the order
of the children of 'layout' directly. This permits elimination of 'coords'
and the two naming functions. Using the depth approach you advocate,
'with' also becomes shorter and I think I have it to the point where it works
with both vpPath and viewport classes. Once Deepayan implements
the use.viewport= argument to print, 'with' can be eliminated too. No
questions this time but I thought I would post the latest version for
completeness. Regards.
[pushLayout is same as before except there are no names on the
children of 'layout' and the rest is new]
library(grid)
library(lattice)
pushLayout - function(nr, nc, name=layout) {
pushViewport(viewport(layout=grid.layout(nr, nc), name=name))
for (i in 1:nr) {
for (j in 1:nc) {
pushViewport(viewport(layout.pos.row=i, layout.pos.col=j))
upViewport()
}
}
upViewport()
}
with.vpPath - with.viewport - function(data, expr, ...) {
# if data is a vpPath it cannot be ROOT since NULL will never
dispatch here
depth - if (data$name == ROOT) 0 else downViewport(data$name)
result - eval.parent(substitute(expr))
upViewport(depth)
invisible(result)
}
grid.newpage()
# specify number of cells to fill and number of rows
n - 5; nr - 3
nc - ceiling(n/nr)
downViewport(pushLayout(nr, nc))
vpt - current.vpTree(all = FALSE)
for(k in 1:n) with(vpt$children[[k]],
print( xyplot(v ~ v, list(v = 1:k)), newpage = FALSE )
)
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[Rd] using so-library involving Taucs
Dear R developers,
The trace of the hat matrix H~(n,n) is computed as follows:
tr(H) = tr(BS^-1B') = tr(S^-1B'B) := tr(X) = sum(diag(X))
with B~(n,p), S~(p,p).
Since p is of the order 10^3 but S is sparse I would like to employ
Taucs linear solver ( http://www.tau.ac.il/~stoledo/taucs/ ) on
SX = B'B.
(Further improvement by implying a looping over i=1,...,p, calling
taucs_linsolve(S, X[,i], (B'B)[,i]) and saving X[i,i] only is pending.)
For this purpose I compiled the C code hattrace.c to a shared object
using:
gcc -g -Wall -I/usr/local/taucs/src -I/usr/local/taucs/build/linux -c
hattrace.c -o hattrace.o
gcc -g -L/usr/local/taucs/external/lib/linux
-L/usr/local/taucs/lib/linux -L/usr/local/lib -L/opt/gnome/lib
-L/usr/lib/R/lib -shared -fpic -o hattrace.so hattrace.o -ltaucs
-llapack -lf77blas -lcblas -latlas -lmetis -lm -lg2c -lR
I tried the following test commands:
library(splines)
library(SparseM)
B - splineDesign(knots = 1:10, x = 4:7)
D - diff(diag(dim(B)[2]), differences = 1)
BB - t(B) %*% B
S - as.matrix.ssc(BB + t(D) %*% D)
if (!is.loaded(symbol.C(hattrace))) { dyn.load(paste(hattrace,
.Platform$dynlib.ext, sep = )) }
out - 0
spur - (.C(hattrace, as.double(as.vector(slot(S, ra))),
as.integer(as.vector(slot(S, ja) - 1)),
as.integer(as.vector(slot(S, ia) - 1)),
as.integer(dim(S)[1]), as.double(as.vector(BB)),
as.double(out), PACKAGE = hattrace))[[6]]
Unfortunately, I get an R process segmentation fault although the C Code
outputs the correct trace value to /tmp/hattrace.log which I checked by
a equivalent R routine. Since this segmentation fault does not occur
every time, I assume a pointer problem. Any help on how to solve it is
greatly appreciated.
I am running R 2.0.0 on SuSE Linux.
Susanne Heim
--
Susanne Heim
Institute of Statistics, Ludwig-Maximilians-University
Ludwigstr.33/II, D-80539 Munich, Germany.
Phone: +49-89-2180-2226
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[Rd] using so-library involving Taucs
Dear R developers,
The trace of the hat matrix H~(n,n) is computed as follows:
tr(H) = tr(BS^-1B') = tr(S^-1B'B) := tr(X) = sum(diag(X))
with B~(n,p), S~(p,p).
Since p is of the order 103 but S is sparse I would like to employ Taucs
linear solver ( http://www.tau.ac.il/~stoledo/taucs/ ) on
SX = B'B.
(Further improvement by implying a looping over i=1,...,p, calling
taucs_linsolve(S, X[,i], (B'B)[,i]) and saving X[i,i] only is pending.)
For this purpose I compiled the C code hattrace.c to a shared object
using:
gcc -g -Wall -I/usr/local/taucs/src -I/usr/local/taucs/build/linux -c
hattrace.c -o hattrace.o
gcc -g -L/usr/local/taucs/external/lib/linux
-L/usr/local/taucs/lib/linux -L/usr/local/lib -L/opt/gnome/lib
-L/usr/lib/R/lib -shared -fpic -o hattrace.so hattrace.o -ltaucs
-llapack -lf77blas -lcblas -latlas -lmetis -lm -lg2c -lR
I tried the following test commands:
library(splines)
library(SparseM)
B - splineDesign(knots = 1:10, x = 4:7)
D - diff(diag(dim(B)[2]), differences = 1)
BB - t(B) %*% B
S - as.matrix.ssc(BB + t(D) %*% D)
if (!is.loaded(symbol.C(hattrace))) { dyn.load(paste(hattrace,
.Platform$dynlib.ext, sep = )) }
out - 0
spur - (.C(hattrace, as.double(as.vector(slot(S, ra))),
as.integer(as.vector(slot(S, ja) - 1)),
as.integer(as.vector(slot(S, ia) - 1)),
as.integer(dim(S)[1]), as.double(as.vector(BB)),
as.double(out), PACKAGE = hattrace))[[6]]
Unfortunately, I get an R process segmentation fault although the C Code
outputs the correct trace value to /tmp/hattrace.log which I checked by
a equivalent R routine. Since this segmentation fault does not occur
every time, I assume a pointer problem. Any help on how to solve it is
greatly appreciated.
I am running R 2.0.0 on SuSE Linux.
Susanne Heim
--
Susanne Heim
Institute of Statistics, Ludwig-Maximilians-University
Ludwigstr.33/II, D-80539 Munich, Germany.
Phone: +49-89-2180-2226
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[Rd] R-bugs will be offline starting June 7
Due to our IT unit moving on Wednesday and Biostat's move the day after, the web interface to r-bugs will be offline from the afternoon of June 7 at least until the afternoon of June 9, possibly going into the 10th. The email interface may come up somewhat earlier. -pd -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] dotcode typo? (PR#7917)
On 6/2/2005 1:27 PM, [EMAIL PROTECTED] wrote: [EMAIL PROTECTED] wrote: Whoops, spoke too soon. This definitely breaks the logic, so I won't commit. With this change the check of demo(lm.glm) in package utils fails with this error message: dead - cbind(x, n - x) summary(glm(dead ~ dose, family = binomial(link = logit))) Error in .Call(logit_link, mu) : cannot resolve native routine Execution halted I'm cc'ing this to R-bugs so we don't forget it, but I'm not going to be able to fix it down myself. Duncan Murdoch __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel That occurs in code that I recently added so I better check that. I think it was that .Call() didn't include PACKAGE=stats in stats/R/family.R. I've fixed that; I'll look for other similar cases. Duncan Murdoch __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] documentation source diff...
Hi, I forgot the name of the function 'colSums', and expected to be able
to find it through the 'see also' section of the documentation for the
'sum' function.
Here is the diff I made of the altered documentation to facilitate this
action... (p.s. I made the diff on the R-2.1.0 source).
diff sum.Rd src/library/base/man/sum.Rd --context=2
*** sum.Rd 2005-06-03 20:24:22.468224056 +0100
--- src/library/base/man/sum.Rd 2005-04-18 22:30:27.0 +0100
***
*** 33,38
Wadsworth \ Brooks/Cole.
}
- \seealso{
- \code{\code{\link{colSums}}.
- }
\keyword{arith}
--- 33,35
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Re: [Rd] using so-library involving Taucs
On 6/3/05, Susanne Heim [EMAIL PROTECTED] wrote:
Dear R developers,
The trace of the hat matrix H~(n,n) is computed as follows:
tr(H) = tr(BS^-1B') = tr(S^-1B'B) := tr(X) = sum(diag(X))
with B~(n,p), S~(p,p).
Since p is of the order 10^3 but S is sparse I would like to employ
Taucs linear solver ( http://www.tau.ac.il/~stoledo/taucs/ ) on
SX = B'B.
(Further improvement by implying a looping over i=1,...,p, calling
taucs_linsolve(S, X[,i], (B'B)[,i]) and saving X[i,i] only is pending.)
For this purpose I compiled the C code hattrace.c to a shared object
using:
gcc -g -Wall -I/usr/local/taucs/src -I/usr/local/taucs/build/linux -c
hattrace.c -o hattrace.o
gcc -g -L/usr/local/taucs/external/lib/linux
-L/usr/local/taucs/lib/linux -L/usr/local/lib -L/opt/gnome/lib
-L/usr/lib/R/lib -shared -fpic -o hattrace.so hattrace.o -ltaucs
-llapack -lf77blas -lcblas -latlas -lmetis -lm -lg2c -lR
I tried the following test commands:
library(splines)
library(SparseM)
B - splineDesign(knots = 1:10, x = 4:7)
D - diff(diag(dim(B)[2]), differences = 1)
BB - t(B) %*% B
S - as.matrix.ssc(BB + t(D) %*% D)
if (!is.loaded(symbol.C(hattrace))) { dyn.load(paste(hattrace,
.Platform$dynlib.ext, sep = )) }
out - 0
spur - (.C(hattrace, as.double(as.vector(slot(S, ra))),
as.integer(as.vector(slot(S, ja) - 1)),
as.integer(as.vector(slot(S, ia) - 1)),
as.integer(dim(S)[1]), as.double(as.vector(BB)),
as.double(out), PACKAGE = hattrace))[[6]]
Unfortunately, I get an R process segmentation fault although the C Code
outputs the correct trace value to /tmp/hattrace.log which I checked by
a equivalent R routine. Since this segmentation fault does not occur
every time, I assume a pointer problem. Any help on how to solve it is
greatly appreciated.
Is S positive definite? If so, it may be more effective to take the
Cholesky decomposition of S and solve the system S^(1/2)X = B then
take the sum of the squares of the elements of X.
If you wish to provide me off-list with examples of the matrices S and
B, I can check how best to do this with the Matrix package.
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