Re: [R] Matrix variable in C code
Selon Gabor Csardi [EMAIL PROTECTED]:
On Thu, Feb 02, 2006 at 06:27:47PM +0100, [EMAIL PROTECTED] wrote:
[...]
The problem is that as.double drops the dim attribute:
b - matrix( 1:4, 2, 2)
b
[,1] [,2]
[1,]13
[2,]24
as.double(b)
[1] 1 2 3 4
You can try:
b - matrix( 1:4, 2, 2)
d - dim(b)
b - as.double(b)
b
[1] 1 2 3 4
dim(b) - d
b
[,1] [,2]
[1,]13
[2,]24
Another thing is that i cannot really see why the ZT parameter of the .Call
should be a matrix anyway. It's just the vector (40 21 30 20). Or am i
missing something?
Sorry, i made a mistake writing the small code, the correct one is the following
with the correct dim for ZT. But it doesn't work...
X-c(4,2,3,2)
Z-c(40,21,30,20)
dX-c(2,1,1)
dyn.load(test.so)
Phi-function(z,a,b)
{
Phi-z
}
VPEfron-function(XType,ZType,dXType,G,c0,c1)
{
ZT-matrix(0,3,2)
ZT[1,1]-Z[2]
ZT[1,2]-Z[4]
ZT[2,1]-Z[3]
ZT[3,1]-Z[1]
# A OPTIMISER
VPCEfron-function(f,XT,ZT,dXT,tailleS=length(XT))
{
f.check-function(x) {
x-f(x)
}
.Call(VPCEfron,body(f.check),as.double(XT),as.double(ZT),as.integer(dXT),as.integer(tailleS),new.env())
}
GG-function(z) G(z,c0,c1)
Vraisemblancepartielle-VPCEfron(GG,XType,ZType,dXType)
}
resultat-VPEfron(X,Z,dX,Phi,0,0)
==
The new piece of code is between ###.
Thanks,
Alex
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Re: [R] (newbie) Saving the workspace in .txt format
Hi you can also try to look at ?savehistory which enables you to save your latest commands to a file. Or use menu item save history. You can edit this saved file and you can use part of it or whole by loadhistory or just by copy/paste to R console. HTH Petr On 3 Feb 2006 at 7:41, Prof Brian Ripley wrote: Date sent: Fri, 3 Feb 2006 07:41:36 + (GMT) From: Prof Brian Ripley [EMAIL PROTECTED] To: Thomas L Jones [EMAIL PROTECTED] Copies to: R-project help r-help@stat.math.ethz.ch Subject:Re: [R] (newbie) Saving the workspace in .txt format On Thu, 2 Feb 2006, Thomas L Jones wrote: (newbie question) How do I save the workspace in Windows text format (with the file extension .txt)? Also, having saved it and edited it, how do I load it back into the workspace? `save' is a command in R, and it has a ascii argument. So you could do save.image(workspace.txt, ascii=TRUE) to save, and load(workspace.txt) to reload. The underlying assumption seems to be that text format files are editable (by a human). Lots of data formats are text files but have many rigid restrictions: PDF is one example and R save formats are others. -- 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 Petr Pikal [EMAIL PROTECTED] __ 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] RHOME
Martyn == Martyn Plummer [EMAIL PROTECTED] on Thu, 02 Feb 2006 22:34:23 +0100 writes: Martyn Quoting Daniel A. Powers Martyn [EMAIL PROTECTED]: R-help -- I built R-2.2.1 in my own directory on a sun (solaris). Now I would like the sysadmin to move the contents to /usr/local/lib and place the binary in /usr/local/bin. No problem. However, the RHOME variable defaults to the directory from which R was built so it is not usable by anyone but me or ROOT. I would like to avoid building this again if possible. Any ideas? Thanks, Dan Martyn R is designed to run from its build directory. But Martyn if your sysadmin installs it with make install (as Martyn root), then the shell wrapper that is installed in Martyn /usr/local/bin/R will have R_HOME pointing to the Martyn right location (/usr/local/lib/R). Literally moving Martyn the build directory to another location is the wrong Martyn thing to do. well, but very easily fixable, and that's what Daniel is asking for: The default value of R_HOME is only set in exactly one place, namely the 'R' shell script; editing that script - once after the move - is really a piece o'cake. __ 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] Matrix variable in C code
I correct a little my code, in R code, i use as.matrix for ZT, so i haven't
got segment fault but it seems that i transmit only the first colon and
because ncol gives 1 and not 2.
So what happen ?
Programs
R CODE - test.R =
X-c(4,2,3,2)
Z-c(40,21,30,20)
dX-c(2,1,1)
dyn.load(test.so)
Phi-function(z,a,b)
{
Phi-z
}
VPEfron-function(XType,ZType,dXType,G,c0,c1)
{
ZT-matrix(0,3,2)
ZT[1,1]-Z[2]
ZT[1,2]-Z[4]
ZT[2,1]-Z[3]
ZT[3,1]-Z[1]
print(ZT)
# A OPTIMISER
VPCEfron-function(f,XT,ZT,dXT,tailleS)
{
f.check-function(x) {
x-f(x)
}
.Call(VPCEfron,body(f.check),as.double(XT),as.matrix(ZT),as.integer(dXT),as.integer(tailleS),new.env())
}
GG-function(z) G(z,c0,c1)
VPEfron-VPCEfron(GG,XType,ZType,dXType,length(XType))
}
resultat-VPEfron(X,Z,dX,Phi,0,0)
END R CODE ==
C CODE of test.c
#include R.h
#include Rdefines.h
#include Rinternals.h
#define RMATRIX(m,i,j) (REAL(m)[ INTEGER(GET_DIM(m))[0]*(j)+(i) ])
SEXP mkans(double x)
{
SEXP ans;
PROTECT(ans = allocVector(REALSXP,1));
REAL(ans)[0]=x;
UNPROTECT(1);
return ans;
}
SEXP VPCEfron(SEXP f, SEXP XR, SEXP ZR, SEXP DIR, SEXP tailleR, SEXP rho)
{
double* X=REAL(XR);
int* DI=INTEGER(DIR);
int taille=INTEGER(tailleR)[0];
int nligne=INTEGER(GET_DIM(ZR))[0];
int ncol=INTEGER(GET_DIM(ZR))[1];
printf(verifie taille: %d\n,taille);
printf(verifie de X: %f - %f - %f - %f\n,X[0],X[1],X[2],X[3]);
printf(verifie dX: %d %d %d\n,DI[0],DI[1],DI[2]);
printf(verifie de Z\n);
printf(%d %d\n,nligne,ncol);
printf(%f %f\n,RMATRIX(ZR,0,0),RMATRIX(ZR,0,1));
printf(%f %f\n,RMATRIX(ZR,1,0),RMATRIX(ZR,1,1));
printf(%f %f\n,RMATRIX(ZR,2,0),RMATRIX(ZR,2,1));
return mkans(0.0);
}
END CODE =
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Re: [R] Matrix variable in C code
No idea, your code (now that you're not using as.double) kinda works for me.
source(test.R)
[,1] [,2]
[1,] 21 20
[2,] 300
[3,] 400
verifie taille: 4
verifie de X: 4.00 - 2.00 - 3.00 - 2.00
verifie dX: 2 1 1
verifie de Z
4 1
40.00 0.00
21.00 0.00
30.00 0.00
The only thing is that your code is very messy (for me at least), and it's
true that you print the value of ZT and it is a 3x3 matrix, but if you print
its value just before the .Call it is just a vector of length 4. Then
as.matrix() creates a 4x1 matrix of this.
Look at this simple R code, it works with your test.c file fine:
##
dyn.load(test.so)
f.check - function(a) a
XT - 1:4
ZT - matrix( c(21,30,40,20,0,0), nr=3, nc=2)
dXT - 1:3
tailleS - 5
.Call(VPCEfron,body(f.check),as.double(XT),as.matrix(ZT),as.integer(dXT),
as.integer(tailleS),new.env())
#
Gabor
On Fri, Feb 03, 2006 at 11:45:24AM +0100, [EMAIL PROTECTED] wrote:
I correct a little my code, in R code, i use as.matrix for ZT, so i haven't
got segment fault but it seems that i transmit only the first colon and
because ncol gives 1 and not 2.
So what happen ?
Programs
R CODE - test.R =
X-c(4,2,3,2)
Z-c(40,21,30,20)
dX-c(2,1,1)
dyn.load(test.so)
Phi-function(z,a,b)
{
Phi-z
}
VPEfron-function(XType,ZType,dXType,G,c0,c1)
{
ZT-matrix(0,3,2)
ZT[1,1]-Z[2]
ZT[1,2]-Z[4]
ZT[2,1]-Z[3]
ZT[3,1]-Z[1]
print(ZT)
# A OPTIMISER
VPCEfron-function(f,XT,ZT,dXT,tailleS)
{
f.check-function(x) {
x-f(x)
}
.Call(VPCEfron,body(f.check),as.double(XT),as.matrix(ZT),as.integer(dXT),as.integer(tailleS),new.env())
}
GG-function(z) G(z,c0,c1)
VPEfron-VPCEfron(GG,XType,ZType,dXType,length(XType))
}
resultat-VPEfron(X,Z,dX,Phi,0,0)
END R CODE ==
C CODE of test.c
#include R.h
#include Rdefines.h
#include Rinternals.h
#define RMATRIX(m,i,j) (REAL(m)[ INTEGER(GET_DIM(m))[0]*(j)+(i) ])
SEXP mkans(double x)
{
SEXP ans;
PROTECT(ans = allocVector(REALSXP,1));
REAL(ans)[0]=x;
UNPROTECT(1);
return ans;
}
SEXP VPCEfron(SEXP f, SEXP XR, SEXP ZR, SEXP DIR, SEXP tailleR, SEXP rho)
{
double* X=REAL(XR);
int* DI=INTEGER(DIR);
int taille=INTEGER(tailleR)[0];
int nligne=INTEGER(GET_DIM(ZR))[0];
int ncol=INTEGER(GET_DIM(ZR))[1];
printf(verifie taille: %d\n,taille);
printf(verifie de X: %f - %f - %f - %f\n,X[0],X[1],X[2],X[3]);
printf(verifie dX: %d %d %d\n,DI[0],DI[1],DI[2]);
printf(verifie de Z\n);
printf(%d %d\n,nligne,ncol);
printf(%f %f\n,RMATRIX(ZR,0,0),RMATRIX(ZR,0,1));
printf(%f %f\n,RMATRIX(ZR,1,0),RMATRIX(ZR,1,1));
printf(%f %f\n,RMATRIX(ZR,2,0),RMATRIX(ZR,2,1));
return mkans(0.0);
}
END CODE =
This message was sent using IMP, the Internet Messaging Program.
--
Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK
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[R] Accessing row names
Hi, I am doing cluster analysis and get back the vector with the clusters. Now I want to access the original data according to the assigned clusters. Therefore, I need the row names of the $cluster vector. Right now I do the following what works but seems a little awkward: dat[rownames(as.data.frame(which(kcl$cluster==1))),] Is there maybe a better or correct way to do this? Thanks a lot! Werner - [[alternative HTML 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] Application of R
Could somebody gives me some advice what is the problem of my analysis as per attached printed file showing the steps of the input and the error occured. I have also attached my data file in Excel file format for your reference. Thanks. Andy result.pdf Description: Adobe PDF document __ 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] Application of R
Hi I do not know anything about mnp but the variables in your data frame has names V1:V23 and you request mnp to use variables x1..., y1..., and z1 Unless you have them somewhere, where do you suppose mnp to know about them? Try to read some basic text about data structures and manipulation with them e.g. R-intro.pdf which is probably in doc directory. HTH Petr On 3 Feb 2006 at 20:24, Andy Wong wrote: Date sent: Fri, 3 Feb 2006 20:24:00 +0800 From: Andy Wong [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject:[R] Application of R Could somebody gives me some advice what is the problem of my analysis as per attached printed file showing the steps of the input and the error occured. I have also attached my data file in Excel file format for your reference. Thanks. Andy Petr Pikal [EMAIL PROTECTED] __ 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] question
Hello, I am a research student and I am using R to access my research. I want to know how to multiple plot , such as for the exponetial distribution, if I give the covariate different value, how to plot these in the same figure, And also I want to add the density plot in the histogramm. How to do these? Thank u in advance nessie __ 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 get the namespace of a function?
Prof Brian Ripley [EMAIL PROTECTED] writes:
On Thu, 2 Feb 2006, Fernando Saldanha wrote:
I am trying to imitate encapsulation from other languages like Java
or C++. Coming from that background, it bothers me that I can commit
errors like the following:
x - 1
f - function(z) { y - x; y + 1 } # Mistake: I should have written y - z
f(10)
[1] 2
In a language like Java the interpreter would have noticed that x was
an undeclared variable and an error message would be issued. R, on the
other hand, allows the code to run, as x exists in the global
environment. I was trying to avoid such situations by setting the
environment of f to be NULL. If there is a better way to catch this
type of errors I would be interested in knowing about it.
The codetools package. See http://www.stat.uiowa.edu/~luke/R/codetools.
(They are not R errors, but the codetools package can tell you that 'x' is
not necessarily in scope.)
Yep, and nor is -, +, and {...
(Does codetools actually check those? Probably not, but it goes to
show why full encapsulation is hard or impossible to achieve in a
language where everything, including functions and operators, are
objects.)
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] How to get the namespace of a function?
On Thu, 2 Feb 2006, Duncan Murdoch wrote:
On 2/2/2006 5:56 PM, Berton Gunter wrote:
Just echoing and slightly amplifying Gabor's comment...
The semantics of R are really based on functional programming (LISP-like)
rather than OOP (JAVA-like)? R's behavior is proper from that point of
view; what is improper is Fernando's expectation that it should behave
some other way.
I don't think it's that so much as trying not to break old code. It
doesn't make sense to me that the search order within a namespace should
pass through the global environment, but something would break if it
didn't. (I suspect it's probably the old S3 object system, which
predates namespaces by a long time, but it's been a while since I've
thought about this.)
S3 dispatch was the primary reason for this design. At some point we
may be able to revisit this but probably not very soon.
Once code analysis becomes a standard part of R, either via byte code
compilation or as bart of R CMD check, there should be warnings issued
automatically for this sort of thing. For now manually using the
codetools ackage Brian pointed to is one option.
Best,
luke
Duncan Murdoch
Of course, one can simulate anything with a Turing machine,
but I consider Fernando's criticisms somewhat unfair because he is
expecting R to behave like something he is familiar with rather than as it
was designed to. For this reason, what bothers him seems wholly desirable to
me -- I want there to be well-defined scoping convention (lexical scoping)
for R to find free variables.
Cheers,
Bert
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch
Sent: Thursday, February 02, 2006 2:16 PM
To: [EMAIL PROTECTED]
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] How to get the namespace of a function?
On 2/2/2006 5:05 PM, Fernando Saldanha wrote:
I am trying to imitate encapsulation from other languages like Java
or C++. Coming from that background, it bothers me that I can commit
errors like the following:
x - 1
f - function(z) { y - x; y + 1 } # Mistake: I should have written y -
z
f(10)
[1] 2
In a language like Java the interpreter would have noticed that x was
an undeclared variable and an error message would be issued. R, on the
other hand, allows the code to run, as x exists in the global
environment. I was trying to avoid such situations by setting the
environment of f to be NULL. If there is a better way to catch this
type of errors I would be interested in knowing about it.
Put your code in a package, and use a namespace. This isn't perfect,
but it gives you more control than you have when running scripts at the
console.
There's an article by Luke Tierney in one of R News 3/1 that explains
the search order when namespaces are involved.
Duncan Murdoch
FS
On 2/2/06, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 2/2/2006 10:56 AM, Fernando Saldanha wrote:
I declared the environment of the function myfun to be NULL as follows:
environment(myfun) - NULL
Since version 2.1.0, it's been recommended that you use
environment(myfun) - baseenv()
and since 2.2.0, you'll get a warning when using NULL (and you'll get an
error in 2.3.0). But why would you want to do that? What are you
trying to achieve?
Duncan Murdoch
Later on I called that myfun and got an error message because the
function index() in the zoo package was called inside myfun and was
not visible:
Error in myfun(args) : couldn't find function index
I tried to use zoo::index() instead of index(), but that did not work.
In fact, zoo::index does not work even in the command line:
z-ts(1:5)
z
Time Series:
Start = 1
End = 5
Frequency = 1
[1] 1 2 3 4 5
index(z)
[1] 1 2 3 4 5
zoo::index(z)
Error in loadNamespace(name) : package 'zoo' does not have a name space
How can I qualify index() so that it is visible inside the body of
myfun?
Thanks for any suggestions,
FS
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone:
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Re: [R] question
x - seq(0, 10, by=.1) plot(x,pexp(x, rate=1)) points(x,pexp(x, rate=2), pch=2, col=blue) See help(plot), help(points), help(lines). Gabor On Fri, Feb 03, 2006 at 01:07:30PM -, Xiao Zhao wrote: Hello, I am a research student and I am using R to access my research. I want to know how to multiple plot , such as for the exponetial distribution, if I give the covariate different value, how to plot these in the same figure, And also I want to add the density plot in the histogramm. How to do these? Thank u in advance nessie __ 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 -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ 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] RHOME
Martin Maechler [EMAIL PROTECTED] writes: Martyn R is designed to run from its build directory. But Martyn if your sysadmin installs it with make install (as Martyn root), then the shell wrapper that is installed in Martyn /usr/local/bin/R will have R_HOME pointing to the Martyn right location (/usr/local/lib/R). Literally moving Martyn the build directory to another location is the wrong Martyn thing to do. well, but very easily fixable, and that's what Daniel is asking for: The default value of R_HOME is only set in exactly one place, namely the 'R' shell script; editing that script - once after the move - is really a piece o'cake. Hmm, I was about to say the same, but there seems to be unexpected references in other places. find `R RHOME` | xargs grep `R RHOME` /usr/lib64/R/bin/R:R_HOME_DIR=/usr/lib64/R /usr/lib64/R/bin/R:R_SHARE_DIR=/usr/lib64/R/share /usr/lib64/R/bin/R:R_INCLUDE_DIR=/usr/lib64/R/include /usr/lib64/R/bin/R:R_DOC_DIR=/usr/lib64/R/doc (this doesn't normally happen - a SUSE RPM specialty, or due to configure flag settings?) Once you start building packages, you also have things like viggo:~/find ~/Rlibrary | xargs grep `R RHOME` Binary file /home/bs/pd/Rlibrary/rgl/libs/rgl.so matches viggo:~/find ~/Rlibrary | xargs grep Rlibrary Binary file /home/bs/pd/Rlibrary/rgl/Meta/hsearch.rds matches Binary file /home/bs/pd/Rlibrary/ISwR/Meta/hsearch.rds matches Binary file /home/bs/pd/Rlibrary/mvtnorm/Meta/hsearch.rds matches Binary file /home/bs/pd/Rlibrary/nlmeODE/Meta/hsearch.rds matches B. on my laptop I had a hit on one of the Sweave support files too. Most likely these are quite harmless, but all in all I think Martyn has the safest advice: Use make install, as root (don't forget umask 022). -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- 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
[R] Problems with ks.test
Hi everybody, while performing ks.test for a standard exponential distribution on samples of dimension 2500, generated everytime as new, i had this strange behaviour: data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0147, p-value = 0.6549 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.019, p-value = 0.3305 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0171, p-value = 0.4580 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0143, p-value = 0.6841 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0145, p-value = 0.6684 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0123, p-value = 0.8435 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0186, p-value = 0.3532 alternative hypothesis: two.sided It seems kind of strange to me that max p-value obtained is 0.8435 and all the best i can have from the rest is a 0.66-0.68. I'm probably not so expert in running this kind of test, but am I doing something wrong? I would expect p values ranging from 0.75 (to be kind) to 0.9, 0.95. How is this possible? Thank you in advance for your answers. See you soon EM __ 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 decide between two theoretical distributions?
Question that I have to ask has two parts: first, related to statistics, in principle, and second, related to R-how-to, in particular. In very brief, I have collected pretty solid sample for a phenomenon that has two possible interpretation of how it is distributed in the population; for example, beta and gamma distributed. How it can be tested which model (theoretical distribution) suits better actual data? Except some vague idea that bootstrapping or jackknifing could be used, I have no further thoughts on that matter. Could it be tested in R and how? Sincerely, Petar Milin __ 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 decide between two theoretical distributions?
Question that I have to ask has two parts: first, related to statistics, in principle, and second, related to R-how-to, in particular. In very brief, I have collected pretty solid sample for a phenomenon that has two possible interpretation of how it is distributed in the population; for example, beta and gamma distributed. How it can be tested which model (theoretical distribution) suits better actual data? Except some vague idea that bootstrapping or jackknifing could be used, I have no further thoughts on that matter. Could it be tested in R and how? Sincerely, Petar Milin __ 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] Matrix variable in C code
On 2/2/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Selon Gabor Csardi [EMAIL PROTECTED]:
On Thu, Feb 02, 2006 at 03:11:42PM +0100, [EMAIL PROTECTED] wrote:
[...]
and my test code in C is:
SEXP VPCEfron(SEXP f, SEXP SR, SEXP ZR, SEXP DIR, SEXP nsR, SEXP rho)
{
int taille=INTEGER(nsR)[0];
[...]
All works, except ZS, the variable ZS is a matrix in R, and when i try to
give
to C code, with ZR, ZR is only a vector.
How to obtain a matrix variable in C ?
A matrix is the same as a vector (stored columnwise), except that is has a
dim attribute. Use can use SET_DIM to set the dim attribute, and GET_dim to
query it. Eg:
int nrow=INTEGER(GET_DIM(ZR))[0];
int ncol=INTEGER(GET_DIM(ZR))[1];
To access the values in the matrix you might use something like:
#define RMATRIX(m,i,j) (REAL(m)[ INTEGER(GET_DIM(m))[0]*(j)+(i) ])
and then
RMATRIX(ZR, 0, 1), etc. works. Note that according to this #define the
matrix
is indexed from zero.
Gabor
--
Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK
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I try but i think that i make some mistake because i obtain segment fault.
To be sure, i reduce the code to permit to test it, the goal is just to print
the variable, i try with vector variables (real X and integer dX in the
following), it works; but with matrix it doesn't work.
The code of the R program - Test.R
=
X-c(4,2,3,2)
Z-c(40,21,30,20)
dX-c(2,1,1)
dyn.load(test.so)
Phi-function(z,a,b)
{
Phi-z
}
VPEfron-function(XType,ZType,dXType,G,c0,c1)
{
# A OPTIMISER
VPCEfron-function(f,XT,ZT,dXT,tailleS=length(XT))
{
f.check-function(x) {
x-f(x)
}
.Call(VPCEfron,body(f.check),as.double(XT),as.double(ZT),as.integer(dXT),as.integer(tailleS),new.env())
}
GG-function(z) G(z,c0,c1)
Vraisemblancepartielle-VPCEfron(GG,XType,ZType,dXType)
}
resultat-VPEfron(X,Z,dX,Phi,0,0)
==
The code of C code - test.c and test.so is obtained by R CMD SHLIB test.c
#include R.h
#include Rdefines.h
#define RMATRIX(m,i,j) (REAL(m)[ INTEGER(GET_DIM(m))[0]*(j)+(i) ])
SEXP mkans(double x)
{
SEXP ans;
PROTECT(ans = allocVector(REALSXP,1));
REAL(ans)[0]=x;
UNPROTECT(1);
return ans;
}
SEXP VPCEfron(SEXP f, SEXP XR, SEXP ZR, SEXP DIR, SEXP rho)
{
double* X=REAL(XR);
int* DI=INTEGER(DIR);
int nligne=INTEGER(GET_DIM(ZR))[0];
int ncol=INTEGER(GET_DIM(ZR))[1];
printf(verifie de X: %f - %f - %f - %f\n,X[0],X[1],X[2],X[3]);
printf(verifie dX: %d %d %d\n,DI[0],DI[1],DI[2]);
printf(verifie de Z\n);
printf(%d %d\n,nligne,ncol);
printf(%f %f\n,RMATRIX(ZR,0,0));
printf(%f %f\n,RMATRIX(ZR,0,1));
printf(%f %f\n,RMATRIX(ZR,1,0));
printf(%f %f\n,RMATRIX(ZR,2,0));
return mkans(0.0);
}
=
You can save these two simple programs in order to test my code.
It's a small point but there is no need to write the C function mkans
- you can use the function ScalarReal (or ScalarLogical, ScalarInt,
...).
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Re: [R] Problems with ks.test
7 repetitions is not nearly enough to get a good estimate of the
variability of the test statistic.
Try this:
nrep - 500
pvals - tstvals - numeric(nrep)
for (i in seq(nrep)) {
tmp - ks.test(rexp(2500,0.4),pexp,0.4)
pvals[i] - tmp$p.value
tstvals[i] - tmp$statistic
}
hist(pvals)
hist(tstvals)
round(quantile(pvals,pr=seq(0.05,.95,.05)),2)
At 2:36 PM + 2/3/06, Emanuele Mazzola wrote:
Hi everybody,
while performing ks.test for a standard exponential distribution on samples
of dimension 2500, generated everytime as new, i had this strange behaviour:
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0147, p-value = 0.6549
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.019, p-value = 0.3305
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0171, p-value = 0.4580
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0143, p-value = 0.6841
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0145, p-value = 0.6684
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0123, p-value = 0.8435
alternative hypothesis: two.sided
data-rexp(2500,0.4)
ks.test(data,pexp,0.4)
One-sample Kolmogorov-Smirnov test
data: data
D = 0.0186, p-value = 0.3532
alternative hypothesis: two.sided
It seems kind of strange to me that max p-value obtained is 0.8435 and all
the best i can have from the rest is a 0.66-0.68.
I'm probably not so expert in running this kind of test, but am I doing
something wrong?
I would expect p values ranging from 0.75 (to be kind) to 0.9, 0.95. How is
this possible?
Thank you in advance for your answers.
See you soon
EM
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--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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Re: [R] Problems with ks.test
The distribution of p-values should be uniform under the null hypothesis. When I do: jj - numeric(1) for(i in 1:1) jj[i] - ks.test(rexp(2500, .4), 'pexp', .4)$p.value Warning messages: 1: cannot compute correct p-values with ties in: ks.test(rexp(2500, 0.4), pexp, 0.4) 2: cannot compute correct p-values with ties in: ks.test(rexp(2500, 0.4), pexp, 0.4) 3: cannot compute correct p-values with ties in: ks.test(rexp(2500, 0.4), pexp, 0.4) 4: cannot compute correct p-values with ties in: ks.test(rexp(2500, 0.4), pexp, 0.4) hist(jj, 50, col='yellow'); abline(h=200, col='green') I get a histogram that looks reasonably flat to me. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Emanuele Mazzola wrote: Hi everybody, while performing ks.test for a standard exponential distribution on samples of dimension 2500, generated everytime as new, i had this strange behaviour: data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0147, p-value = 0.6549 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.019, p-value = 0.3305 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0171, p-value = 0.4580 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0143, p-value = 0.6841 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0145, p-value = 0.6684 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0123, p-value = 0.8435 alternative hypothesis: two.sided data-rexp(2500,0.4) ks.test(data,pexp,0.4) One-sample Kolmogorov-Smirnov test data: data D = 0.0186, p-value = 0.3532 alternative hypothesis: two.sided It seems kind of strange to me that max p-value obtained is 0.8435 and all the best i can have from the rest is a 0.66-0.68. I'm probably not so expert in running this kind of test, but am I doing something wrong? I would expect p values ranging from 0.75 (to be kind) to 0.9, 0.95. How is this possible? Thank you in advance for your answers. See you soon EM __ 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] How to get all the data in a specific column from a dataframe?
Dear R-helpers: Suppose I have a datafram called test_frame like this col1 col2 col3 col4 r1 xxx x r2 xxx x r3 xxx x ..xxx x rn xxx x I know I can get data of col3 by using test_frame[,3]. My question is, if I want to do this by specifying col3 rather than 3, what should I do? Many thanks [[alternative HTML 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
Re: [R] RHOME
Far be it for me to tell people what they can and cannot do. Perhaps I
can rephrase myself in a less inflammatory way.
R runs from the build directory as a convenience for developers, so you
don't have to reinstall R every time you change something. But for
users, the standard mechanism make install has a number of advantages
over moving the build directory to a publicly accessible location: it is
guaranteed to work, you don't have to do any post-hoc editing of files,
it takes up a lot less space, about 4.6 times less on my system
[EMAIL PROTECTED] r-devel]$ du -sh R
356MR
[EMAIL PROTECTED] r-devel]$ du -sh /usr/local/lib64/R
77M /usr/local/lib64/R
But if you do want to copy the build directory the, as Martin says,
you can edit the file bin/R so that the line that starts
R_HOME_DIR points to the correct location, e.g.
R_HOME_DIR=/usr/local/lib/R
M.
On Fri, 2006-02-03 at 14:48 +0100, Peter Dalgaard wrote:
Martin Maechler [EMAIL PROTECTED] writes:
Martyn R is designed to run from its build directory. But
Martyn if your sysadmin installs it with make install (as
Martyn root), then the shell wrapper that is installed in
Martyn /usr/local/bin/R will have R_HOME pointing to the
Martyn right location (/usr/local/lib/R). Literally moving
Martyn the build directory to another location is the wrong
Martyn thing to do.
well, but very easily fixable, and that's what Daniel is asking
for:
The default value of R_HOME is only set in exactly one place,
namely the 'R' shell script; editing that script - once after
the move - is really a piece o'cake.
Hmm, I was about to say the same, but there seems to be unexpected
references in other places.
find `R RHOME` | xargs grep `R RHOME`
/usr/lib64/R/bin/R:R_HOME_DIR=/usr/lib64/R
/usr/lib64/R/bin/R:R_SHARE_DIR=/usr/lib64/R/share
/usr/lib64/R/bin/R:R_INCLUDE_DIR=/usr/lib64/R/include
/usr/lib64/R/bin/R:R_DOC_DIR=/usr/lib64/R/doc
(this doesn't normally happen - a SUSE RPM specialty, or due to
configure flag settings?)
I think this is normal. But the RedHat RPM behaves differently.
(because the RPM build process installs into a temporary build root
which is distinct from the final installation directory, requiring more
sed voodoo).
Once you start building packages, you also have things like
viggo:~/find ~/Rlibrary | xargs grep `R RHOME`
Binary file /home/bs/pd/Rlibrary/rgl/libs/rgl.so matches
viggo:~/find ~/Rlibrary | xargs grep Rlibrary
Binary file /home/bs/pd/Rlibrary/rgl/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/ISwR/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/mvtnorm/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/nlmeODE/Meta/hsearch.rds matches
B.
on my laptop I had a hit on one of the Sweave support files too.
Most likely these are quite harmless, but all in all I think Martyn
has the safest advice: Use make install, as root (don't forget
umask 022).
---
This message and its attachments are strictly confidential. ...{{dropped}}
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[R] Infinite loop running Mod_R/Rapache
I installed mod_r according to the specifications, and have been trying
to get the demo script to work correctly. I am running debian, the
latest build of R, apache 2 with prefork mpm, and the latest mod_r. Is
anyone else using this module successfully? I added:
LoadModule R_module mod_R.so
Location /test/hello
SetHandler r-handler
Rsource /var/www/html/test.R
RreqHandler handler
/Location
to my http.conf and
test.R in /var/www/html is:
handler-function(r){
apache.write(r,h1Hello World!/h1)
OK
}
When I start apache2, my /tmp directory fills with rtmp directories
until memory is exausted. The first time it created 32,000 before I
noticed. Does anyone have any idea as to what I could be doing wrong, or
have a software configuration that works? Thank you for all of your
help. ~BJ
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Re: [R] How to get all the data in a specific column from a dataframe?
test_frame[,col3] or subset(test_frame, select = col3) Vincent Deng wrote: Dear R-helpers: Suppose I have a datafram called test_frame like this col1 col2 col3 col4 r1 xxx x r2 xxx x r3 xxx x ..xxx x rn xxx x I know I can get data of col3 by using test_frame[,3]. My question is, if I want to do this by specifying col3 rather than 3, what should I do? Many thanks [[alternative HTML 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 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ 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 get all the data in a specific column from a dataframe?
Chuck Cleland [EMAIL PROTECTED] writes: test_frame[,col3] or subset(test_frame, select = col3) or test_frame$col3 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- 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
[R] statistical modelling SAS vs R
Hello, Recently I have been reading a lot of material about statistical modeling using R. There seems to be conflicting opinions about what the best approach is between the SAS community and the R community. 1) In R one might start with a model that has all possible effects of interest in it and then simplify by eliminating/adding insignificant effects using a stepwise procedure. 2) In SAS one may starts with a reasonable model and look at type 3 SS's to test hypotheses and report LSMEANS. This can be done in R too I think. Does anyone have current opinions about this? I know it's been discussed before but I would be very interested in hearing about the advantages and pitfalls of both approaches. Bill __ 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] workspace question
All, When starting R, how does one prevent the loading the previous workspace which was saved? I'd like to start a new project and save the new image in a different directory, but I'd like to partition this from the old project. Does there exist a better way than just deleting the files associated w/ the old project manually? I looked in the Intro to R manual and searched for workspace and didn't see anything on this aspect. Kind regards, Dave ps - please reply directly to [EMAIL PROTECTED] __ 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] statistical modelling SAS vs R
Bill Szkotnicki wrote: Hello, Recently I have been reading a lot of material about statistical modeling using R. There seems to be conflicting opinions about what the best approach is between the SAS community and the R community. 1) In R one might start with a model that has all possible effects of interest in it and then simplify by eliminating/adding insignificant effects using a stepwise procedure. 2) In SAS one may starts with a reasonable model and look at type 3 SS's to test hypotheses and report LSMEANS. This can be done in R too I think. Does anyone have current opinions about this? I know it's been discussed before but I would be very interested in hearing about the advantages and pitfalls of both approaches. Bill You'll get lots of opinions about this. Both R and SAS can be abused terribly, and both approaches you mentioned have major problems if you use P-values to specify models. Better and more replicable results can be obtained using modern shrinkage methods and being more liberal with inclusion of variables, or by using Bayesian model averaging. Note that LSMEANS and Type III tests are SAS concoctions and that if you have interactions in the model, type III tests have been criticized. If there are no interactions, type Type III = Type II. Frank Harrell -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Clustering for social/complex networks
Hi group, Here is another clustering question. Is there anything available in R that I can cluster groups with overlaps? It looks like a Venn Diagram with two or more circles overlapping one another. I realize that Hierarchical Clustering (hclust in Stats) only group individuals into distinct groups. My scenario is I have to group Physicians that each of them may belong to more than one group. That reflects the complexity of relationhip, something analogous to Social Network. Thanks! kel __ 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] is there a way to visualize 3D normal distributions?
In response to your last question -- Duncan already gave you the answer in his last e-mail -- to give an explicit example, for a particular set of means and variance-covariance matrix: library(rgl) demo(shapes3d) rgl.clear() sphere - ellipsoid3d(2,2,2,qmesh=TRUE) means - c(0,0,0) S - matrix(c(3,1,-1,1,2,-1,-1,-1,2),nrow=3) ellipsoid - translate3d(rotate3d(sphere,matrix=chol(S)*qnorm(0.975)), means[1],means[2],means[3]) shade3d(ellipsoid) axis3d() Duncan Murdoch wrote: On 2/2/2006 5:01 PM, Michael wrote: shape3d only gives rigid sphere... not the free form ellipsoid that I want... ? If you run the demo, you'll see ellipsoids... You just need to work out the appropriate transform to apply to a sphere to get the ellipsoid you want. I imagine something like this: sphere - ellipsoid3d(2,2,2, qmesh=TRUE) ellipsoid - translate3d(rotate3d(sphere, matrix=chol(S)), xbar, ybar, zbar) shade3d(ellipsoid) is what you want, where S is the covariance matrix, and xbar,ybar,zbar have the obvious meaning. (rotate3d() is used with a matrix that isn't a rotation matrix; it may not be obvious that this is allowed, but it is.) Duncan Murdoch On 2/2/06, Ben Bolker [EMAIL PROTECTED] wrote: Duncan Murdoch murdoch at stats.uwo.ca writes: On 2/2/2006 3:39 AM, Michael wrote: Hi all, How do I visualize a contour of a tri-variate normal distribution? I just like to see the ellipsoid very much. I hope there is a easy way or existing method in R. The misc3d package includes a function for 3d contour plots; that should do what you want. is contour3d really necessary or could you just plot ellipsoids? (library(rgl); demo(shapes3d)) -- still a little bit of figuring to do, but this should get you most of the way there. Ben Bolker __ 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 [[alternative HTML 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 -- 620B Bartram Hall[EMAIL PROTECTED] Zoology Department, University of Floridahttp://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704 __ 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] Infinite loop running Mod_R/Rapache
BJ wrote:
I installed mod_r according to the specifications, and have been trying
to get the demo script to work correctly. I am running debian, the
latest build of R, apache 2 with prefork mpm, and the latest mod_r. Is
anyone else using this module successfully? I added:
LoadModule R_module mod_R.so
Location /test/hello
SetHandler r-handler
Rsource /var/www/html/test.R
RreqHandler handler
/Location
to my http.conf and
test.R in /var/www/html is:
handler-function(r){
apache.write(r,h1Hello World!/h1)
OK
}
When I start apache2, my /tmp directory fills with rtmp directories
until memory is exausted. The first time it created 32,000 before I
noticed. Does anyone have any idea as to what I could be doing wrong, or
have a software configuration that works? Thank you for all of your
help. ~BJ
This is definitely an apache configuration problem. After responding to
you privately about this issue, I got paranoid and checked the latest
R/Apache code release (rapache-0.1.1) with the following debian packages:
apache2-common/unstable uptodate 2.0.55-4
apache2-utils/unstable uptodate 2.0.55-4
apache2-mpm-prefork/unstable uptodate 2.0.55-4
apache2-prefork-dev/unstable uptodate 2.0.55-4
I could not reproduce the behavior you are witnessing. Maybe you can
send me (off-list) your /etc/apache2/apache2.conf,
/etc/apache2/sites-enabled/* and see if I can't help you troubleshoot.
But this bit of R creating a temp dir (for transient files?) needs to be
handled more delicately in a server environment. I'm going to do some
more digging in the R source... I hope I haven't made some glaringly
wrong assumptions.
--
Jeffrey Horner Computer Systems Analyst School of Medicine
615-322-8606 Department of Biostatistics Vanderbilt University
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[R] R-2.2.1-INSTALL Issue with TCLTK
Hi
I am not able to have a working tcltk library in R-2.2.1 inspite of
trying different options suggested in the FAQ's. I am using the
following configure option and I do get the tcltk package installed but
with a missing libs folder.
./configure -prefix= ~R-2.2.1 --enable-R-shlib --enable-linux-lfs
--with-zlib --with-gnu-ld --with-tcltk
--with-tcl-config=~tcl-8.4.12/lib --with-tk-config=~tk-8.4.12/lib
I have ensured that I have a valid tclsh in my path and have even
provided the include path for covering the tcl.h
Operating system: RHEL
The error I get while trying to invoke the libarary for tcltk is:
Error in firstlib(which.lib.loc, package) :
Tcl/Tk support is not available on this system
Error in library(tcltk) : .First.lib failed for 'tcltk'
Execution halted
Any help to identify the cause is highly appreciated.
Respectfully
Gautam
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Re: [R] workspace question
If you start R with the argument --no-restore (or even --vanilla, I think), no workspace will be loaded. Personally I almost never save a workspace image. Whatever I need I explicitly save() and load() or attach(). Andy From: Afshartous, David All, When starting R, how does one prevent the loading the previous workspace which was saved? I'd like to start a new project and save the new image in a different directory, but I'd like to partition this from the old project. Does there exist a better way than just deleting the files associated w/ the old project manually? I looked in the Intro to R manual and searched for workspace and didn't see anything on this aspect. Kind regards, Dave ps - please reply directly to [EMAIL PROTECTED] __ 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] Difficulty with qqline in logarithmic context
[Brian Ripley]
Is there a good reason to use qqnorm in a single-log context?
Yes. Googling around reveals this is not so uncommon.
Should one not rather use
qqnorm(log(freq))
qqline(log(freq))
In the display produced by qqnorm, the y-axis would then show
log(value) labels, while the user (me!) expects value labels.
since you are (I guess) looking at log-normality of freq?
Once again, I was merely toying with qqplot. I found intriguing that,
while shuffling messages around between folders, for a good while, the
distribution of log(number of messages) per folder appears vagueley
normal, as I do not quickly see a reasonable justification for this.
Another way to look at that is
qqplot(qlnorm(ppoints(length(freq))), freq, log=xy)
the same plot, different scales.
Interesting, thanks for teaching me about ppoints. Yet, I stay more
happy with the abcissa scale produced by qqnorm. Besides, how would
one uses qqline with the above?
(I believe a QQ plot should always have comparable scales on the two
axes.)
While comparable scales are somewhat simpler to compare, this is not
necessarily what is most adequate for the user. Proof is that while
quantiles are being compared here, scales do not show quantiles, but
units as meaningful to the user. One might want to compare variables
scaled very differently, maybe because of different units from the same
distribution, of from different but similar distributions using
different scales and shifted to different means. Or even, why not, if
this is what is meaningful for users, a log scale.
The point is that qqline is tied to normality, not to log-normality.
As it stands, yes. As a convenience, it could be extended (probably
easily) to log-normality. qqnorm already does something sensible in
log-context, so a user might expect qqline to do equally well.
The real point might be that qqline is tied to abline a bit too
blindly. What is the meaning of intercept and slope of a straight line
on a graphic in log context? First, the intercept might not even exist.
Second, abline interpretation depends on the clippling, and possibly
on the extrema of the pretty breakpoints chosen for scales, so making it
hard to predict on average use. There ought to be some reason for the
log-aware code in abline, yet I did not find documentation for it.
The wisest for abline, in my very humble opinion, would be for it to
complain if ever called in log context. Then, qqline would indirectly
complain through abline, if qqline is not modified to do something
more proper. Moreover, if it is definitely out of question that
qqline be ever meaningfully called in log context, then so qqnorm,
which should then complain as well.
Currently, qqline misbehaves, in that it silently produces
a meaningless result, while it could either diagnose that the result is
meaningless, or produce a mearningful result.
[Remainder of the reply top-quoted, as usual on r-help.]
On Wed, 1 Feb 2006, François Pinard wrote:
Hi, R friends. I had some difficulty with the following code:
qqnorm(freq, log='y')
qqline(freq)
as the line drawn was seemingly random. The exact data I used appears
below. After wandering a bit within the source code for abline,
I figured out I should rather write:
qqnorm(freq, log='y')
par(ylog=FALSE)
qqline(log10(freq))
par(ylog=TRUE)
I'm proposing that this little stunt be rather be hidden and
automatically effected within qqline proper, whenever par('ylog') is
TRUE. I thought about providing a patch, as qqline is so small. Yet
it would be more noise than useful, as I'm not familiar with the datax
argument usage, which should probably be addressed as well.
Here is the data, in case useful:
freq -
as.integer(c(33, 79, 21, 436, 58, 18, 1106, 498, 1567, 393, 2,
104, 50, 67, 113, 76, 327, 331, 196, 145, 86, 59, 12, 215, 293,
154, 500, 314, 246, 587, 85, 23, 323, 3, 13, 576, 29, 37, 24,
21, 1230, 137, 13, 93, 3, 101, 72, 218, 59, 17, 2, 8, 86, 143,
150, 22, 19, 234, 119, 157, 4, 255, 146, 126, 76, 15, 271, 170,
4, 6, 16, 3048, 2175, 3350, 5017, 5706, 1610, 665, 322, 1, 16,
47, 51, 168, 94, 66, 154, 99, 11, 547, 953, 1, 1071, 80, 184,
168, 52, 187, 103, 187, 361, 46, 85, 135, 597, 121, 283, 26,
12, 20, 169, 9, 79, 15, 114, 75, 30, 111, 556, 173, 32, 99, 438,
2, 2, 1, 117, 5, 3, 51, 8, 41, 12, 23, 2, 13, 5, 1, 9, 4, 1,
7, 15, 5, 48, 16, 112, 6, 1, 39, 60, 5, 23, 5, 19, 1, 8, 32,
4, 13, 1, 14, 71, 5, 1, 35, 30, 100, 389, 22, 8, 1, 192, 40,
6, 3, 17, 2, 14, 71, 14, 1, 5, 4, 32, 21, 18, 13, 2, 2, 45, 342,
46, 144, 18, 131, 188, 112, 37, 85, 90, 8, 195, 173, 5, 53, 96,
37, 16, 16, 281, 64, 50, 92, 336, 31, 744, 4, 134, 74, 1, 227,
6, 48, 418, 64, 66, 59, 20, 45, 20, 370, 148, 22, 7, 30, 601,
29, 82, 113, 938, 252, 65, 137, 72, 22, 98, 12, 152, 212, 13,
8, 35, 3, 77))
Yet this really is the value of courriel$freq after data(courriel),
with a file .../R/data/courriel.R here, holding:
courriel - read.table(pipe('grep -c
Re: [R] Clustering for social/complex networks
try: cmeans Fuzzy C-Means Clustering in library(e1071) regards, christian Hi group, Here is another clustering question. Is there anything available in R that I can cluster groups with overlaps? It looks like a Venn Diagram with two or more circles overlapping one another. I realize that Hierarchical Clustering (hclust in Stats) only group individuals into distinct groups. My scenario is I have to group Physicians that each of them may belong to more than one group. That reflects the complexity of relationhip, something analogous to Social Network. Thanks! kel __ 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] Function assign
I'm trying to apply the function assign( ) to a subset of a matrix, but it doesn't work... i.e. example-matrix(nrow=5,ncol=5) assign(example[c(1,3),],matrix(1:10,nrow=2,ncol=5)) but matrix example doesn't change ( get(example[c(1,3),]) is not useful to me)...how can I do this assignment? Thanks in advance, Marco [[alternative HTML 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
Re: [R] Function assign
example-matrix(nrow=5,ncol=5) example[c(1,3),]-matrix(1:10,nrow=2,ncol=5) Marco Venanzi wrote: I'm trying to apply the function assign( ) to a subset of a matrix, but it doesn't work... i.e. example-matrix(nrow=5,ncol=5) assign(example[c(1,3),],matrix(1:10,nrow=2,ncol=5)) but matrix example doesn't change ( get(example[c(1,3),]) is not useful to me)...how can I do this assignment? Thanks in advance, Marco [[alternative HTML 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 -- Ferdinand Alimadhi Programmer / Analyst Harvard University The Institute for Quantitative Social Science (617) 496-0187 [EMAIL PROTECTED] www.iq.harvard.edu __ 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] R-2.2.1-INSTALL Issue with TCLTK
Those don't look like valid paths to config files to me. On FC3 they
would be
/usr/lib/tclConfig.sh
/usr/lib/tkConfig.sh
So even if you have users tcl-8.4.12 and tk-8.4.12 (do you?), your paths
are almost surely not to config files.
Configure reports what works, including that it is not going to build
tcl/tk support. Look back at the relevant parts of its output.
On Fri, 3 Feb 2006, Bhola, Gautam wrote:
Hi
I am not able to have a working tcltk library in R-2.2.1 inspite of
trying different options suggested in the FAQ's. I am using the
following configure option and I do get the tcltk package installed but
with a missing libs folder.
./configure -prefix= ~R-2.2.1 --enable-R-shlib --enable-linux-lfs
--with-zlib --with-gnu-ld --with-tcltk
--with-tcl-config=~tcl-8.4.12/lib --with-tk-config=~tk-8.4.12/lib
I have ensured that I have a valid tclsh in my path and have even
provided the include path for covering the tcl.h
Operating system: RHEL
The error I get while trying to invoke the libarary for tcltk is:
Error in firstlib(which.lib.loc, package) :
Tcl/Tk support is not available on this system
Error in library(tcltk) : .First.lib failed for 'tcltk'
Execution halted
Any help to identify the cause is highly appreciated.
Respectfully
Gautam
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--
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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[R] all.equal() and which()
Please excuse the lack of a complete dataset here, if its needed I'll be happy to provide it. Can anyone show me how to rewrite this? Browse[1] time(data)[24210:24220] [1] 24.209 24.210 24.211 24.212 24.213 24.214 24.215 24.216 24.217 [10] 24.218 24.219 Browse[1] which(time(data)==24.211) numeric(0) I'm assuming its an eps fault but which(all.equal(time(data),24.211)) dosnt seem to work __ 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] all.equal() and which()
On Fri, 2006-02-03 at 10:41 -0500, tom wright wrote: Please excuse the lack of a complete dataset here, if its needed I'll be happy to provide it. Can anyone show me how to rewrite this? Browse[1] time(data)[24210:24220] [1] 24.209 24.210 24.211 24.212 24.213 24.214 24.215 24.216 24.217 [10] 24.218 24.219 Browse[1] which(time(data)==24.211) numeric(0) I'm assuming its an eps fault but which(all.equal(time(data),24.211)) dosnt seem to work There might be an easier way, but here is one approach: mydat [1] 24.209 24.210 24.211 24.212 24.213 24.214 24.215 24.216 24.217 [10] 24.218 24.219 which(sapply(mydat, function(x) isTRUE(all.equal(24.211, x [1] 3 This uses sapply() to check each element of 'mydat' against the target value of 24.211. The use of 'isTRUE(all.equal(...))' returns a boolean result of either TRUE or FALSE, enabling the use of which() against the vector returned from sapply(): sapply(mydat, function(x) isTRUE(all.equal(24.211, x))) [1] FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE See ?all.equal and ?isTRUE for more information. HTH, Marc Schwartz __ 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] Using string vectors as for loop arguments
Is there a mechanism to interate through a vector of strings? Say I
have a data frame of 50 variables (VAR1 to VAR50), each with 100
measurements along with some coding factors (EXP and DOSE). I want to
calculate the mean of a subset of each of VAR1 to VAR 50 (selecting
by EXP and DOSE). Rather than just copy/pasting the same code 50
times, I thought of using a for loop to go through a vector of VAR1
to VAR50 (VAR.LIST below). Each iteration would be the variable name
for which the mean would be calculated.
Trying this, I get an error that the argument is not numeric or
logical. So I assume that for loops with vectors of strings are
disallowed. What I am wondering is whether there a way to mimic this
sort of procedure?
The code looked something like this:
VAR.LIST-paste(c(VAR), 1:50, sep=)
for (i in VAR.LIST){
mean(i[EXP==1 DOSE==1], na.rm=T)
}
Thanks
Kevin Middleton
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Re: [R] statistical modelling SAS vs R
bill, what kind of modeling are you talking about? based on your desc on SAS, you are doing general linear model, aren't you? Frank gave you a great suggestion of using shrinkage methods, such as lasso, instead of stepwise/backforward/forward methods. But no matter shrinkage or stepwise, both can be implemented in R and SAS. At this point, there is no difference at all. On 2/3/06, Bill Szkotnicki [EMAIL PROTECTED] wrote: Hello, Recently I have been reading a lot of material about statistical modeling using R. There seems to be conflicting opinions about what the best approach is between the SAS community and the R community. 1) In R one might start with a model that has all possible effects of interest in it and then simplify by eliminating/adding insignificant effects using a stepwise procedure. 2) In SAS one may starts with a reasonable model and look at type 3 SS's to test hypotheses and report LSMEANS. This can be done in R too I think. Does anyone have current opinions about this? I know it's been discussed before but I would be very interested in hearing about the advantages and pitfalls of both approaches. Bill __ 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 -- WenSui Liu (http://statcompute.blogspot.com) Senior Decision Support Analyst Health Policy and Clinical Effectiveness Cincinnati Children Hospital Medical Center [[alternative HTML 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] How to generate pitch strings
If I calculate a transition probability matrix, first order markov 12x12 or second order 144x144 from musical pitch classes (0-11), is it possible to generate pitch class strings similar as those original strings using those probability matrix with R? If, how? Atte Tenkanen, Turku, Finland __ 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] Using string vectors as for loop arguments
?apply
as in:
answer-apply(yourframe,2,function(x)x[EXP==1 DOSE==1])
Note that there are slicker ways to do this call.
Note also for that for the particular case of column means, you have a
built-in much faster alternative:
answer-colMeans(yourframe[EXP==1 DOSE==1,],na.rm=TRUE)
Also note that the == construction may be problematic if EXP or DOSE are not
factors, say.
Finally, you need to start reading the R docs to learn about this yourself.
An Introduction to R is a good place to start.
Oh... and your attempt below will certainly not work. After you read the
basic docs, you'll see why not.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kevin Middleton
Sent: Friday, February 03, 2006 1:41 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Using string vectors as for loop arguments
Is there a mechanism to interate through a vector of strings? Say I
have a data frame of 50 variables (VAR1 to VAR50), each with 100
measurements along with some coding factors (EXP and DOSE). I
want to
calculate the mean of a subset of each of VAR1 to VAR 50 (selecting
by EXP and DOSE). Rather than just copy/pasting the same code 50
times, I thought of using a for loop to go through a vector of VAR1
to VAR50 (VAR.LIST below). Each iteration would be the variable name
for which the mean would be calculated.
Trying this, I get an error that the argument is not numeric or
logical. So I assume that for loops with vectors of strings are
disallowed. What I am wondering is whether there a way to mimic this
sort of procedure?
The code looked something like this:
VAR.LIST-paste(c(VAR), 1:50, sep=)
for (i in VAR.LIST){
mean(i[EXP==1 DOSE==1], na.rm=T)
}
Thanks
Kevin Middleton
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Re: [R] RHOME
On Fri, 3 Feb 2006, Peter Dalgaard wrote: Martin Maechler [EMAIL PROTECTED] writes: Martyn R is designed to run from its build directory. But Martyn if your sysadmin installs it with make install (as Martyn root), then the shell wrapper that is installed in Martyn /usr/local/bin/R will have R_HOME pointing to the Martyn right location (/usr/local/lib/R). Literally moving Martyn the build directory to another location is the wrong Martyn thing to do. well, but very easily fixable, and that's what Daniel is asking for: The default value of R_HOME is only set in exactly one place, namely the 'R' shell script; editing that script - once after the move - is really a piece o'cake. Hmm, I was about to say the same, but there seems to be unexpected references in other places. find `R RHOME` | xargs grep `R RHOME` /usr/lib64/R/bin/R:R_HOME_DIR=/usr/lib64/R /usr/lib64/R/bin/R:R_SHARE_DIR=/usr/lib64/R/share /usr/lib64/R/bin/R:R_INCLUDE_DIR=/usr/lib64/R/include /usr/lib64/R/bin/R:R_DOC_DIR=/usr/lib64/R/doc (this doesn't normally happen - a SUSE RPM specialty, or due to configure flag settings?) That only happens in the installed copy. Martin is right if one is talking about moving the build tree (and Martyn is right that there is a lot of stuff that does not need to be installed in the build tree and that `make install' takes all the strain of copying the right bits). -- 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
[R] Cause of Error 1:nrow(X) : argument NA / NaN
Dear R Helpers I am trying to get function smedian.hilow to work using Hmisc summarize on variable conc in dataframe pkindivmtd by time and dose using: attach(pkindivmtd) sconc - summarize(conc,llist(time,dose),smedian.hilow) I get the error message Erreur dans 1:nrow(X) : argument NA / NaN Contents of pkindivmtd is contents(pkindivmtd) Data frame:pkindivmtd 1296 observations and 9 variablesMaximum # NAs:0 Labels Units Levels Storage dose Dosemginteger day integer hourinteger subjectSubject integer conc Concentration ng/mL double fday 10 integer fsubject 37 integer fdose Dose4 integer time Time hoursinteger . What I am doing wrong ? Sorry for not providing a reproducible example as when I generate randomly the 3 variables it works ! Many thanks, Jean-Louis __ 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] Tobit Regression
I'm statistician I have thesis : Tobit Regression my book : Greene, William H. 1997. Econometric Analysis. Third Edition, prentice Hall Is there the program in R ? may I ask the manual how make the program? and also how to test the assumption ? If there are anyone have Amemiya journal may I asked ? please help me! I already googling and I don't get the answer. Before i use STATA 6 to analyze. but I don't get the manual. __ 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] rgl install problem on Solaris 10 X86
Hi, Could you help me to install the rgl package on Solaris 10 x86? I tried and got the following error messages. When I compiled my R as 64bit, I used the SUN ProW compilers. However, gcc seems to being used below as well as missing some information. Thank you in advance, Dongseok install.packages(rgl) --- Please select a CRAN mirror for use in this session --- * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries /usr/openwin/lib, headers /usr/openwin/include checking for libpng-config... yes configure: creating ./config.status config.status: creating src/Makevars ** libs CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c api.cpp -o api.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Background.cpp -o Background.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise Background.cpp, line 54: Warning: boundingBox hides Shape::boundingBox. 1 Warning(s) detected. CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c BBoxDeco.cpp -o BBoxDeco.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Color.cpp -o Color.oCC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise Color.cpp, line 142: Error: The function realloc must have a prototype. Color.cpp, line 159: Error: The function realloc must have a prototype. Color.cpp, line 160: Error: The function memcpy must have a prototype. Color.cpp, line 168: Error: The function free must have a prototype. Color.cpp, line 175: Error: The function realloc must have a prototype. Color.cpp, line 196: Error: The function realloc must have a prototype. Color.cpp, line 247: Error: The function realloc must have a prototype. 7 Error(s) detected. *** Error code 7 make: Fatal error: Command failed for target `Color.o' ERROR: compilation failed for package 'rgl' ** Removing '/export/home/choid/bin/R2.2.1/lib/R/library/rgl' The downloaded packages are in /tmp/Rtmp9Yaawc/downloaded_packages [[alternative HTML 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
Re: [R] rgl install problem on Solaris 10 X86
On 2/3/2006 6:37 PM, Dongseok Choi wrote: Hi, Could you help me to install the rgl package on Solaris 10 x86? No, but there have been a lot of changes to it since the last upload to CRAN. You might want to grab a new copy from http://rgl.neoscientists.org/About.html by getting the latest Subversion checkout. Duncan Murdoch I tried and got the following error messages. When I compiled my R as 64bit, I used the SUN ProW compilers. However, gcc seems to being used below as well as missing some information. Thank you in advance, Dongseok install.packages(rgl) --- Please select a CRAN mirror for use in this session --- * Installing *source* package 'rgl' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for X... libraries /usr/openwin/lib, headers /usr/openwin/include checking for libpng-config... yes configure: creating ./config.status config.status: creating src/Makevars ** libs CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c api.cpp -o api.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Background.cpp -o Background.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise Background.cpp, line 54: Warning: boundingBox hides Shape::boundingBox. 1 Warning(s) detected. CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c BBoxDeco.cpp -o BBoxDeco.o CC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise CC -xtarget=generic64 -I/export/home/choid/bin/R2.2.1/lib/R/include -I/usr/openwin/include -DHAVE_PNG_H -I/usr/include/libpng12 -I/mounts/devel/SUNWspro/prd/include -I/mounts/devel/GNU/repoz/readline43/include -KPIC -O -xlibmil -dalign -I/mounts/devel/SUNWspro/prod/include -c Color.cpp -o Color.oCC: Warning: Option -dalign passed to ld, if ld is invoked, ignored otherwise Color.cpp, line 142: Error: The function realloc must have a prototype. Color.cpp, line 159: Error: The function realloc must have a prototype. Color.cpp, line 160: Error: The function memcpy must have a prototype. Color.cpp, line 168: Error: The function free must have a prototype. Color.cpp, line 175: Error: The function realloc must have a prototype. Color.cpp, line 196: Error: The function realloc must have a prototype. Color.cpp, line 247: Error: The function realloc must have a prototype. 7 Error(s) detected. *** Error code 7 make: Fatal error: Command failed for target `Color.o' ERROR: compilation failed for package 'rgl' ** Removing '/export/home/choid/bin/R2.2.1/lib/R/library/rgl' The downloaded packages are in /tmp/Rtmp9Yaawc/downloaded_packages [[alternative HTML 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RHOME
R-help
My thanks goes out to all who responded to this. I am tying to avoid
burdening the sysadmin with this project so I opted for the simple fix of
modifying the shell script. My aim here is to build the libraries in my
local directory and copy those as needed to /usr/local/lib/R/library. I will
have to direct the sysadmin in the installation of future versions of R.
Cheers,
Dan
Daniel A. Powers, Ph.D.
Department of Sociology
University of Texas at Austin
1 University Station A1700
Austin, TX 78712-0118
phone: 512-232-6335
fax: 512-471-1748
[EMAIL PROTECTED]
-Original Message-
From: Martyn Plummer [mailto:[EMAIL PROTECTED]
Sent: Friday, February 03, 2006 9:46 AM
To: Peter Dalgaard
Cc: Martin Maechler; Daniel A. Powers; r-help@stat.math.ethz.ch
Subject: Re: [R] RHOME
Far be it for me to tell people what they can and cannot do. Perhaps I
can rephrase myself in a less inflammatory way.
R runs from the build directory as a convenience for developers, so you
don't have to reinstall R every time you change something. But for
users, the standard mechanism make install has a number of advantages
over moving the build directory to a publicly accessible location: it is
guaranteed to work, you don't have to do any post-hoc editing of files,
it takes up a lot less space, about 4.6 times less on my system
[EMAIL PROTECTED] r-devel]$ du -sh R
356MR
[EMAIL PROTECTED] r-devel]$ du -sh /usr/local/lib64/R
77M /usr/local/lib64/R
But if you do want to copy the build directory the, as Martin says,
you can edit the file bin/R so that the line that starts
R_HOME_DIR points to the correct location, e.g.
R_HOME_DIR=/usr/local/lib/R
M.
On Fri, 2006-02-03 at 14:48 +0100, Peter Dalgaard wrote:
Martin Maechler [EMAIL PROTECTED] writes:
Martyn R is designed to run from its build directory. But
Martyn if your sysadmin installs it with make install (as
Martyn root), then the shell wrapper that is installed in
Martyn /usr/local/bin/R will have R_HOME pointing to the
Martyn right location (/usr/local/lib/R). Literally moving
Martyn the build directory to another location is the wrong
Martyn thing to do.
well, but very easily fixable, and that's what Daniel is asking
for:
The default value of R_HOME is only set in exactly one place,
namely the 'R' shell script; editing that script - once after
the move - is really a piece o'cake.
Hmm, I was about to say the same, but there seems to be unexpected
references in other places.
find `R RHOME` | xargs grep `R RHOME`
/usr/lib64/R/bin/R:R_HOME_DIR=/usr/lib64/R
/usr/lib64/R/bin/R:R_SHARE_DIR=/usr/lib64/R/share
/usr/lib64/R/bin/R:R_INCLUDE_DIR=/usr/lib64/R/include
/usr/lib64/R/bin/R:R_DOC_DIR=/usr/lib64/R/doc
(this doesn't normally happen - a SUSE RPM specialty, or due to
configure flag settings?)
I think this is normal. But the RedHat RPM behaves differently.
(because the RPM build process installs into a temporary build root
which is distinct from the final installation directory, requiring more
sed voodoo).
Once you start building packages, you also have things like
viggo:~/find ~/Rlibrary | xargs grep `R RHOME`
Binary file /home/bs/pd/Rlibrary/rgl/libs/rgl.so matches
viggo:~/find ~/Rlibrary | xargs grep Rlibrary
Binary file /home/bs/pd/Rlibrary/rgl/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/ISwR/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/mvtnorm/Meta/hsearch.rds matches
Binary file /home/bs/pd/Rlibrary/nlmeODE/Meta/hsearch.rds matches
B.
on my laptop I had a hit on one of the Sweave support files too.
Most likely these are quite harmless, but all in all I think Martyn
has the safest advice: Use make install, as root (don't forget
umask 022).
---
This message and its attachments are strictly confidential. ...{{dropped}}
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Re: [R] weights argument in the lmer function in lme4
I agree: The lmer weights argument seems not to have any effect. To check this, I modified the first example in the lmer documentation as follows: Sleep - sleepstudy Sleep$wts - 1:180 (fm1 - lmer(Reaction ~ Days + (Days|Subject), Sleep)) (fm1w - lmer(Reaction ~ Days + (Days|Subject), weights=wts, Sleep)) The numbers from both seemed to be the same. To try to help diagnose this, I listed lmer, and found that it consisted of a call to standardGeneric. Then 'getMethods(lmer)' listed only one method for the case where the argument formula had class formula. I tried to trace this further, e.g., by giving it a different name and using debug. After being stopped a couple of time by functions hidden in the Matrix namespace, I gave ups. However, at least you know that it's not you. And I've included Doug Bates as a cc so he can use this info as he sees fit. hope this helps. spencer graves sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: lme4 latticeMatrix 0.995-2 0.12-11 0.995-4 Patrick Connolly wrote: I suspect the weights argument is not having any effect. Package: Matrix Version: 0.995-2 Date: 2006-01-19 Beginning with this: Browse[1] resp.lmer - lmer(SensSSC ~ Block + Season + (1 | Plot) + (1 | Ma) + (1 | Pa) + + (1 | MaPa), weights = SensSSC.N, data = xx) I group the output into a table with my ran.eff function and get this: Browse[1] ran.eff(resp.lmer) 01 02 03 04 05 06 07 GCAf RankF A 13.714 13.709 13.886 14.124 15.120 13.546 14.586 0.472 1 B 13.452 NA 13.426 13.632 14.439 13.512 13.713 0.069 3 C 13.922 13.770 14.353 NA 14.661 13.529 14.367 0.453 2 D NA NA 13.353 NA NA NA NA -0.051 4 E 12.775 12.767 12.823 12.767 14.036 12.631 13.645 -0.495 6 F 13.043 13.338 12.641 12.977 13.848 12.425 13.530 -0.448 5 GCAm -0.200 -0.169 -0.165 -0.103 0.736 -0.428 0.329 NANA RankM 6.000 5.000 4.000 3.000 1.000 7.000 2.000 NANA Despite any shortcomings in my ran.eff function, those values look alright, but they're the same (to any number of decimal places) as I'd get without a weights argument. Just to check that the weights really don't effect it, I tried using only the rows with a weight of 5 (almost 90% of the data) but it was substantially different. Browse[1] resp.lmer5 - lmer(SensSSC ~ Block + Season + (1 | Plot) + (1 | Ma) + (1 | Pa) + + (1 | MaPa), subset = SensSSC.N == 5, data = xx) Browse[1] ran.eff(resp.lmer5) 01 02 03 04 05 06 07 GCAf RankF A 13.435 13.349 13.595 13.914 14.722 13.161 14.414 0.345 2 B 13.068 NA 13.110 13.447 14.121 13.296 13.637 -0.014 4 C 13.702 13.537 14.256 NA 14.371 13.575 14.247 0.469 1 D NA NA 13.276 NA NA NA NA -0.001 3 E 12.717 12.659 12.786 12.719 13.642 12.659 13.556 -0.425 6 F 13.015 13.101 12.549 12.920 13.629 12.438 13.474 -0.374 5 GCAm -0.210 -0.230 -0.146 -0.049 0.596 -0.353 0.391 NANA RankM 5.000 6.000 4.000 3.000 1.000 7.000 2.000 NANA That seems to indicate that weights cannot be readily ignored. Has anyone had experience to indicate that the weights argument does produce a difference, and so I should be looking somewhere else for the reason why I'm getting such results? TIA __ 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] Density estimation with monotonic constaints
There are multiple functions for density estimation in R, but I don't
know of any for estimating a monotonically decreasing density. If you
haven't already, I encourage you to use, e.g., the help.search and
RSiteSearch functions to find and explore their capabililties.
Why do you ask? Are you interested in analyzing particular data
set(s) or are you doing research on density estimation?
If it were my problem, I might just try something like the function
density and then evaluate the results to find out if it satisfied my
constraints. If it did and if I were only interested in that data set,
I'd be done. If not, I'd increase the smoothing until I got something
that was monotonic. If I wanted a more general method, I might wrap a
call to a function like density inside another function, and
automatically adjust the smoothing until it satisfied some optimality
criterion I might devise. If I didn't get what I wanted doing that, I
might list, e.g., the density function and walk through it line by
line until I figured out what I needed to change to get what I wanted.
I just listed density and found that it consists solely of a call to
UseMethod. To get beyond that, I tried 'methods(density), which
told me there was only one method called density.default. Then
requesting density.default gave me the code for that. Another tip: I
find debug extrememly helpeful for walking through code like this.
I suspect this will not solve your problem, but I hope at least it
helps. If you'd like further assistance from this listserve, please
submit another post. However, I encourage you first to PLEASE do read
the posting guide! www.R-project.org/posting-guide.html. Doing so
might increase your chances for getting useful information more quickly.
spencer graves
Debayan Datta wrote:
Hi All,
I have a sample x={x1,x2,..,xn} fom a distribution with density f. I
wish to estimate the density. I know a priori that the density is
monotonically decreasing. Is there a way to do this in R?
Thanks
Debayan
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Re: [R] output hessian matrix in constrOptim
The documentation for constrOptim says it has a ... argument,
which can contain Other arguments passed to 'optim', which will pass
them to 'f' and 'grad' if it does not used them. I routinely get an
estimated hessian from 'optim' just by specifying the argument
'hessian=TRUE'. This led me to try the following
# an example from 'constrOptim' that works:
fQP - function(b) {-sum(c(0,5,0)*b)+0.5*sum(b*b)}
Amat - matrix(c(-4,-3,0,2,1,0,0,-2,1),3,3)
bvec - c(-8,2,0)
constrOptim(c(2,-1,-1), fQP, NULL, ui=t(Amat),ci=bvec)
# The following generated an error:
constrOptim(c(2,-1,-1), fQP, NULL, ui=t(Amat),ci=bvec,
hessian=TRUE)
Error in f(theta, ...) : unused argument(s) (hessian ...)
If it were my problem, I might first try 'fit - constrOptim(...)'.
Then if the optimum was NOT at a constraint, I'd use the outpt from
'constrOptim' as an input to optim with 'hessian=TRUE'. If it was at
a constraint, I'd have to think very carefully about what I wanted in
terms of a hessian, because that does not seem obvious to me at the
moment. Then I'd program something to get that. If I wanted more than
that, I'd list 'constrOptim' and / or 'optim', and walk through them
line by line using debug until I figured out what I wanted to do next.
If you'd like more help from this listserve, please submit another
post -- but first, PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html.
hope this helps,
spencer graves
liu wrote:
Hi,
Is there any way to get the hessian matrix from the constrOptim
function without supplying gradient function? Thanks.
-
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[R] RUnit - need advice on a good directory structure or tips...
I made my own RUnit testing convention, and I want to introduce this to one
of my friends.
Before that, I'd like to review my codes.
The problem that I met when I tried to polish my codes is: How can I get the
file path in the file???
I.e., I want to get the path to the file that I'm writing using some magic R
functions. But I couldn't find any good magic.
Is there any magic?
So, I made a convention.
1. Put both testr files and suite...r files in the same directory.
2. Current working path should be the same directory as that of test files.
3. In test files, use .setUp and .tearDown functions to properly modify
current working directory.
4. 'source' the source codes to test them.
This is pretty much restriction, and I want to reduce the number of
restrictions.
More specifically, if the function defineTestSuite support optionally
setting current working directory to that of test files, it would be great
help, because it can remove the need of placing both test files and suite
files in the same directory.
But the best solution is the way to get the path to the file of the current
file.
BTW, here is an example. I welcome any kind of advice.
==
There are three files. Two are in the tests
directory(suite_foo.r test_foo.r), and the other one is in the codes
directory (foo.r).
In your R prompt, do setwd(path to test directory) and then do
source(suite_foo.r) to run tests.
==
##
## ../tests/test_foo.r
##
## A test file sample.
##
## Restrictions.
##Because of current directory problem, here I suggest convention.
##
##1. The testSuite files and test files should be in the same directory
like this example.
##
##2. Always include the following five objects in your own test file
##as it is shown in this example and modify them as you want.
## (- pathToCode, codeFileName, currentPath, .setUp, .tearDown)
##
##3. Then, properly change the pathToCode and the codeFileName.
##You can add your own codes to .setUP and .tearDown.
##
##4. Use one test file for each code file. This is a good practice.
##
##
pathToCode - ../codes## relative path to code directory.
codeFileName - foo.r ## code file name in 'pathToCode' directory
currentPath - getwd()
.setUp - function() { ## called before each test case. Add your own codes.
setwd(paste(currentPath,pathToCode,sep=/))
source(codeFileName)
print(.setUp)
}
.tearDown - function() { ## called before each test case. Add your own
codes.
setwd(currentPath)
print(.tearDown)
}
##
##
## Start of test functions.
##
## Add your own test functions with names starting with test
##
##
test.c2f - function() {
# print(currentPath)
checkEquals(c2f(0), 32)
checkEquals(c2f(10), 50)
checkException(c2f(xx))
}
test.f2c - function() {
checkEquals(f2c(32), 0)
checkEquals(f2c(50), 10)
checkTrue(identical(f2c(50),10))
checkException(f2c(xx))
}
test.errordemo - function() {
DEACTIVATED(Fanta long star king)
stop(this is just to show what an error looks like as opposed to a
failure)
}
==
##
## ../tests/suite_foo.r
##
## A testSuite file sample
##
## Restrictions.
##Because of current directory problem, here I suggest convention.
##
##1. A testSuite file should be in the same directory as that of test
files.
##
##2. A testSuite file should be sourced (or executed)
##ONLY WHEN the 'current working directory' of R is in that of the
restSuite file.
##
##3. The name of a testSuite file must start with 'suite', not 'test'.
##
##
library(RUnit)
suite_foo - defineTestSuite(foo,
dirs = .,
testFileRegexp = ^test.+\\.r,
testFuncRegexp = ^test.+
)
result_foo - runTestSuite(suite_foo)
printTextProtocol(result_foo)
## printHTMLProtocol(result_foo, fileName=result_foo.html)
## runTestFile(test_foo.r)
==
##
## ../codes/foo.r
##
## A code file sample
##
##
## centigrade to fahrenheit
c2f - function(a) return(9/5 * a + 32)
## fahrenheit to centigrade
f2c - function(f) return(5/9 * (f - 32))
=
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