Re: [R] socket clusters on snow dies easily
On Thu, Apr 08, 2004 at 11:18:43AM -0500, Luke Tierney wrote: If you absolutely have to use the socket approach you will probably have to track down the particular reason for this failure in your environment by looking at what is going on under the hood and checking the pieces. The master sets up a server socket, the slave noted connect to that socket, and for some reason the first read on that connection seems to be failing. It could be a timing issues--you may need to adjust socket timeouts, it could be a permission or firewall issue; hard to tell without experimenting. You are probably better off using the PVM version if at all possible. Overall it more solid than the socket version and likely to have fewer issues. er, due to some historical reason, we want to use socket instead of MPI or PVM. My friend and I will trace the socket code and see how to solve this problem. If there is anything new, i'll post here. Regards, Rong-En Fan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] bootstrap function coefficients
Dear R community,
Please, can you help me with a problem concerning bootstrap. The data table
called «RMika», contained times (Tps) and corresponding concentration of a
chemical in a soil (SolA). I would like to get, by bootstraping, 10
estimations of the parameters C0 and k from the function: SolA =
C0*exp(-k*Tps).
# First, I fit the data and all is OK
tabMika-read.delim(RMika.txt)
library(nls)
attach(tabMika)
Expon-function(Tps,parm){
+ C0-parm[1]
+ k-parm[2]
+ }
DegSA.nls-nls(SolA~C0*exp(-k*Tps),start=c(C0=35, k=1),tabMika)
summary(DegSA.nls)
Formula: SolA ~ C0 * exp(-k * Tps)
Parameters:
Estimate Std. Error t value Pr(|t|)
C0 25.682104 1.092113 23.52 2e-16 ***
k 0.087356 0.007582 11.52 6.36e-13 ***
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
Residual standard error: 2.584 on 32 degrees of freedom
Correlation of Parameter Estimates:
C0
k 0.7101
# Second, I try to use bootstrap to get the 10 estimates of k and C0
library(bootstrap)
theta-function(tabMika){coef(eval(DegSA.nls$call))}
bootSolA.nls-bootstrap(tabMika,10,theta)
Warning message:
multi-argument returns are deprecated in: return(thetastar, func.thetastar,
jack.boot.val, jack.boot.se,
bootSolA.nls
$thetastar
[,1][,2][,3][,4][,5][,6]
C0 25.68210358 25.68210358 25.68210358 25.68210358 25.68210358 25.68210358
k 0.08735615 0.08735615 0.08735615 0.08735615 0.08735615 0.08735615
[,7][,8][,9] [,10]
C0 25.68210358 25.68210358 25.68210358 25.68210358
k 0.08735615 0.08735615 0.08735615 0.08735615
# As you can notify, the 10 estimations have the same values for C0 and k.
Moreover, this correspond to the values of k and C0 determined by fitting
all the data without bootstrap!!!???
I cannot find what is wrong. Please, if you find a solution, thank you to
send it to me.
Sincerely
Michael Coeurdassier
Michaël COEURDASSIER, PhD
Department of Environmental Biology
UC INRA EA3184MRT
Institute for Environmental Sciences and Technology
University of Franche-Comte
Place Leclerc
25030 Besançon cedex
FRANCE
Tel : +33 (0)381 665 741
Fax : +33 (0)381 665 797
[EMAIL PROTECTED]: [EMAIL PROTECTED]
http://lbe.univ-fcomte.fr/
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[R] generating 00Index.html
Hi, I've started to create the documentation of my package. I've generate a pdf and the different html files from .Rd files. However I don't know how to automatically generate the 00Index.html. Do I have to write one in latex style and convert it or can I use the CONTENTS, INDEX, or Rd files. Thanks Nolwenn Nolwenn Le Meur INSERM U533 Faculté de médecine 1, rue Gaston Veil 44035 Nantes Cedex 1 France Tel: (+33)-2-40-41-29-86 (office) (+33)-2-40-41-28-44 (secretary) Fax: (+33)-2-40-41-29-50 mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bootstrap function coefficients
Package bootstrap is ORPHANED (that is, unsupported by anyone). Do try
package boot instead.
10 is a very small number of bootstrap replications: I do suggest you try
100 or more.
On Fri, 9 Apr 2004, Michaël Coeurdassier wrote:
Dear R community,
Please, can you help me with a problem concerning bootstrap. The data table
called «RMika», contained times (Tps) and corresponding concentration of a
chemical in a soil (SolA). I would like to get, by bootstraping, 10
estimations of the parameters C0 and k from the function: SolA =
C0*exp(-k*Tps).
# First, I fit the data and all is OK
tabMika-read.delim(RMika.txt)
library(nls)
attach(tabMika)
Expon-function(Tps,parm){
+ C0-parm[1]
+ k-parm[2]
+ }
DegSA.nls-nls(SolA~C0*exp(-k*Tps),start=c(C0=35, k=1),tabMika)
summary(DegSA.nls)
Formula: SolA ~ C0 * exp(-k * Tps)
Parameters:
Estimate Std. Error t value Pr(|t|)
C0 25.682104 1.092113 23.52 2e-16 ***
k 0.087356 0.007582 11.52 6.36e-13 ***
---
Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1
Residual standard error: 2.584 on 32 degrees of freedom
Correlation of Parameter Estimates:
C0
k 0.7101
# Second, I try to use bootstrap to get the 10 estimates of k and C0
library(bootstrap)
theta-function(tabMika){coef(eval(DegSA.nls$call))}
bootSolA.nls-bootstrap(tabMika,10,theta)
Warning message:
multi-argument returns are deprecated in: return(thetastar, func.thetastar,
jack.boot.val, jack.boot.se,
bootSolA.nls
$thetastar
[,1][,2][,3][,4][,5][,6]
C0 25.68210358 25.68210358 25.68210358 25.68210358 25.68210358 25.68210358
k 0.08735615 0.08735615 0.08735615 0.08735615 0.08735615 0.08735615
[,7][,8][,9] [,10]
C0 25.68210358 25.68210358 25.68210358 25.68210358
k 0.08735615 0.08735615 0.08735615 0.08735615
# As you can notify, the 10 estimations have the same values for C0 and k.
Moreover, this correspond to the values of k and C0 determined by fitting
all the data without bootstrap!!!???
I cannot find what is wrong. Please, if you find a solution, thank you to
send it to me.
Sincerely
Michael Coeurdassier
--
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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Re: [R] generating 00Index.html
It happens automatically when you INSTALL the package sources ... sounds as if you are not actually doing that. On Fri, 9 Apr 2004, Nolwenn Le Meur wrote: I've started to create the documentation of my package. I've generate a pdf and the different html files from .Rd files. However I don't know how to automatically generate the 00Index.html. Do I have to write one in latex style and convert it or can I use the CONTENTS, INDEX, or Rd files. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nlme on Windows 2000 (v1.8.1)
See the rw-FAQ, specifically Q2.19. It is very likely some piece of rogue software on your machines. On Thu, 8 Apr 2004, Kent Holsinger wrote: I have a problem with nlme on Windows 2000, and I'm having a devil of a time determining whether the problem is with my computer or with something in R. I'm running v1.8.1 on a Dell Pentium III with 512MB of RAM and all of the recommended Windows 2000 updates applied. If I use Rterm, I can run analyses with NLME to my heart's content. But when I run Rgui, I encounter a floating point exception. To be concrete if I library(nlme) Loading required package: lattice data(Rail) lme(travel ~ 1, data = Rail, random = ~ 1 | Rail) (the first example in Pinheiro and Bates), R churns for a while and a window pops up informing me of an application error. Specifically, The exception Floating-point division by zero. (0xc08e) occurred in the application at location 0x639b50ff. There error occurs every time. The same analysis runs flawlessly in Rterm. To make it even stranger, I get the same error on a Toshiba Pentium laptop (also with 512MB of memory, although I haven't tried the analyses in Rterm on that machine). On that machine, I get a blue screen after acknowledging the error. The laptop is a dual boot on which I run Linux (Fedora Core 1). R works perfectly on it under Linux. I've downloaded and re-installed the binaries on both machines several times, so I don't think I have a corrupted download. Any ideas on how to diagnose (and solve) this problem would be greatly appreciated. Kent -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nlme on Windows 2000 (v1.8.1)
On Thu, 08 Apr 2004 08:03:56 -0400, you wrote: If I use Rterm, I can run analyses with NLME to my heart's content. But when I run Rgui, I encounter a floating point exception. I agree with Prof Ripley: I'd suspect video (or other) drivers messing up the floating point control word. Identifying the exact cause is quite hard, but you can probably confirm this by rebooting in safe mode (i.e. with minimal drivers loaded). You do this by hitting F8 during the boot sequence. R can run fine in safe mode; if you don't get the error, then it's pretty clearly one of the drivers that you usually load that is causing the trouble. Figuring out which one won't be easy... Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] %+=% and eval.parent()
On 7 Apr 2004, Peter Dalgaard wrote:
Robin Hankin [EMAIL PROTECTED] writes:
Hi again everybody.
Yesterday I had a problem with c-style += functions. One suggestion
was to define
R plus- - function(x,value){x+value}
Then
R a - matrix(1:9,3,3)
R plus(a[a%%2==1]) - 1000
works as desired.
QUESTION: why does this behave differently:
R plus- - function(x,y){x+y}
R a - matrix(1:9,3,3)
R plus(a[a%%2==1]) - 1000
Error in plus-(`*tmp*`, value = 1000) :
unused argument(s) (value ...)
R
The only change seems to be changing the second argument from value
to y. Why does this affect anything? Where do I look for
documentation on things like plus- ?
These assignment functions work basically by
plus(x) - foo
getting internally transcribed as
x - plus-(x, value=foo)
(actually, there's an intermediate alias for the target to avoid
multiple evaluation; this is what shows up as *tmp*, but you're not
supposed to know that...)
The use of the keyword matching form was prompted by some problems
with indexing functions that take a variable number of indices in
addition to x. (Think [-(x,i,value) vs. [-(x,i,j,value) and the
hoops you have to jump through when the value gets passed in the j
argument.) However, keyword matching of course implies that you need
to use the matching keyword in the function definition.
This *should* be somewhere in the R Language Definition, although I'm
not sure it is actually there. Or the blue book, although I suspect
that S v.3 actually used positional matching (and jumped through
hoops).
It did. This is in the FAQ, 3.2.3:
* In R, the argument of a replacement function which corresponds to the
right hand side must be named `value'. E.g., `f(a) - b' is evaluated
as `a - f-(a, value = b)'. S always takes the last argument,
irrespective of its name.
I seem to recall I discovered the discrepancy in ca 1998.
R-lang is minimalist about what it calls `assignment functions', most of
the time.
--
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] Question
Could you please help me. How can I get indexes of matrix elements equal to the specified value. Thanks in advance. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] looking for a tutorial on exception handling
Hi, I would like to learn how to do exception handling in R. I had a look at the help page for tryCatch and I am trying to understand it (I am sure it is well-written, but I have not used exception handling before in any language, so I have no experience in that area). Is there a tutorial or an introduction into exception handling in R with tryCatch friends? Preferably with lots of examples. It would be nice if there was one online, but references to books would also be appreciated. Thanks, Tamas -- Tamás K. Papp E-mail: [EMAIL PROTECTED] Please try to send only (latin-2) plain text, not HTML or other garbage. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R-estimators
Dear all, could you please suggest me the package I have to install in order to use ranks statistics in regression models (R-Estimators, wilcoxon scores ...) Thanks and Happy Easter Paolo Radaelli [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RODBC on FreeBSD 4.9
Hello. I have found a number of posts/threads on this subject and remain unsuccessful to determine the solution. In brief, my situation is: 1. Running FreeBSD 4.9 Stable in x86 2. Installed, and running, R 1.8.1 3. Installed, and running, postgreSQL 7.4.2 4. Installed, and running, unixODBC 2.2.8 5. Failed, repeatedly, to install RODBC. The following is my error log: tsunami# R CMD INSTALL RODBC * Installing *source* package 'RODBC' ... checking for gcc... gcc checking for C compiler default output... 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 for library containing SQLTables... no configure: error: no ODBC driver manager found ERROR: configuration failed for package 'RODBC' ** Removing '/usr/local/lib/R/library/RODBC' I have set up the DSN/databases using ODBCConfig, viewed/confirmed through DataManager and have even used isql to further confirm that all is set up correctly. I have read, numerous times, the README within RODBC. Unfortunately, I am out of ideas. Therefore, I am asking for ideas of others. Also, I found, and employed, the results from a previous post, https://stat.ethz.ch/pipermail/r-help/2001-October/014693.html, and reset my LIBS and LD_LIBRARY_PATH to those suggested by the author. Again, no joy. So, any thoughts, with successful ones perhaps resulting in an FAQ/how-to, would be most appreciated. (Also, please let me know what more info you may need to help and I will gladly provide it.) Charles [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] %+=% and eval.parent()
Prof Brian Ripley [EMAIL PROTECTED] writes: This *should* be somewhere in the R Language Definition, although I'm not sure it is actually there. Or the blue book, although I suspect that S v.3 actually used positional matching (and jumped through hoops). It did. This is in the FAQ, 3.2.3: * In R, the argument of a replacement function which corresponds to the right hand side must be named `value'. E.g., `f(a) - b' is evaluated as `a - f-(a, value = b)'. S always takes the last argument, irrespective of its name. I seem to recall I discovered the discrepancy in ca 1998. I seem to recall when we introduced it, and that it was deliberate. What I can't remember is what the occasion was. R-lang is minimalist about what it calls `assignment functions', most of the time. `replacement functions' would be correct terminology, right? - and - are the assignment functions. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nlme on Windows 2000 (v1.8.1)
Duncan Murdoch wrote: On Thu, 08 Apr 2004 08:03:56 -0400, you wrote: If I use Rterm, I can run analyses with NLME to my heart's content. But when I run Rgui, I encounter a floating point exception. You do this by hitting F8 during the boot sequence. R can run fine in safe mode; if you don't get the error, then it's pretty clearly one of the drivers that you usually load that is causing the trouble. Figuring out which one won't be easy... It *is* one of my drivers. NLME works fine in safe mode. If/when I manage to find the offending driver I'll report it to the list. Thanks to you and Dr. Ripley for the advice. (As I suspected, the fault lies in my computers, not R.) Kent -- Kent E. Holsinger[EMAIL PROTECTED] http://darwin.eeb.uconn.edu -- Department of Ecology Evolutionary Biology -- University of Connecticut, U-3043 -- Storrs, CT 06269-3043 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Cross-compiling packages for (ARM) Zaurus ideas and tips?
Hello All, A bit of a long one (background mainly), this is really just a request for some ideas. I ported R 1.7.x for use on the Sharp Zaurus ( iPAQ, simpad, yopy, etc.) some time ago and have just ported 1.8.1 but had never quite realised that you actually need to install some packages to make the system useful (I don't use R, I did it as a favour and of course for the fun of it). I use a GCC3.x cross compiler running on an x86 Linux box to do the compilation. Packaging programs after they have been cross-compiled is a pain in general (unfortunately you can't just run 'make install') but normally it only has to be done once. However for the packages it's a different matter, especially as I don't have enough space to host compiled packages for everyone to access and in any case there'll always be one that I've missed, etc. I'm thinking about creating a small native GCC for the Z (there are already some out there, but they need to be GCC 3.x and need g77 neither of which they currently have). My biggest concern here is that it'll use quite a lot of space just to be able to create R packages occasionally. The other method is for people to use a desktop cross compiler to compile and package the resulting libraries. To this end I've been looking at the INSTALL script in the hope of modifying it so that it will compile and then create a .ipk package file (subset of debian .deb file) which is the standard for the Zaurus. I've modified the INSTALL script quite heavily - to try and remove extraneous env vars and reduce the number of external scripts which are called, and to create the directory structure in a temp directory so I can package it up. After battling with sed (steep learning curve there) I temporarily gave up this morning trying to work out why shlib.mk can't be found (despite, probably because of, my alterations). What do people think, is this the best way to go about doing this? Would I be better starting from scratch? Has anyone tried making a cross-compiler package handling script before? I actually thought that the INSTALL script would be fairly simple (having seen the output when I INSTALLed a package on my desktop box) but it doesn't seem quite so simple while I'm wading through it. My gut feeling is that it probably is quite simple to do what I want (which is only a very small subset of what the INSTALL script can do) and it's just that there's so much extra in there. I was really just after a quick (and dirty?) script to get up and running as soon as possible. I presume the INSTALL script has developed from a more simple one? If so are there any old (simple) copies lying about anywhere or has the process changed? Sorry for the rambling, Cheers, Simon Simon Pickering MEng Research Officer Dept. of Engineering and Applied Science University of Bath Bath, BA2 7AY, UK Tel: +44 (0)1225 383314 Fax: +44 (0)1225 386928 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Question (on matrix indexes)
I am not sure what you mean but you might be interested in the functions row() and col(). Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc -- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ivan Yegorov Sent: Friday, April 09, 2004 1:56 PM To: [EMAIL PROTECTED] Subject: [R] Question Could you please help me. How can I get indexes of matrix elements equal to the specified value. Thanks in advance. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] loess' robustness weights in loess
hi! i want to change the robustness weights used by loess. these are described on page 316 of chambers and hastie's statistical models in S book as r_i = B(e_i,6m) where B is tukey's biweight function, e_i are the residulas, and m is the median average distance from 0 of the residuals. i want to change 6m to, say, 3m. is there a way to do this? i cant figure it out from the help files. thanks, rafael __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loess' robustness weights in loess
On Fri, 9 Apr 2004, Rafael A. Irizarry wrote: hi! i want to change the robustness weights used by loess. these are described on page 316 of chambers and hastie's statistical models in S book as r_i = B(e_i,6m) where B is tukey's biweight function, e_i are the residulas, and m is the median average distance from 0 of the residuals. i want to change 6m to, say, 3m. is there a way to do this? i cant figure it out from the help files. Well, they say loess in R is an interface to C/Fortran code, and not the same code as the S code described in Chambers Hastie. I translated the C driver routines to R for some added flexibility. At a quick look, in function simpleLoess() you will find the weights in object `robust', calculated by Fortran function lowesw. You could replace that by a call to an R-level alternative, or play with the Fortran source code. You'll have to do what I did way back, and read the source code to see how it works in detail. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] question regarding vector ops
Hi, I was playing with some code and came upon this situation. x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - 1:10 x[idx] - x[idx] + 1 x [1] 2 1 1 1 1 1 1 1 1 1 This is expected. But if I do: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(0,10) idx [1] 0 0 0 0 0 0 0 0 0 0 x[idx] - x[idx] +1 x [1] 1 0 0 0 0 0 0 0 0 0 I was expoecting that when all the elements of idx are set to 0, x[0] would become 11. Could somebody explain why this behavior occurs? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- A computer lets you make more mistakes faster than any other invention, with the possible exceptions of handguns and Tequilla. -- Mitch Ratcliffe __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question regarding vector ops
Rajarshi Guha wrote: Hi, I was playing with some code and came upon this situation. x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - 1:10 x[idx] - x[idx] + 1 x [1] 2 1 1 1 1 1 1 1 1 1 This is expected. But if I do: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(0,10) idx [1] 0 0 0 0 0 0 0 0 0 0 x[idx] - x[idx] +1 x [1] 1 0 0 0 0 0 0 0 0 0 I was expoecting that when all the elements of idx are set to 0, x[0] would become 11. Could somebody explain why this behavior occurs? Why do you expect anything to become 11? And what is x[0] in your expectation? x[0] is empty (indexing is starting from 1 in R) and returns numeric(0), hence x[0] - anything consequently does nothing ... (alternatively, one might expect an error message). Uwe Ligges Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- A computer lets you make more mistakes faster than any other invention, with the possible exceptions of handguns and Tequilla. -- Mitch Ratcliffe __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question regarding vector ops
On Fri, 2004-04-09 at 12:03, Rajarshi Guha wrote: Hi, I was playing with some code and came upon this situation. x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - 1:10 x[idx] - x[idx] + 1 x [1] 2 1 1 1 1 1 1 1 1 1 This is expected. But if I do: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(0,10) idx [1] 0 0 0 0 0 0 0 0 0 0 x[idx] - x[idx] +1 x [1] 1 0 0 0 0 0 0 0 0 0 Aah, I realize that the second code snippet is not supposed to work. What I meant was: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(1,10) idx [1] 1 1 1 1 1 1 1 1 1 1 x[idx] - x[idx] + 1 [1] 2 0 0 0 0 0 0 0 0 0 I expected that x would be [1] 11 0 0 0 0 0 0 0 0 0 Or am I thinking about it wrong? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Disembowelling takes guts. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question regarding vector ops
Rajarshi Guha wrote: On Fri, 2004-04-09 at 12:03, Rajarshi Guha wrote: Hi, I was playing with some code and came upon this situation. x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - 1:10 x[idx] - x[idx] + 1 x [1] 2 1 1 1 1 1 1 1 1 1 This is expected. But if I do: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(0,10) idx [1] 0 0 0 0 0 0 0 0 0 0 x[idx] - x[idx] +1 x [1] 1 0 0 0 0 0 0 0 0 0 Aah, I realize that the second code snippet is not supposed to work. What I meant was: x - c(1, rep(0,9)) x [1] 1 0 0 0 0 0 0 0 0 0 idx - rep(1,10) idx [1] 1 1 1 1 1 1 1 1 1 1 x[idx] - x[idx] + 1 [1] 2 0 0 0 0 0 0 0 0 0 I expected that x would be [1] 11 0 0 0 0 0 0 0 0 0 Or am I thinking about it wrong? Yes, you are wrong: You are indexing 10 times the first value. Writing 10 times the same value 10 times into the same location does not sum it up. Consider x[idx] - 1:10 Then you are writing 1 into x[1], 2 into x[1], 3 into x[1], ... and finally 10 into x[1], hence at the end x[1] is 10. Uwe Ligges Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Disembowelling takes guts. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] missing values for mda package
Thanks. I was able to use na.omit to remove NAs. But it seems to me this kills one of the advantages of the original algorithm for handling missing values. On Tue, 2004-04-06 at 11:54, Uwe Ligges wrote: zhu wang wrote: Dear helpers, I am trying to use the mda package downloaded from the R website, but the data set has missing values so I got an error message. Should I manually handle these missing values? I was trying to read the documents to specify any option related to missing values, but I did not find it. Please forgive me if I ignore something obvious. If it is not documented (hence probably not available) and you don't know how to tell the functions to handle missing values, try to do it yourself. ?NA suggests: See Also: [...] 'na.action', 'na.omit', 'na.fail' on how methods can be tuned to deal with missing values. Uwe Ligges Thanks, Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 Phone: (214)768-2453 Fax: (214)768-4035 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 Phone: (214)768-2453 Fax: (214)768-4035 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] rectangles without borders
Hi, I want to draw rectangles with rect without borders, but with shading (ie setting density). ?rect says lty: line type for borders; defaults to 'solid'. but if I set it to 0, the border disappears, but the shading also vanishes! But the above says that lty is the line type for BORDERS, and does not mention density at all -- how do I get around this? Thanks, Tamas -- Tamás K. Papp E-mail: [EMAIL PROTECTED] Please try to send only (latin-2) plain text, not HTML or other garbage. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] missing values for mda package
Package mda covers many things, including bruto, mars, polyreg and mda itself. Which `the original algorithm' for which option did you have in mind? More concretely, what where you trying to do with the package? Given that the package is the original authors' own code, it seems unlikely that they `killed one of the advantages' of their methodology, so elucidation is sorely needed. On 9 Apr 2004, zhu wang wrote: Thanks. I was able to use na.omit to remove NAs. But it seems to me this kills one of the advantages of the original algorithm for handling missing values. On Tue, 2004-04-06 at 11:54, Uwe Ligges wrote: zhu wang wrote: Dear helpers, I am trying to use the mda package downloaded from the R website, but the data set has missing values so I got an error message. Should I manually handle these missing values? I was trying to read the documents to specify any option related to missing values, but I did not find it. Please forgive me if I ignore something obvious. If it is not documented (hence probably not available) and you don't know how to tell the functions to handle missing values, try to do it yourself. ?NA suggests: See Also: [...] 'na.action', 'na.omit', 'na.fail' on how methods can be tuned to deal with missing values. Uwe Ligges Thanks, Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 Phone: (214)768-2453 Fax: (214)768-4035 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rectangles without borders
The person who added shading did not update the help page for rect Try border=FALSE (and look at ?polygon for more details as to why). On Fri, 9 Apr 2004, Tamas Papp wrote: Hi, I want to draw rectangles with rect without borders, but with shading (ie setting density). ?rect says lty: line type for borders; defaults to 'solid'. but if I set it to 0, the border disappears, but the shading also vanishes! But the above says that lty is the line type for BORDERS, and does not mention density at all -- how do I get around this? Thanks, Tamas -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] missing values for mda package
I basically wanted to use MARS to reproduce results using the dataset Marketing in the following book http://www-stat-class.stanford.edu/~tibs/ElemStatLearn/ The authors actually provided S-Plus functions for mars, bruto ,etc. I used all default options of mars in R but there was an error due to NAs and I could not find any option to handle missing values. Zhu Wang -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Fri 4/9/2004 12:53 PM To: Wang, Zhu Cc: Uwe Ligges; [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject:Re: [R] missing values for mda package Package mda covers many things, including bruto, mars, polyreg and mda itself. Which `the original algorithm' for which option did you have in mind? More concretely, what where you trying to do with the package? Given that the package is the original authors' own code, it seems unlikely that they `killed one of the advantages' of their methodology, so elucidation is sorely needed. On 9 Apr 2004, zhu wang wrote: Thanks. I was able to use na.omit to remove NAs. But it seems to me this kills one of the advantages of the original algorithm for handling missing values. On Tue, 2004-04-06 at 11:54, Uwe Ligges wrote: zhu wang wrote: Dear helpers, I am trying to use the mda package downloaded from the R website, but the data set has missing values so I got an error message. Should I manually handle these missing values? I was trying to read the documents to specify any option related to missing values, but I did not find it. Please forgive me if I ignore something obvious. If it is not documented (hence probably not available) and you don't know how to tell the functions to handle missing values, try to do it yourself. ?NA suggests: See Also: [...] 'na.action', 'na.omit', 'na.fail' on how methods can be tuned to deal with missing values. Uwe Ligges Thanks, Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 Phone: (214)768-2453 Fax: (214)768-4035 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] missing values for MARS (was mda package)
On Fri, 9 Apr 2004, Wang, Zhu wrote: I basically wanted to use MARS to reproduce results using the dataset Marketing in the following book http://www-stat-class.stanford.edu/~tibs/ElemStatLearn/ The authors actually provided S-Plus functions for mars, bruto ,etc. I used all default options of mars in R but there was an error due to NAs and I could not find any option to handle missing values. Friedman originated MARS and has code for it. The code in mda by Hastie/Tibshirani is different, and the code on that website is a direct ancestor of the mda package for R. I see no option in the code for mars there to handle missing values, so you would do better to ask the authors how they did it (if you really believe they have such an option). And PLEASE read the posting guide and try to learn to ask precise questions with enough background information! -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Pfizer - Open position for Statistician - emphasis computational statistics
All:
The Nonclinical Statistics Group at Pfizer Inc., New London, CT, is
currently seeking a Statistician with an interest and experience in
computational statistics.
Please use the following link for more information and application
information:
If Interested please apply on-line at www.pfizer.com/are/careers/index.html
http://www.pfizer.com/are/careers/index.html and search for Job#
29Mar0428519.
Peg Romansky
PGRD
Staffing - Development
A2148 - NL
860-732-9675
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
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[R] Regression models w/ splines
Hi - I am fitting various Cox PH models with spline predictors. After fitting the model, I would like to use termplot() to examine the functional form of the fitted model (e.g., to obtain a plot of the relative risk (or log r.r.) versus the predictors). When there is only 1 predictor in the model, termplot returns a ?. In this case, I have not been able to figure out how to create the desired plot. Otherwise,termplot is easy to use. Example: library(survival) library(splines) data(pbc) fit1-coxph(Surv(time,status)~ns(bili,4)+ns(age,4), data=pbc) fit2-coxph(Surv(time,status)~ns(bili,4), data=pbc) par(mfrow=c(2,2)) termplot(fit1) # returns two plots (one for bili and one for age) termplot(fit2) # returns a ? prompt Does anyone have any suggestions for obtaining a plot of the log relative risk as a function of bili in the second example (or for this type of model in general)? On a similar note, I would like to be able to obtain predicted values for new subjects. I tried using: temp-data.frame(bili=0.8) predict(fit2,newdata=temp, safe=T) This gives the following error message: Error in qr(t(const)) : NA/NaN/Inf in foreign function call (arg 1) Is there a simple method available for obtaining predicted values for new subjects when using these types of models? I have encountered similar problems when trying to use smoothing splines w/ the above examples (i.e., 'pspline' in the survival package). I am currently using R version 1.8.1 for windows. Any help would be greatly appreciated! John John Fieberg, Ph.D. Wildlife Biometrician, MN DNR 5463-C W. Broadway Forest Lake, MN 55434 Phone: (651) 296-2704 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Regression models w/ splines
John Fieberg [EMAIL PROTECTED] writes: Hi - I am fitting various Cox PH models with spline predictors. After fitting the model, I would like to use termplot() to examine the functional form of the fitted model (e.g., to obtain a plot of the relative risk (or log r.r.) versus the predictors). When there is only 1 predictor in the model, termplot returns a ?. In this case, I have not been able to figure out how to create the desired plot. Otherwise,termplot is easy to use. Kasper Hansen and Per Jensen from my department reported this recently, AFAIR with a suggested fix. You might want to go over the archives for the last month or so. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] von Mises
Dear All, I am trying to plot von Mises density on the circle. One can use dvm function from the CircStats package, by giving a set of angles, mu and kappa to plot the circular density on the line. Does any one have a macro that does it on the circle? These plots are displayed in Nick Fisher's book. Any help will be appreciated. Thanks, G. Subramaniam __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Regression models w/ splines
On Fri, 09 Apr 2004 15:16:34 -0500 John Fieberg [EMAIL PROTECTED] wrote: Hi - I am fitting various Cox PH models with spline predictors. After fitting the model, I would like to use termplot() to examine the functional form of the fitted model (e.g., to obtain a plot of the relative risk (or log r.r.) versus the predictors). This kind of application is why the Design package was created. It is very easy to obtain such plots: library(Design) dd - datadist(mydata); options(datadist='dd') f - cph(Surv(y,d) ~ sex*rcs(age,4)+rcs(bp,5)) plot(f, age=NA, sex='female') --- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] adding text in (pair) panels (splom)
Hi,
I would like to add text in each panel got from the following:
splom(~Cs5bis,
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
This could be a correlation coefficient or the statistical significance of the
correlation or both, or a star if p 0.05, etc...
The function text() is useless (probably because I cannot pass appropriates
coordinates in each panel). Googling the R-archives, I
have found only one hint of Andy Liaw relating a rather complex (to me) script within
a home-made panel.myfitline() function.
Is there a simple way to add text in panels created eg with:
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
?
Any hint appreciated,
Patrick Giraudoux
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Re: [R] adding text in (pair) panels (splom)
Hi
Patrick Giraudoux wrote:
Hi,
I would like to add text in each panel got from the following:
splom(~Cs5bis,
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
This could be a correlation coefficient or the statistical significance of the
correlation or both, or a star if p 0.05, etc...
The function text() is useless (probably because I cannot pass appropriates
coordinates in each panel). Googling the R-archives, I
have found only one hint of Andy Liaw relating a rather complex (to me) script within
a home-made panel.myfitline() function.
Is there a simple way to add text in panels created eg with:
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
text() is useless because splom is a lattice function and lattice is
based on grid. To add text in a panel you could use lattice's ltext(),
but I think the best way would be to use grid.text() as below. This
example draws the correlation coefficient 1mm in from the top-left
corner of the panel.
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
grid.text(round(cor(x, y), 2),
x=unit(1, mm), y=unit(1, npc) - unit(1, mm),
just=c(left, top))
})
Does that do what you want?
Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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Re: [R] adding text in (pair) panels (splom)
OK Paul and Kjetil
I understand that grid.text is part of the library grid. I have tried with Paul's
arguments. It works perfectly well.
Thanks a lot both,
Patrick
- Original Message -
From: Paul Murrell [EMAIL PROTECTED]
To: Patrick Giraudoux [EMAIL PROTECTED]
Cc: r-help [EMAIL PROTECTED]
Sent: Saturday, April 10, 2004 4:39 AM
Subject: Re: [R] adding text in (pair) panels (splom)
Hi
Patrick Giraudoux wrote:
Hi,
I would like to add text in each panel got from the following:
splom(~Cs5bis,
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
This could be a correlation coefficient or the statistical significance of the
correlation or both, or a star if p 0.05,
etc...
The function text() is useless (probably because I cannot pass appropriates
coordinates in each panel). Googling the R-archives,
I
have found only one hint of Andy Liaw relating a rather complex (to me) script
within a home-made panel.myfitline() function.
Is there a simple way to add text in panels created eg with:
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
})
text() is useless because splom is a lattice function and lattice is
based on grid. To add text in a panel you could use lattice's ltext(),
but I think the best way would be to use grid.text() as below. This
example draws the correlation coefficient 1mm in from the top-left
corner of the panel.
panel=function(x,y,...){
panel.xyplot(x,y,...)
panel.abline(lm(y~x),...)
grid.text(round(cor(x, y), 2),
x=unit(1, mm), y=unit(1, npc) - unit(1, mm),
just=c(left, top))
})
Does that do what you want?
Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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[R] Density Estimation
Dear Sir/Madam; Would you please tell me what is the command that allows the estimation of the Kernel Density for some data. Thanks, Thami Rachidi [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Density Estimation
-Original Message- From: [EMAIL PROTECTED] Dear Sir/Madam; Would you please tell me what is the command that allows the estimation of the Kernel Density for some data. Thanks, ?density __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
