Re: [R] Problem installing Hmisc (more info)
On Sat, 5 Feb 2005, Michael Kubovy wrote:
Following Brian Ripley's advice:
$ which g77
/sw/bin/g77
So I think you have fink.
I then found Makeconf, in
/Library/Frameworks/R.framework/Versions/2.0.1/Resources/etc
I edited it according to Brian's advice. It had:
You didn't. You need to replace
L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 appropriately.
FLIBS = -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
-lg2c -lSystem
which now is:
FLIBS = -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin -lg2c
-lSystem
Nevertheless the install failed just as below. But the console complaint was
slightly different from before:
WARNING: ignoring environment value of R_HOME
* Installing *source* package 'Hmisc' ...
** libs
g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
g77 -fno-common -g -O2 -c largrec.f -o largrec.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o rcorr.o
wclosest.o -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin -lg2c
-lSystem -lcc_dynamic -framework R
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not exist
ld: can't locate file for: -lg2c
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package 'Hmisc'
** Removing
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/Hmisc'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/Hmisc'
On Feb 5, 2005, at 4:59 PM, Prof Brian Ripley wrote:
On Sat, 5 Feb 2005, Michael Kubovy wrote:
Frank Harrell suggested I re-post with information about the version of
R
Thanks, that starts to make sense. You appear to have g77 installed, but
not in the place the person who prepared the binary install of R has it.
Where do you have it installed? ('whereis g77' or 'which g77' should tell
you.) Then you need to alter FLIBS in R_HOME/etc/Makeconf to point to it.
(You can remove -lfrtbegin from FLIBS: it is not needed: your R_HOME looks
to be /Library/Frameworks/R.framework/Versions/2.0.1.)
However, I believe there is a more fundamental problem: because libg2c is
a static library on current MacOS X, most packages using Fortran cannot be
compiled there. That's presumably the case with Hmisc, as the automated
package builder is not providing a binary build. (There is supposedly a
check directory on CRAN, but it is not there at present.)
Heres's the information:
version
_
platform powerpc-apple-darwin6.8
arch powerpc
os darwin6.8
system powerpc, darwin6.8
status
major2
minor0.1
year 2004
month11
day 15
language R
Here's what happens when I try to install:
install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdirfc4111
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
Here's what the Console had to say:
* Installing *source* package 'Hmisc' ...
** libs
g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
g77 -fno-common -g -O2 -c largrec.f -o largrec.o
gcc -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
rcorr.o wclosest.o -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
-lg2c -lSystem -lcc_dynami
Re: [R] Problem installing Hmisc (more info)
I had problem installing Hmisc and Dedign a couple of weeks ago,
repetitively.
It failed at the stage compiling the last help file (summary, I
remember), after long time sucking up system resource. What I did was
updated some development tools, such as glibc, gcc, automake, etc., I
can't tell which one worked for me, but eventually I managed to
compile those two packages with success. If you really want to know what
exactly development tools I have updated, I'd love to take a look at my
log files.
Hope this helps;-)
My information:
R.version
_
platform i586-pc-linux-gnu
arch i586
os linux-gnu
system i586, linux-gnu
status
major2
minor0.1
year 2004
month11
day 15
language R
Jindan
On Sat, 5 Feb 2005, Michael Kubovy wrote:
> Frank Harrell suggested I re-post with information about the version of
> R
>
> Heres's the information:
> > > version
> > _
> > platform powerpc-apple-darwin6.8
> > arch powerpc
> > os darwin6.8
> > system powerpc, darwin6.8
> > status
> > major2
> > minor0.1
> > year 2004
> > month11
> > day 15
> > language R
>
> Here's what happens when I try to install:
> > > install.packages("Hmisc")
> > trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
> > Content type `text/plain; charset=iso-8859-1' length 47565 bytes
> > opened URL
> > ==
> > downloaded 46Kb
> >
> > trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
> > Content type `application/x-tar' length 453567 bytes
> > opened URL
> > ==
> > downloaded 442Kb
> >
> > Delete downloaded files (y/N)?
> >
> > The packages are in /tmp/Rtmp1911/Rinstdirfc4111
> > Warning message:
> > Installation of package Hmisc had non-zero exit status in:
> > install.packages("Hmisc")
>
> Here's what the Console had to say:
> > * Installing *source* package 'Hmisc' ...
> > ** libs
> > g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
> > g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
> > g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
> > g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
> > g77 -fno-common -g -O2 -c largrec.f -o largrec.o
> > gcc -no-cpp-precomp
> > -I/Library/Frameworks/R.framework/Resources/include
> > -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
> > g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
> > g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
> > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> > Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
> > rcorr.o wclosest.o -L/usr/local/lib
> > -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
> > -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
> > -lg2c -lSystem -lcc_dynamic -framework R
> > ld: warning -L: directory name
> > (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
> > ld: warning -L: directory name
> > (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
> > exist
> > ld: can't locate file for: -lfrtbegin
> > make: *** [Hmisc.so] Error 1
> > ERROR: compilation failed for package 'Hmisc'
> > ** Removing
> > '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> > Hmisc'
> > ** Restoring previous
> > '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> > Hmisc'
>
>
> _
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
> Parcels: Room 102Gilmer Hall
> McCormick Road Charlottesville, VA 22903
> Office: B011+1-434-982-4729
> Lab: B019+1-434-982-4751
> Fax: +1-434-982-4766
> WWW: http://www.people.virginia.edu/~mk9y/
> [[alternative text/enriched version deleted]]
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem installing Hmisc (more info)
Following Brian Ripley's advice:
> $ which g77
> /sw/bin/g77
I then found Makeconf, in
/Library/Frameworks/R.framework/Versions/2.0.1/Resources/etc
I edited it according to Brian's advice. It had:
> FLIBS = -L/usr/local/lib
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
> -lg2c -lSystem
which now is:
> FLIBS = -L/usr/local/lib
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin
> -lg2c -lSystem
Nevertheless the install failed just as below. But the console
complaint was slightly different from before:
> WARNING: ignoring environment value of R_HOME
> * Installing *source* package 'Hmisc' ...
> ** libs
> g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
> g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
> g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
> g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
> g77 -fno-common -g -O2 -c largrec.f -o largrec.o
> gcc -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
> g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
> g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
> rcorr.o wclosest.o -L/usr/local/lib
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -L/sw/bin
> -lg2c -lSystem -lcc_dynamic -framework R
> ld: warning -L: directory name
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
> ld: warning -L: directory name
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
> exist
> ld: can't locate file for: -lg2c
> make: *** [Hmisc.so] Error 1
> ERROR: compilation failed for package 'Hmisc'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> Hmisc'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> Hmisc'
> On Feb 5, 2005, at 4:59 PM, Prof Brian Ripley wrote:
>
>> On Sat, 5 Feb 2005, Michael Kubovy wrote:
>>
>>> Frank Harrell suggested I re-post with information about the version
>>> of
>>> R
>>
>> Thanks, that starts to make sense. You appear to have g77 installed,
>> but not in the place the person who prepared the binary install of R
>> has it.
>> Where do you have it installed? ('whereis g77' or 'which g77' should
>> tell you.) Then you need to alter FLIBS in R_HOME/etc/Makeconf to
>> point to it. (You can remove -lfrtbegin from FLIBS: it is not
>> needed: your R_HOME looks to be
>> /Library/Frameworks/R.framework/Versions/2.0.1.)
>>
>> However, I believe there is a more fundamental problem: because
>> libg2c is a static library on current MacOS X, most packages using
>> Fortran cannot be compiled there. That's presumably the case with
>> Hmisc, as the automated package builder is not providing a binary
>> build. (There is supposedly a check directory on CRAN, but it is not
>> there at present.)
>>
>>>
>>> Heres's the information:
> version
_
platform powerpc-apple-darwin6.8
arch powerpc
os darwin6.8
system powerpc, darwin6.8
status
major2
minor0.1
year 2004
month11
day 15
language R
>>>
>>> Here's what happens when I try to install:
> install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL
`http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdirfc4111
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
>>>
>>> Here's what the Console had to say:
* Installing *source* package 'Hmisc' ...
** libs
g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
g77 -fno-common -g -O2 -c largrec.f -o largrec.o
gcc -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c ranksort.c -o
ranksort.o
g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
gcc -bundle -flat_na
[R] MC using hclus
Has anyone used hclus to determine p-values of a subset of features that give good class separation after clustering ? What I mean is sampling a set of features and checking for class separation by clustering and then determining if the features that give the actual class separation are not random. Cheers ../Murli __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] plot smooth density estimates for bivariate data
Hi, there. Suppose I have a bivarariate data matrix y1 and y2. I want to plot a 3-D picture of the estimated density f(y1, y2) against y1 and y2? How can I do that? Do I use persp() or density()? Thanks for your help. Yulei $$$ Yulei He 1586 Murfin Ave. Apt 37 Ann Arbor, MI 48105-3135 [EMAIL PROTECTED] 734-647-0305(H) 734-763-0421(O) 734-763-0427(O) 734-764-8263(fax) $$ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Labelling and formatting of graphics
In the output of the code below, I want to do the following:
- get hats over some of the betas
- get the polygons stippled, not coloured grey
- remove the tick marks at the ends of the axes. If I put tick =
false, the whole axis disappears.
betahat <- c(0.04*0:150)
betahatdens <- dnorm(betahat, 3, 1)
plot(betahat, betahatdens, xlim = c(-0.2, 6.2), ylim = c(-0.09, 1),
type = "l", lwd = 2, xlab = NA, ylab = NA, axes = FALSE)
axis(1, pos = 0, labels = FALSE, tick = TRUE, at = c(0, 2, 3, 4, 6))
axis(2, pos = 0, labels = FALSE, tick = TRUE, at = c(0, 0.5))
text (5.5, -0.05,
labels = expression(italic(beta)), pos = 4, cex = 1.2)
text (c(-0.3, -0.3, -0.3), c(0.25, 0.3, 0.35),
labels = expression('f(',italic(beta),')'),
pos = 4, cex = 1.2, srt = 90)
text (2, -0.05,
labels = expression(italic(beta - sigma[beta])), pos = 4, cex = 1.2)
text (3, -0.05,
labels = expression(italic(beta)), pos = 4, cex = 1.2)
text (4, -0.05,
labels = expression(italic(beta + sigma[beta])), pos = 4, cex = 1.2)
selx1 <- c(4 + (6 - 4) * 0:100/100)
selx2 <- c(4 + (6 - 4) * 100:0/100)
sely1 <- dnorm(selx1, 3, 1)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, col = "gray")
selx1 <- c(2 * 0:100/100)
selx2 <- c(2 * 100:0/100)
sely1 <- dnorm(selx1, 3, 1)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, col = "gray")
Moreover, in the output of the code below, I want to:
- get values placed by every tickmark, not just every alternate
tickmark
- give the values to fewer places of decimals.
t <- c(0.01*0:900 - 4.5)
tdens <- dt(t, 6)
plot(t, tdens, xlim = c(-4.7, 4.7), ylim = c(-0.09, 0.5),
type = "l", lwd = 2, xlab = NA, ylab = NA, axes = FALSE)
axis(1, pos = 0, labels = FALSE, tick = TRUE, at = c(-4.5, 3.21, 4.5))
tcrit025 <- qt(0.975, 6)
tcrit005 <- qt(0.995, 6)
axis(1, pos = 0, labels = TRUE, tick = TRUE,
at = c(-tcrit005, -tcrit025, -1, 0, 1, tcrit025, tcrit005))
axis(2, pos = 0, labels = FALSE, tick = TRUE, at = c(0, 0.4))
text (4.2, -0.05,
labels = expression(italic(T)), pos = 4, cex = 1.2)
text (c(-0.4, -0.4, -0.4), c(0.2, 0.25, 0.3),
labels = expression('f(',italic(T),')'),
pos = 4, cex = 1.2, srt = 90)
text (c(2.91, 3.11), c(-0.06, -0.06),
labels = expression(italic(t), '= 3.21'), pos = 4, cex = 1.2)
points (c(3.21, 3.21), c(0, -0.05), type = "l")
selx1 <- c(1 + (4.5 - 1) * 0:100/100)
selx2 <- c(1 + (4.5 - 1) * 100:0/100)
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, col = "gray")
selx1 <- -selx1
selx2 <- -selx2
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, col = "gray")
selx1 <- c(tcrit025 + (4.5 - tcrit025) * 0:100/100)
selx2 <- c(tcrit025 + (4.5 - tcrit025) * 100:0/100)
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, density = 20)
selx1 <- -selx1
selx2 <- -selx2
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, density = 20)
selx1 <- c(tcrit005 + (4.5 - tcrit005) * 0:100/100)
selx2 <- c(tcrit005 + (4.5 - tcrit005) * 100:0/100)
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, density = 20, angle = 135)
selx1 <- -selx1
selx2 <- -selx2
sely1 <- dt(selx1, 6)
sely2 <- seq(length = 101, from = 0, by = 0)
selx <- c(selx1, selx2)
sely <- c(sely1, sely2)
polygon(selx, sely, density = 20, angle = 135)
text (1.4, 0.32,
labels = "Hatched area = 0.025", pos = 4, cex = 1.2)
points (c(1.5, 3), c(0.3, 0.005), type = "l")
text (c(2.3, 2.3), c(0.25, 0.22),
labels = c("Cross-hatched", "area = 0.005"), pos = 4, cex = 1.2)
points (c(3, 4), c(0.2, 0.005), type = "l")
Can anyone advise?
Best wishes,
Nick Galwey
[[alternative HTML version deleted]]
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem installing Hmisc (more info)
On Sat, 5 Feb 2005, Michael Kubovy wrote:
Frank Harrell suggested I re-post with information about the version of
R
Thanks, that starts to make sense. You appear to have g77 installed, but
not in the place the person who prepared the binary install of R has it.
Where do you have it installed? ('whereis g77' or 'which g77' should tell
you.) Then you need to alter FLIBS in R_HOME/etc/Makeconf to point to
it. (You can remove -lfrtbegin from FLIBS: it is not needed: your R_HOME
looks to be /Library/Frameworks/R.framework/Versions/2.0.1.)
However, I believe there is a more fundamental problem: because libg2c is
a static library on current MacOS X, most packages using Fortran cannot be
compiled there. That's presumably the case with Hmisc, as the automated
package builder is not providing a binary build. (There is supposedly a
check directory on CRAN, but it is not there at present.)
Heres's the information:
version
_
platform powerpc-apple-darwin6.8
arch powerpc
os darwin6.8
system powerpc, darwin6.8
status
major2
minor0.1
year 2004
month11
day 15
language R
Here's what happens when I try to install:
install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdirfc4111
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
Here's what the Console had to say:
* Installing *source* package 'Hmisc' ...
** libs
g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
g77 -fno-common -g -O2 -c largrec.f -o largrec.o
gcc -no-cpp-precomp
-I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
rcorr.o wclosest.o -L/usr/local/lib
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
-lg2c -lSystem -lcc_dynamic -framework R
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
ld: warning -L: directory name
(/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
exist
ld: can't locate file for: -lfrtbegin
make: *** [Hmisc.so] Error 1
ERROR: compilation failed for package 'Hmisc'
** Removing
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
Hmisc'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
Hmisc'
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative text/enriched version deleted]]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Brian D. Ripley, [EMAIL PROTECTED]
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
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problem installing Hmisc (more info)
Frank Harrell suggested I re-post with information about the version of
R
Heres's the information:
> > version
> _
> platform powerpc-apple-darwin6.8
> arch powerpc
> os darwin6.8
> system powerpc, darwin6.8
> status
> major2
> minor0.1
> year 2004
> month11
> day 15
> language R
Here's what happens when I try to install:
> > install.packages("Hmisc")
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
> Content type `text/plain; charset=iso-8859-1' length 47565 bytes
> opened URL
> ==
> downloaded 46Kb
>
> trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
> Content type `application/x-tar' length 453567 bytes
> opened URL
> ==
> downloaded 442Kb
>
> Delete downloaded files (y/N)?
>
> The packages are in /tmp/Rtmp1911/Rinstdirfc4111
> Warning message:
> Installation of package Hmisc had non-zero exit status in:
> install.packages("Hmisc")
Here's what the Console had to say:
> * Installing *source* package 'Hmisc' ...
> ** libs
> g77 -fno-common -g -O2 -c cidxcn.f -o cidxcn.o
> g77 -fno-common -g -O2 -c cidxcp.f -o cidxcp.o
> g77 -fno-common -g -O2 -c hoeffd.f -o hoeffd.o
> g77 -fno-common -g -O2 -c jacklins.f -o jacklins.o
> g77 -fno-common -g -O2 -c largrec.f -o largrec.o
> gcc -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c ranksort.c -o ranksort.o
> g77 -fno-common -g -O2 -c rcorr.f -o rcorr.o
> g77 -fno-common -g -O2 -c wclosest.f -o wclosest.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> Hmisc.so cidxcn.o cidxcp.o hoeffd.o jacklins.o largrec.o ranksort.o
> rcorr.o wclosest.o -L/usr/local/lib
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../.. -lfrtbegin
> -lg2c -lSystem -lcc_dynamic -framework R
> ld: warning -L: directory name
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2) does not exist
> ld: warning -L: directory name
> (/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2/../../..) does not
> exist
> ld: can't locate file for: -lfrtbegin
> make: *** [Hmisc.so] Error 1
> ERROR: compilation failed for package 'Hmisc'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> Hmisc'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/
> Hmisc'
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative text/enriched version deleted]]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] loess problems
The problem is that 90% of your data sit on the boundary. Loess is a nearest neighbor smoother (using (100 x span) % of the data to estimate at each point). If you call loess() directly with span=2/3 (the default in scatter.smooth), or something smaller than about 0.91, you'll see that it has trouble. Strangely, if you set span=.8, scatter.smooth() will also complain, but not at the default span... (Re-generating the data yet again does trigger the warnings, so seems like it does catches things some of the time.) For your second example, I think loess becomes undefined when the span is set too small (and 1/n is surely too small): You are asking the algorithm to take the nearest 1/n of the data to do the smooth. You would think that should just mean _the_ nearest data point, but the problem is: > n <- 100 > 1 / n < 1 [1] TRUE so you're asking the algoithm to take fewer than 1 data point to estimate at each point. The warnings you see for that example is pointing you in the right direction. Andy > From: Jean Eid > > I have a problem either understanding what loess is doing or > that loess > has a problem itself. > > As the x-axis variables become more concentrated on a > particular point,the > estimated loess tends to zero. the examples below show what i am > talking about, why is that? my intution tells me > that it should tend to the mean of the variable which is been > smoothed. > > Here's a worked up example > > x <- c(seq(0,100), rep(100,1000)) > y <- rnorm(length(x), mean=10, sd=2) > scatter.smooth(x,y) > > > > Although it does give warnings, I don't understand why it is > giving the > estimate as zero. > > > another example would be > > x <- seq(0,100) > y <- rnorm(length(x), mean=50, sd=2) > scatter.smooth(x,y, span=1/length(x)) > > > shoudn't this give just the points at which the smoothing algorithm is > applied? > > > > thank you > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[Fwd: Re: [R] Problems compiling (configure) R on Ubuntu linux (debian)]
Original Message Subject: Re: [R] Problems compiling (configure) R on Ubuntu linux (debian) Date: Sat, 5 Feb 2005 12:47:42 -0600 From: Dirk Eddelbuettel <[EMAIL PROTECTED]> To: Ulises M. Alvarez <[EMAIL PROTECTED]> References: <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> Ulises, Thanks -- but I am not the Ubuntu user who asked. Could you resend this to him, and the list? On 5 February 2005 at 12:37, Ulises M. Alvarez wrote: | Hello! | | I agree that the easiest way to get R in Ubuntu is with apt-get or with | the GUI-based synaptic. Just make yourself sure that both the 'universe' | and 'multiverse' repositories are available in your | /etc/apt/sources.list, something like: | | ### /etc/apt/sources.list (partial view) | deb http://archive.ubuntu.com/ubuntu warty universe multiverse | deb-src http://archive.ubuntu.com/ubuntu warty universe multiverse | ### | | Then, all you have to type is: | | sudo aptitude update | sudo aptitude install r-base r-base-core r-base-latex r-cran-hmisc Or apt-get, or wajig, or ... | On the other hand, if you insist on compile R for your Ubuntu box, I'll | recommend you to install (all in a long line): | | sudo aptitude install build-essential g77 libmagick++6-dev libpng3-dev | libtiff-tools libtk-img libtiff4-dev tcl8.4 tcl8.4-dev tk8.4 tk8.4-dev | a2ps libedit-dev libreadline4-dev tclreadline tetex-base tetex-bin | tetex-extra 'apt-get build-dep r-base' is much easier, and possibly more complete :-) That was a helpful post, though. Please send it to the list. Cheers, Dirk | | And that's all I can remember now. Beware that this may take time, | depending on your Internet connection. | | Let me know if you need more help. | | | Dirk Eddelbuettel wrote: | > On 5 February 2005 at 14:25, Peter Dalgaard wrote: | > | =?windows-1250?Q?Ale=9A_=8Eiberna?= <[EMAIL PROTECTED]> writes: | > | > I am new to Linux and I tried to compile R on my Ubuntu Warty linux. I | > | > There is really no need to do this, especially when you're new to Linux. The | > command | > | >$ apt-get install r-base | > | > (or is graphical equivalent via aptitude et al) is your friend. You may have | > to add Debian archives to the list of archives search when you do 'apt-get | > update'. I'm sure the Ubunto docs explain how to do that. | > | > Dirk, whose free Ubunto cdrom is still unused for lack of time | > | | -- | U.M.A. | http://sophie.fata.unam.mx/ -- Better to have an approximate answer to the right question than a precise answer to the wrong question. -- John Tukey as quoted by John Chambers -- U.M.A. http://sophie.fata.unam.mx/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] loess problems
I have a problem either understanding what loess is doing or that loess has a problem itself. As the x-axis variables become more concentrated on a particular point,the estimated loess tends to zero. the examples below show what i am talking about, why is that? my intution tells me that it should tend to the mean of the variable which is been smoothed. Here's a worked up example x <- c(seq(0,100), rep(100,1000)) y <- rnorm(length(x), mean=10, sd=2) scatter.smooth(x,y) Although it does give warnings, I don't understand why it is giving the estimate as zero. another example would be x <- seq(0,100) y <- rnorm(length(x), mean=50, sd=2) scatter.smooth(x,y, span=1/length(x)) shoudn't this give just the points at which the smoothing algorithm is applied? thank you __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compressed communication with DB using RMySQL?
Uri wrote: > Dear All, > I have a setup where R pulls entries from a MySQL db server. I wanted > to know whether the R interface can pull encrypted / compressed data > from MySQLD. MySQL supports compressed communication on the server > side, but I couldn't find any references to such options on the client > (RMySQL) side. Right, this is not properly documented (buried in ?mysqlNewConnection). You can simply add the argumet client.flag = 32 to dbConnect(), e.g., con <- dbConnect(MySQL(), ..., client.flag=32) The number 32 comes from the mysql_com.h version 4.1.17 header file #define CLIENT_COMPRESS 32 /* Can use compression protocol */ I'd be curious to know whether you find compressed connections significantly faster over raw connections. Hope this helps, -- David > > Best, > Uri Hasson. > --- > Uri Hasson. > Brain Research Imaging Center > The University of Chicago. > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem installing Hmisc
On Sat, 5 Feb 2005, Michael Kubovy wrote:
What am I doing wrong?
You can look at the console log (eg start Console.app in
/Applications/Utilities) to see what the problem is, but the fact that
Hmisc is not available as a binary package probably means that it does not
compile for the Mac (at least without some modification)
-thomas
> install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdir77a4044d
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
[[alternative text/enriched version deleted]]
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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Re: [R] How to access results of survival analysis
Heinz Tuechler wrote: At 15:19 05.02.2005 +0100, Uwe Ligges wrote: Heinz Tuechler wrote: Hello, it seems that the main results of survival analysis with package survival are shown only as side effects of the print method. If I compute e.g. a Kaplan-Meier estimate by km.survdur<-survfit(s.survdur) then I can simply print the results by km.survdur Call: survfit(formula = s.survdur) n events median 0.95LCL 0.95UCL 100.058.046.841.079.3 Is there a simple method to access these results, e.g. if I want to print only the median with the confidence limits? ... No, the print methods do not return those values. But you can copy code for calculation of the required values from those print methods into your own functions... Uwe Ligges Thank you for your answer. I assume, you suggest to use capture.output(print(...)). No, I suggested to copy the code from survival:::print.survfit and Co. that calculates the values you are looking for... Uwe > Without your response I would have believed that I had missed an important possibility of R. Regarding the Cox-Model Ales Ziberna gave me a useful hint to use summary() which returns a list. Thanks to both of you, Heinz Tüchler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Compressed communication with DB using RMySQL?
Dear All, I have a setup where R pulls entries from a MySQL db server. I wanted to know whether the R interface can pull encrypted / compressed data from MySQLD. MySQL supports compressed communication on the server side, but I couldn't find any references to such options on the client (RMySQL) side. Best, Uri Hasson. --- Uri Hasson. Brain Research Imaging Center The University of Chicago. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to access results of survival analysis
At 15:19 05.02.2005 +0100, Uwe Ligges wrote: >Heinz Tuechler wrote: >> Hello, >> >> it seems that the main results of survival analysis with package survival >> are shown only as side effects of the print method. >> >> If I compute e.g. a Kaplan-Meier estimate by >> >>>km.survdur<-survfit(s.survdur) >> >> then I can simply print the results by >> >>>km.survdur >> >> Call: survfit(formula = s.survdur) >> >> n events median 0.95LCL 0.95UCL >> 100.058.046.841.079.3 >> >> Is there a simple method to access these results, e.g. if I want to print >> only the median with the confidence limits? ... > >No, the print methods do not return those values. >But you can copy code for calculation of the required values from those >print methods into your own functions... > >Uwe Ligges > > Thank you for your answer. I assume, you suggest to use capture.output(print(...)). Without your response I would have believed that I had missed an important possibility of R. Regarding the Cox-Model Ales Ziberna gave me a useful hint to use summary() which returns a list. Thanks to both of you, Heinz Tüchler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to make an empty screen
Hi I want to plot control charts for several events grouped by employees. As every employees doesn't encounter every event, a variable number of control charts is produced in turn. Now what I need is a way to get a new empty screen when the printout for one employee has finished as the title lines is somhow mixed between the changing of employees The screen setup: par(mfrow=c(4,4)) And I make the title like this: title(main=event, outer=T) Regards soren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to access results of survival analysis
Hello Ales, thank you for your hint regarding names(summary(fit)). Summary(fit) is a list containig all important results of the Cox-model. So it helps a lot! Regarding the results of a Kaplan-Meier estimate summary does not help, because it does not contain the main results. Thanks again, Heinz Tüchler ps. If I understood it right, you answered only to me and not to the list. So I assumed that you prefer not to put your answer on the list and therefore I answer to you off-list. At 09:24 05.02.2005 +0100, Ales Ziberna wrote: >Hi! > >I don't now how to reach the median directly. However I can help you whit >cox-PH coefficients. > >if fit is the resoult of the coxph, then > >fit$coefficients should give you the coefficients. To see whatother things >you can acces in similar way, see >names(fit) >or >names(summary(fit)). > >I hope this helps at least a little! > >Ales Ziberna > > >- Original Message - >From: "Heinz Tuechler" <[EMAIL PROTECTED]> >To: >Sent: Friday, February 04, 2005 11:17 PM >Subject: [R] How to access results of survival analysis > > >Hello, > >it seems that the main results of survival analysis with package survival >are shown only as side effects of the print method. > >If I compute e.g. a Kaplan-Meier estimate by >> km.survdur<-survfit(s.survdur) >then I can simply print the results by >> km.survdur >Call: survfit(formula = s.survdur) > > n events median 0.95LCL 0.95UCL > 100.058.046.841.079.3 > >Is there a simple method to access these results, e.g. if I want to print >only the median with the confidence limits? >Regarding the results of a Cox-PH-model I face the same situation. The >printed results are: >> cx.survdur.ipss_mds.sex >Call: >coxph(formula = s.survdur ~ x1 + x2, method = "efron") > > coef exp(coef) se(coef) z p >x1 0.6424 1.900.206 3.123 0.0018 >x2.L 0.0616 1.060.263 0.234 0.8100 > >Likelihood ratio test=9.56 on 2 df, p=0.0084 n=58 (42 observations >deleted due to missing) > >Is there a simple method to copy e.g. the coefficients and p-values in a >new object? > >I am working with: >R : Copyright 2004, The R Foundation for Statistical Computing >Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 >Survival package version: survival_2.16 >Operating System: Windows 98SE > >Thanks, >Heinz Tüchler > >__ >R-help@stat.math.ethz.ch mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide! >http://www.R-project.org/posting-guide.html > > > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems compiling (configure) R on Ubuntu linux (debian)
On 5 February 2005 at 14:25, Peter Dalgaard wrote: | =?windows-1250?Q?Ale=9A_=8Eiberna?= <[EMAIL PROTECTED]> writes: | > I am new to Linux and I tried to compile R on my Ubuntu Warty linux. I There is really no need to do this, especially when you're new to Linux. The command $ apt-get install r-base (or is graphical equivalent via aptitude et al) is your friend. You may have to add Debian archives to the list of archives search when you do 'apt-get update'. I'm sure the Ubunto docs explain how to do that. Dirk, whose free Ubunto cdrom is still unused for lack of time -- Better to have an approximate answer to the right question than a precise answer to the wrong question. -- John Tukey as quoted by John Chambers __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Rép : [R] 2 small problems: integer division and the nature of NA
Thanks to the many R users who convinced me that the sum of NAs should be zero and gave me a solution if I did not want it to be zero. Thank you also for the explanations of rounding errors with floating point arithmetics. I did not expect it. This small error was a real problem for me as I was trying to find a way to recode numeric values into intervals. Because I wanted to retain numeric values as a result, I tried not to use cut or cut2. Hence to convert a range of temperatures into 0.2 degree intervals I had written: (lets first make a fake temperature variable k for testing) k <- seq(-5,5,0.1) k1 <- ifelse(k<0,-0.2*(abs(k) %/% 0.2) - 0.1, 0.2 *(k %/% 0.2) + 0.1) Note that this works well to quickly recode a numeric variable that only takes integer values. But it produces the problem that prompted my call for help when there are decimals: some values end up in a different class than what you'd expect. Considering your answers, I found 3 solutions: k2 <- ifelse(k<0,-0.2*(abs(round(10*k)) %/% 2) - 0.1, 0.2 *(round(10*k) %/% 2) + 0.1) k3 <- (-0.1+min(k)) + 0.2 * as.numeric(cut(k, seq(min(k),max(k)+0.2,0.2), right=F, labels=F)) k4 <- cut2(k, seq(min(k), max(k)+0.2, 0.2), levels.mean=T) k5 <- as.numeric(levels(k7))[k7] I could "round" to 1 decimal to be even more exact but this is good enough. If it can be more elegant, please let me know! Denis Subject: [R] 2 small problems: integer division and the nature of NA Hi, I'm wondering why 48 %/% 2 gives 24 but 4.8 %/% 0.2 gives 23... I'm not trying to round up here, but to find out how many times something fits into something else, and the answer should have been the same for both examples, no? On a different topic, I like the behavior of NAs better in R than in SAS (at least they are not considered the smallest value for a variable), but at the same time I am surprised that the sum of NAs is 0 instead of NA. The sum of a vector having at least one NA but also valid data gives NA if we do not specify na.rm=T. But with na.rm=T, we are telling sum to give the sum of valid data, ignoring NAs that do not tell us anything about the value of a variable. I found out while getting the sum of small subsets of my data (such as when subsetting by several variables), sometimes a "cell" only contained NAs for my response variable. I would have expected the sum to be NA in such cases, as I do not have a single data point telling me the value of my response here. But R tells me the sum was zero in that cell! Was this behavior considered "desirable" when sum was built? If not, any hope it will be fixed? Sincerely, Denis Chabot __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem installing Hmisc
Michael Kubovy wrote:
What am I doing wrong?
> install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
No further messages here? E.g. something like
* Installing *source* package 'Hmisc' ...
** libs
?
Have you installed other packages with/without success before?
What happens when trying to install from the command line using
R CMD INSTALL
?
Uwe Ligges
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdir77a4044d
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels: Room 102 Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011 +1-434-982-4729
Lab: B019 +1-434-982-4751
Fax: +1-434-982-4766
WWW: http://www.people.virginia.edu/~mk9y/
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Re: [R] How to access results of survival analysis
Heinz Tuechler wrote: Hello, it seems that the main results of survival analysis with package survival are shown only as side effects of the print method. If I compute e.g. a Kaplan-Meier estimate by km.survdur<-survfit(s.survdur) then I can simply print the results by km.survdur Call: survfit(formula = s.survdur) n events median 0.95LCL 0.95UCL 100.058.046.841.079.3 Is there a simple method to access these results, e.g. if I want to print only the median with the confidence limits? Regarding the results of a Cox-PH-model I face the same situation. The printed results are: cx.survdur.ipss_mds.sex Call: coxph(formula = s.survdur ~ x1 + x2, method = "efron") coef exp(coef) se(coef) z p x1 0.6424 1.900.206 3.123 0.0018 x2.L 0.0616 1.060.263 0.234 0.8100 Likelihood ratio test=9.56 on 2 df, p=0.0084 n=58 (42 observations deleted due to missing) Is there a simple method to copy e.g. the coefficients and p-values in a new object? I am working with: R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 Survival package version: survival_2.16 Operating System: Windows 98SE Thanks, Heinz Tüchler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html No, the print methods do not return those values. But you can copy code for calculation of the required values from those print methods into your own functions... Uwe Ligges __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems compiling (configure) R on Ubuntu linux (debian)
=?windows-1250?Q?Ale=9A_=8Eiberna?= <[EMAIL PROTECTED]> writes: > Hello! > > I would first like to appologice if this question does not fit on this > mailing-list. > > I am new to Linux and I tried to compile R on my Ubuntu Warty linux. I > followed the instructions in "R Installation and Administration" manual. It > seams that there was a problem with "configure", since when running "make" > afterward gave me this reply: > make: *** No targets specified and no makefile found. Stop. Presumably configure told you something before that? > I have copied the content of the "config.log" at the end of the file. If > someone would give me some instructions on how to read this file, I would be > very grateful. > > Thank you in advance! > Ales Ziberna So you thought that sending 2800 lines to 2000+ people probably wouldn't bother anyone? You seem to be lacking a Fortran compiler as configure is picking up "fc" (which is bash's "fix command"), but we could have found that out based on more concentrated output than the entire config.log. -- 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-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Rare Cases and SOM
Manuel Gutierrez yahoo.es> writes: : : I am trying to understand how the SOM algorithm works : using library(class) SOM function. : I have a 1000*10 matrix and I want to be able to : summarize the different types of 10-element vectors. : In my real world case it is likely that most of the : 1000 values are of one kind the rest of other (this is : an oversimplification). : Say for example: : : InputA<-matrix(cos(1:10),nrow=900,ncol=10,byrow=TRUE) : InputB<-matrix(sin(5:14),nrow=100,ncol=10,byrow=TRUE) : Input<-rbind(InputA,InputB) : : I though that a small grid of 3*3 would be enough to : extract the patterns in such simple matrix : : GridWidth<-3 : GridLength<-3 : gr <- somgrid(xdim=GridWidth,ydim=GridLength,topo = : "hexagonal") : test.som <- SOM(Input, gr) : par(mfrow=c(GridLength,GridWidth)) : for(i in 1:(GridWidth*GridLength)) : plot(test.som$codes[i,],type="l") : : Only when I use a larger grid (say for example 7*3 ) I : get some of the representatives for the sin pattern. : This must have something to do with the initialization : of the grid, as the sin is so rare it is unlikely that : I get it as a reference vector. Afterwards, because : the selection for the training is also random it is : also unlikely they are picked. : I've been trying to modify some of the other : parameters for the SOM also, but I would appreciatte : some input to keep me going until I receive the : reference books from my bookstore. : : Are my suspictions right? : Should I be using the SOM for my study or should I : look somewhere else? : NOTE: I have no prior knowledge of whether the : datasets I want to analyse will have rare cases or not : or where they will be located. I don't have a direct answer to your question as I have not used that package but I have used randomForest and it does have stratified sampling facitilities so that you can be sure that a rare case is represented. Check out the sampsize= argument. Also there is an article in RNews on randomForest and search this list where you can find some relevant comments by the author of randomForest. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problem installing Hmisc
What am I doing wrong?
> install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length 453567 bytes
opened URL
==
downloaded 442Kb
Delete downloaded files (y/N)?
The packages are in /tmp/Rtmp1911/Rinstdir77a4044d
Warning message:
Installation of package Hmisc had non-zero exit status in:
install.packages("Hmisc")
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400 Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick Road Charlottesville, VA 22903
Office: B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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Re: [R] Installing R packages in windows
Liaw, Andy wrote:
A half-way decent ftp client would allow you to get all files in a
directory, so that ought to be quite easy.
... or wget ... or in R:
download.packages(CRAN.packages()[,1], destdir = ..)
Uwe Ligges
Andy
From: Vikas Rawal
Thank you. That is useful. But is it possible to download all
the packages in one go, or would one have download each one by one?
Vikas
-Original Message-
From: Uwe Ligges <[EMAIL PROTECTED]>
To: Vikas Rawal <[EMAIL PROTECTED]>
Date: Fri, 04 Feb 2005 13:55:42 +0100
Subject: Re: [R] Installing R packages in windows
Vikas Rawal wrote:
I need to install a selected set of packages on a number of
machines (in a computer lab). Some of these machines are not
connected to internet. Is it possible to download all the
packages and make a kind of repository on a CD, and then
install.packages from the CD?
Yes, just download the packages and install.packages with
CRAN=NULL ...
Instead, you might want to mount the installed packages from
a network
volume instead, adding a second library path for R. So you
only need to
install stuff once.
Uwe Ligges
Vikas
==
This Mail was Scanned for Virus and found Virus free
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Re: [R] Std Err on Concentration measures
David Giles has a paper on calculating standard errors for the Gini: http://web.uvic.ca/econ/ewp0202.pdf Tim Original message >Date: Sat, 5 Feb 2005 11:43:02 +0100 >From: Angelo Secchi <[EMAIL PROTECTED]> >Subject: [R] Std Err on Concentration measures >To: r-help@stat.math.ethz.ch > > >Hi, >I'm using the ineq package to calculate some concentration measures (Gini, Herfindal, ...) and I was wondering if there's around also a function to calculate standard error on these measures. If not, is anybody aware of where I can find a reference on this point? >Thanks. > >-- > > Angelo Secchi PGP Key ID:EA280337 > >__ >R-help@stat.math.ethz.ch mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Std Err on Concentration measures
Hi, I'm using the ineq package to calculate some concentration measures (Gini, Herfindal, ...) and I was wondering if there's around also a function to calculate standard error on these measures. If not, is anybody aware of where I can find a reference on this point? Thanks. -- Angelo Secchi PGP Key ID:EA280337 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] arrow head styles?
> "IvoW" == <[EMAIL PROTECTED]> > on Fri, 04 Feb 2005 12:33:52 -0800 writes: IvoW> dear R wizards: is it possible to specify different IvoW> arrow head styles? E.g., a solid arrow head? Or a IvoW> bent arrow head? Or a longer or shorter arrow head? IvoW> (perhaps through an add in?) I guess I could write IvoW> this myself, but since arrows is built-in, I was IvoW> hoping it had some flexibility hidden in it that I did IvoW> not see in "?arrows". The are several "extensions" to the arrows() function around. package 'sfsmisc' has p.arrows() package 'IDPmisc' has Arrows() Did you try to search for "arrows" on Jonathan Baron's search site http://search.R-project.org/ ? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Internationalization and localization of R
This pre-announcement is being sent for information to both R-help and BioC. Please use [EMAIL PROTECTED] for any follow-up discussion. --- We are about at the end of a several-week process of adding support for non-Latin character sets and non-Western-European languages to R. - For Linux users, R works in the UTF-8 locales that are rapidly becoming the standard in the latest distributions: for example if in Fedora Core 3 I select English (United Kingdom) I get locale en_GB.utf8. This is also true of those commercial Unixes which support such locales. - For Linux/Unix users, R works in many non-English locales with other encodings such as EUC-JP. The only one that we are having problems with is vi_VN.tcvn (but the Vietnamese UTF-8 locale appears to work). - For Windows users, R works in the double-byte `East Asian' locales as well as many others, if support is selected at installation time. (See the current rw-FAQ for more discussion of this: this is supported in the current automated builds of r-devel on CRAN.) - There are built-in facilities to convert between encodings, so that e.g. Japanese in SHIFT-JIS can be read by R running under UTF-8 or EUC-JP. - There are mechanisms to translate both C and R error messages from both base R and for packages, and also the menus etc of the Windows and MacOS X GUIs. The purpose of this pre-announcement is to alert developers that these changes will be coming in 2.1.0 in a couple of months. - Package writers who would like to translate messages in their packages, or to prepare their packages for translation by others should consult http://developer.r-project.org/210update.txt and the latest version of `Writing R Extensions' in the R-devel sources. All the standard packages and a few of the recommended ones have been prepared and updates will be appearing on CRAN shortly. - People might like to start organizing translation teams for their own languages, and early experience from such a team would be helpful in polishing the instructions and mechanisms. There is a document for translators at http://developer.r-project.org/Translations.html If translations are available by early April they can be shipped with 2.1.0 (although there are planned to be mechanisms to add them to an R installation). - We will be looking for testers in the alpha/beta period in about a month's time, and would-be users of R in unusual languages (e.g. Vietnamese) would be especially helpful as testers. This is particularly important for Windows 95/98/ME to which we only have very limited access, to English versions. --- -- Brian D. Ripley, [EMAIL PROTECTED] 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] genetic algorithm
After a little search, I found on CRAN: - gafit: genetic algorithm for curve fitting, - rgenout: R version of genetic optimization using derivatives - subselect: Selecting variable subsets, with function genetic(): genetic algorithm searching for an optimal k-variable subset I don't know if it fits your needs. Best, Philippe ..<°}))>< ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. WeiWei Shi wrote: Hi, I am doing some research on feature selection for classfication problem using genetic algorithm in a wrapper approach. I am wondering if there is some package which is already built for this purpose. I was advised before about dprep package but I don't think it used GA there (if I am wrong, please correct me!) Thanks, Ed __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
