[R] problem downloading Red Hat R-1.7.1-1.i386.rpm
System info: Red Hat 9.0 R Version 1.7.0 ESS 5.1.21 Emacs 21.2.1 --- Colleagues At work I've had to migrate from Mandrake 9.1 to Red Hat 9.0 and I'm reinstalling R. I am having a problem downloading from R-1.7.1-1.i386.rpm from /bin/linux/redhat/9/i386. Basically the download does not complete. I am using mozilla, and when I click on the link the screen corrupts with odd symbols. Is there a problem with the site? (I don't have any problem downloading the user-contributed packages or the R-1.7.1.tgz. Sam -- Sam McClatchie, Research scientist (fisheries acoustics)) NIWA (National Institute of Water Atmospheric Research Ltd) PO Box 14 901, Kilbirnie, Wellington, New Zealand [EMAIL PROTECTED] Research home page http://www.smcc.150m.com/ /\ xX( /// \\\ /// %)Xx / \\ (((@ (((% ..xX(?O?)Xx __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] problem downloading Red Hat R-1.7.1-1.i386.rpm
Sam McClatchie [EMAIL PROTECTED] writes: System info: Red Hat 9.0 R Version 1.7.0 ESS 5.1.21 Emacs 21.2.1 --- Colleagues At work I've had to migrate from Mandrake 9.1 to Red Hat 9.0 and I'm reinstalling R. I am having a problem downloading from R-1.7.1-1.i386.rpm from /bin/linux/redhat/9/i386. Basically the download does not complete. I am using mozilla, and when I click on the link the screen corrupts with odd symbols. Is there a problem with the site? (I don't have any problem downloading the user-contributed packages or the R-1.7.1.tgz. Sam Mozilla gets confused about the .rpm ending I think. Just use Shift-Button1 to download, or right-click, save target as... -- 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
Re: [R] problem downloading Red Hat R-1.7.1-1.i386.rpm
*right* click the link and then left click Save Target As (or something similar. Arne On Wednesday 01 October 2003 08:31, Sam McClatchie wrote: System info: Red Hat 9.0 R Version 1.7.0 ESS 5.1.21 Emacs 21.2.1 --- Colleagues At work I've had to migrate from Mandrake 9.1 to Red Hat 9.0 and I'm reinstalling R. I am having a problem downloading from R-1.7.1-1.i386.rpm from /bin/linux/redhat/9/i386. Basically the download does not complete. I am using mozilla, and when I click on the link the screen corrupts with odd symbols. Is there a problem with the site? (I don't have any problem downloading the user-contributed packages or the R-1.7.1.tgz. Sam -- Arne Henningsen Department of Agricultural Economics Christian-Albrechts-University Kiel 24098 Kiel, Germany Tel: +49-431-880-4445 Fax: +49-431-880-1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] installing DBI_0.1-6.tar.gz
Dear,
I tried to install the DBI package in R-1.7.1, but this gave the
following error:
/volume1/scratch/jallemee/R/lib/R/bin/INSTALL: line 1: 1856
Done( echo
options(save.image.defaults=${save_image_defaults}); if test
-s R_PROFILE.R; then
cat R_PROFILE.R;
fi; echo invisible(.libPaths(c(\${lib}\, .libPaths(; cat
${R_PACKAGE_DIR}/R/${pkg} )
1857 Segmentation fault | ${R_EXE} --slave --save
${save_args}
ERROR: execution of package source for 'DBI' failed
Can somebody help me?
Thanks a lot,
Kind regards,
Joke.
Joke Allemeersch
Kasteelpark Arenberg 10
3001 Heverlee (Leuven)
http://www.esat.kuleuven.ac.be/~dna/BioI/
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Re: [R] truncating axis
Diego Riano wrote: Hello Does anyone know how to truncate and axis in R? Not sure what you mean, but do to plot arguments xlim and ylim do what you want? See help(par) for these and other plot controls. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] truncating axis
On 1 Oct 2003, Diego Riano wrote: Does anyone know how to truncate and axis in R? What do you mean by truncate? Do you mean to change the range of the axes? If so then something like plot(x, xlim = range(), ylim = range()) should do (just put the desired range -- Cheers, Kevin -- On two occasions, I have been asked [by members of Parliament], 'Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?' I am not able to rightly apprehend the kind of confusion of ideas that could provoke such a question. -- Charles Babbage (1791-1871) From Computer Stupidities: http://rinkworks.com/stupid/ -- Ko-Kang Kevin Wang Master of Science (MSc) Student SLC Tutor and Lab Demonstrator Department of Statistics University of Auckland New Zealand Homepage: http://www.stat.auckland.ac.nz/~kwan022 Ph: 373-7599 x88475 (City) x88480 (Tamaki) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] FW: error predicting values from the LME
Thanks for the hint. And it's a general one I intend to use more often. I managed to sort out the problem proceeding with the simpler models first and getting to more komplex ones. Even the one I presented in my question suddenly worked. However I think I found the problem, but I'm unable to solve it. With the problematic prediction I used the prespecified model using the as.formula. This is my exapmle: # first way m.gr-as.formula(y ~ v11+v21+v22+v23 | inter) m.fix-as.formula(y ~ v11+v21+v22+v23+v21:v11+v22:v11+v23:v11) m.ran-as.formula(~ v11 | inter) d.n.gr.1-grouped.data(m.gr data=d.n) m.1-lme(m.fix, random=m.ran, data=d.n.gr.1, na.action=na.omit) dnNew-subset(d.n,is.na(d.n$y),select=c(v11,v21,v22,v23,inter)) p.1-predict(m.1,dnNew) # second way d.n.gr.2-grouped.data(y ~ v11+v21+v22+v23 | inter data=d.n) m.2-lme(y ~ v11+v21+v22+v23+v21:v11+v22:v11+v23:v11, random=~ v11 | inter, data=d.n.gr.2, na.action=na.omit) p.2-predict(m.1,dnNew) Second way works, while the first way doesn't. I get all the model specifications from the first one including fitted and residuals, everything that is derived from the lme object itself. However with the predictions I get the error. Error in eval(expr, envir, enclos) : 1 argument passed to $ which requires 2. I have saved the 3 objects: both models and the test dataset and attached it to the message in hope to help solve my problem, however my message was rejected as being to big (the attached file is 80K). If somebody has an idea how to solve the problem, I can send the data to him/her. Is there a solution to the problem? Thanks for the help so far. I would appreciate any other suggestions. Andrej -Original Message- From: Spencer Graves [mailto:[EMAIL PROTECTED] Sent: Tuesday, September 30, 2003 3:13 PM To: Andrej Kveder Cc: R-Help Subject: Re: [R] FW: error predicting values from the LME Could you dumb it down to a toy example with 4 observations for a model like y ~ 1 | inter, 2 observations for each of 2 levels of inter? If that works, then you can play with the example that works and the example that doesn't; this is one of the strategies mentioned in Poly (1971) How to Solve It (Princeton U. Pr.). With luck, this will help you figure out what you need to do to get the answers you want. If not, it should help you produce a small toy example that doesn't work, which you can then send us. Please include a data.frame call, so someone can copy your example into R and try it in 2 seconds. That should increase the chances that you would get a helpful reply. Also, have you read Pinhiero and Bates (2000) Mixed-Effect Models in S and S-Plus (Springer)? I've found that book to be indispensible for using lme. hope this helps. spencer graves Andrej Kveder wrote: HI all, I might add some more information in order to possibly solve my problem. I'm really stuck and no obvious solutions do the trick. I'm using R 1.7.1 on Windows 2000 with the packages regurarly updated. I'm using hypothetical data constructed as a pseudo population conforming to a certain Var-Cov structure. I might add that just predict(level2) works. But when I add the new dataset it doesn't. Following a suggestion I even tried refactoring of the grouping variable (inter) after I created the subset. It didn't work. I have no other factor variables in the model. I really have got no clue what could be wrong. There is a sample from my data: dnNew Grouped Data: y ~ v11 + v21 + v22 + v23 | inter v11 v21 v22 v23inter 4 5.55186635 5.6620022 24.18033 5.003409 1 13 2.03852426 5.6620022 24.18033 5.003409 1 15 2.19825772 7.5676798 31.03986 4.746891 2 16 4.51368278 7.5676798 31.03986 4.746891 2 18 3.35322702 7.5676798 31.03986 4.746891 2 19 2.46414346 7.5676798 31.03986 4.746891 2 20 2.66670834 7.5676798 31.03986 4.746891 2 and this is the model: level2 Linear mixed-effects model fit by REML Data: d.n.gr.2 Log-restricted-likelihood: -533.0011 Fixed: model$fixed (Intercept) v11 v21 v22 v23 v11:v21 3.205519074 0.298941539 -0.017743958 0.016007280 -0.410760471 0.002700954 v11:v22 v11:v23 -0.003680952 -0.018005717 Random effects: Formula: ~v11 | inter Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 0.385620605 (Intr) v11 0.003147431 -0.048 Residual 0.450012367 Number of Observations: 729 Number of Groups: 50 If this give you some more insight to my problem. I would reallly appreciate any suggestion. Thanks Andrej -Original Message- From: Andrej Kveder [mailto:[EMAIL PROTECTED] Sent: Monday, September 29, 2003 7:05 PM To: R-Help Subject: predicting values from the LME Dear listers, I experinced a problem prdicting the values using the LME with multilevel data. I have NA's in my dependent variable and the model is fitted only on the completed cases. I want to estimate the predicted values for the rest of the data (those cases with missing dep. variable) I extracted a
[R] R-1.7.1 for Redhat 9
Dear, I have problems with installing R-1.7.1 for Redhat 9. When I applied `./configure' and `make', I get the following error: make check make[1]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[2]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[3]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1 make[4]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests' make: *** [check] Error 2 I found on the web that one has to change something in the file src/main/arithmetic.c, but this was already done in my file, so that can`t cause the error. Is there somebody who knows how to solve this? Thanks a lot, kind regards, Joke Joke Allemeersch Kasteelpark Arenberg 10 3001 Heverlee (Leuven) http://www.esat.kuleuven.ac.be/~dna/BioI/ [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Evaluating outer, numeric, variables in an lme object.
Hello! I´m working with a dateset from twelve fertilizer experiments (Trial) with a block structure of three replicats (Block). The treatment levels consist of application method and product but only one intensity. The factor TrCode could for example be BC(CAN) for broadcast calcium ammonium nitrate. I´ve used the following call to fit a lme-object to the data: ejna1t4b.lme - lme( Yield ~ TrCode, data = ejna1t4, + random = ~ 1 | Trial/Block) This seems, for me, to work quite well. Or should I code differently? What I want to do now, is to evaluate the impact from a load of soil and weather data where I only have one reading from each Trial/variable. These variables are all numeric. Is this possible in the lme context? It is naturally possible to calculate treatment means of all Trials and run a regression analysis on the new dataset, but I have a feeling there are smarter ways of doing this. Or? Is there anything on this type of problem in MASS or Pinheiro Bates? So far, if I have found the proper texts, I have not understood it... ;-) Thanks /CG CG Pettersson, MSc, PhD-stud Department of Ecology and Crop Production Science, SLU P.O. Box 7043 S-750 07 Uppsala, Sweden Phone: +46 (0)18 67 12 24; Fax: +46 (0)18 67 29 06 +46 (0)70 330 66 85 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Text cutoff in legends
Dear r-help If I display plots on the X11 device, the legends looks fine. But if make an EPS, the longer entry in the legend is cutoff (and also in the .pdf I do from the .eps) Can you give me a hint and tell me what I do wrong, please ? postscript(plot.eps,paper=special,horizontal=F,onefile=F,width=8.0,height=7.0) dev.set (2) dev.copy (which=3) dev.off (3) R Version 1.6.1 (2002-11-01) on SuSE Linux 8.0 Thank you very much Marcel -- Marcel Sutter PMOD/WRC Dorfstrasse 33 CH-7260 Davos Dorf Switzerland http://www.pmodwrc.ch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] R-1.7.1 for Redhat 9
Tell us the output of something like tail -20 /volume1/scratch/jallemee/R-1.7.1/tests/Examples/base-Ex.Rout so we know where it bombed (and may be how it bombed). Andy -Original Message- From: Joke Allemeersch [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 01, 2003 6:02 AM To: [EMAIL PROTECTED] Subject: [R] R-1.7.1 for Redhat 9 Dear, I have problems with installing R-1.7.1 for Redhat 9. When I applied `./configure' and `make', I get the following error: make check make[1]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[2]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[3]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: `Makedeps' is up to date. make[4]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[4]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1 make[4]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests' make: *** [check] Error 2 I found on the web that one has to change something in the file src/main/arithmetic.c, but this was already done in my file, so that can`t cause the error. Is there somebody who knows how to solve this? Thanks a lot, kind regards, Joke Joke Allemeersch Kasteelpark Arenberg 10 3001 Heverlee (Leuven) http://www.esat.kuleuven.ac.be/~dna/BioI/ [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Text cutoff in legends
Marcel Sutter wrote: Dear r-help If I display plots on the X11 device, the legends looks fine. But if make an EPS, the longer entry in the legend is cutoff (and also in the .pdf I do from the .eps) Can you give me a hint and tell me what I do wrong, please ? Probably nothing. The X11 and postscript devices have different boundaries. The plot is made to fit them, and the legend added to that. I don't usually use dev.copy(); I just repeat the plot commands after the postscript() device is opened. Try that; if that doesn't work, adjust your legend placement. postscript(plot.eps,paper=special,horizontal=F,onefile=F,width=8.0,height=7.0) dev.set (2) dev.copy (which=3) dev.off (3) R Version 1.6.1 (2002-11-01) on SuSE Linux 8.0 Might as well upgrade R while you're at it. 1.8 will be out Real Soon Now. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Simulation of Levy Processes and Fractional Brownian motion
Dear R users, Are there any functions that can be used for the Simulation of Levy Processes and Fractional Brownian motion? Paul. - ÁðïêôÞóôå ôçí äùñåÜí [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] R-1.7.1 for Redhat 9
In that Examples directory I have the files base-Ex.Rout.fail and
base-Ex.R. If I perform tail -50 on base-Ex.R, I get
data(esoph) # following on from help(esoph)
model3 - glm(cbind(ncases, ncontrols) ~ agegp + C(tobgp, , 1) +
C(alcgp, , 1), data = esoph, family = binomial())
summary(model3)
options(contrasts = c(unordered = contr.treatment,ordered =
contr.poly))
cleanEx(); ..nameEx - zMachine
### * zMachine
### Name: .Machine
### Title: Numerical Characteristics of the Machine
### Aliases: .Machine
### Keywords: sysdata programming math
### ** Examples
str(.Machine)
cleanEx(); ..nameEx - zScript
### * zScript
### Name: .Script
### Title: Scripting Language Interface
### Aliases: .Script
### Keywords: interface
### ** Examples
.Script(perl, massage-Examples.pl,
paste(tools, system.file(R-ex, package = tools)))
### * FOOTER
###
cat(Time elapsed: , proc.time() - get(ptime, env =
.CheckExEnv),\n)
dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: \\( \\)?### [*]+ ***
### End: ***
quit('no')
If I perform tail -20 on base-Ex.Rout.fail, I just get the text you
see when starting R in the terminal.
R : Copyright 2003, The R Development Core Team
Version 1.7.1 (2003-06-16)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type `license()' or `licence()' for distribution details.
R is a collaborative project with many contributors.
Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.
Thanks,
Joke
On Wed, 2003-10-01 at 12:43, Liaw, Andy wrote:
Tell us the output of something like
tail -20 /volume1/scratch/jallemee/R-1.7.1/tests/Examples/base-Ex.Rout
so we know where it bombed (and may be how it bombed).
Andy
-Original Message-
From: Joke Allemeersch [mailto:[EMAIL PROTECTED]
Sent: Wednesday, October 01, 2003 6:02 AM
To: [EMAIL PROTECTED]
Subject: [R] R-1.7.1 for Redhat 9
Dear,
I have problems with installing R-1.7.1 for Redhat 9. When I
applied `./configure' and `make', I get the following error:
make check
make[1]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests'
make[2]: Entering directory `/volume1/scratch/jallemee/R-1.7.1/tests'
make[3]: Entering directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
make[4]: Entering directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
make[4]: Entering directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
make[4]: Leaving directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory
`/volume1/scratch/jallemee/R-1.7.1/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/volume1/scratch/jallemee/R-1.7.1/tests'
make: *** [check] Error 2
I found on the web that one has to change something in the
file src/main/arithmetic.c, but this was already done in my
file, so that can`t cause the error. Is there somebody who
knows how to solve this?
Thanks a lot,
kind regards,
Joke
Joke Allemeersch
Kasteelpark Arenberg 10
3001 Heverlee (Leuven)
http://www.esat.kuleuven.ac.be/~dna/BioI/
[[alternative HTML version deleted]]
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Joke Allemeersch
Kasteelpark Arenberg 10
3001 Heverlee (Leuven)
http://www.esat.kuleuven.ac.be/~dna/BioI/
[[alternative HTML version deleted]]
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RE: [R] Simulation of Levy Processes and Fractional Brownian mot
On 01-Oct-03 Paul Divid wrote:
Dear R users,
Are there any functions that can be used for the
Simulation of Levy Processes and Fractional Brownian motion?
Warning: computer simulation of fractal/chaotic processes can be
danegrously misleading:
chaos-function(xstart,n) {
x-xstart; y-x;
for(i in (1:n)){
if(y=0.5){y-2*y} else {y-2*(1-y)}
x-c(x,y)
}
return(x)
}
Mathematically, this function is genuinely chaotic, for almost all
values of 0 xstart 1.
Try it with
chaos(sqrt(2)/2,100)
With tongue (somewhat) in cheek,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 167 1972
Date: 01-Oct-03 Time: 13:09:51
-- XFMail --
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[R] Solving a tridiagonal system
I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/01pa/hyb74/node24.html. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: Mandelbrot set and C code
I decided to take on the 'proper' solution to calculate the
Mandelbrot set in R, i.e. to do the raw calculations in C and then link
that code with R. I thought it would be a hard task, but I was pleasantly
surprised when I saw how easily was to write the bit of C code (I am not a
C programmer myself!) and how even easier was to link it with R using .C()
and R CMD SHLIB. If you are interested (or anyone else) here is the (very
fast) code to calculate the mandelbrot set, I hope you enjoy playing with
it as much as I did.
# BEGINNING OF R CODE:
###
# Function to calculate the Mandelbrot set. This function calls a #
# C routine in order to perform the calculations faster. #
# #
# Written by Mario dos Reis. September 2003 #
###
mandelbrot - function(x = c(-3, 1),# x limits
y = c(-1.8, 1.8),# y limits
nx = 600,# x resolution
ny = 600,# y resolution
iter = 20) # maximun number of iterations
{
xcoo - seq(x[1], x[2], len = nx) # x coordinates
ycoo - seq(y[1], y[2], len = ny) # y coordinates
set = numeric(nx*ny) # this will store the output of
# the C routine
# This is the call to the C function itself
the.set = .C(mandelbrot,
xcoo = as.double(xcoo),
ycoo = as.double(ycoo),
nx = as.integer(nx),
ny = as.integer(ny),
set = as.integer(set),
iter = as.integer(iter))$set
# Create a list with elements x, y and z,
# suitable for image(), persp(), etc. and return it.
return(list(x = xcoo, y = ycoo, z = matrix(the.set, ncol = ny, byrow = T)));
}
# END OF R CODE. ###
/* BEGINNING OF C CODE: ***/
#include stdio.h
/***
* Function to evaluate a series of complex numbers that *
* form a subset of the Argand plane, to see if *
* they belong to the Mandelbrot set. *
* This function has been written with the intention of *
* linking it to some R code in order to create a *
* practical way to play with the set.*
* *
* Written by Mario dos Reis. September 2003 *
* *
***/
void mandelbrot(double *xcoo, double *ycoo, int *nx,
int *ny, int *set, int *iter)
/* 'xcoo' and 'ycoo' are the x and y coordinates respectively
* of all the points to be evaluated.
* 'nx' and 'ny' number of divisions along the x and y axes
* 'set' will store the practical output of the function
* 'iter' is the maximun number of iterations
*/
{
int i, j, k;
double z[2], c[2], oldz[2];
for(i = 0; i *nx; i++) {
for(j = 0; j *ny; j++) {
/* initialise the complex point to be tested
* c[0] (or z[0]) is the real part
* c[1] (or z[1]) is the imaginary part
*/
c[0] = xcoo[i]; c[1] = ycoo[j];
z[0] = 0; z[1] = 0;
for(k = 1; k *iter + 1; k++) {
oldz[0] = z[0]; oldz[1] = z[1];
// the mandelbrot mapping z - z^2 + c
z[0] = oldz[0]*oldz[0] - oldz[1]*oldz[1] + c[0];
z[1] = 2 * oldz[0]*oldz[1] + c[1];
if((z[0]*z[0] + z[1]*z[1]) 4) {
break;
}
}
/* fills the set vector
* notice the trick 'i * (*ny) + j' to find
* the apporpiate position of the output in the
* vector set. The R function will take care of
* transforming this vector into a suitable matrix
* for plotting, etc.
*/
set[i * (*ny) + j] = k;
}
}
return;
}
/* END OF C CODE. **
To anyone interested in trying out these functions, just save the C code
into a file, say 'mandelbrot.c', to be able to use the C code with R a
shared object needs to be created. This is done simple running the
following command from the directory where 'mandelbrot.c' is stored (note
this code was tried in Linux, for Win users I think the instructions are
similar but you need you check it out):
R CMD SHLIB mandelbrot.c
This will create the file 'mandelbrot.so' in that same directory.
Start R from this directory and paste the above R code into the console.
Re: [R] installing DBI_0.1-6.tar.gz
Hi,
I've never seen R core dumping during a package installation,
if indeed the 1857 Segmentation Fault message applies to R.
Could you give us more details (OS, etc.)? Also, have you had
problems with any other packages or is this the only one you're
having problems with, etc.?
Regards,
--
David
Joke Allemeersch wrote:
Dear,
I tried to install the DBI package in R-1.7.1, but this gave the
following error:
/volume1/scratch/jallemee/R/lib/R/bin/INSTALL: line 1: 1856
Done( echo
options(save.image.defaults=${save_image_defaults}); if test
-s R_PROFILE.R; then
cat R_PROFILE.R;
fi; echo invisible(.libPaths(c(\${lib}\, .libPaths(; cat
${R_PACKAGE_DIR}/R/${pkg} )
1857 Segmentation fault | ${R_EXE} --slave --save
${save_args}
ERROR: execution of package source for 'DBI' failed
Can somebody help me?
Thanks a lot,
Kind regards,
Joke.
Joke Allemeersch
Kasteelpark Arenberg 10
3001 Heverlee (Leuven)
http://www.esat.kuleuven.ac.be/~dna/BioI/
[[alternative HTML version deleted]]
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--
David A. James
Statistics Research, Room 2C-253Phone: (908) 582-3082
Bell Labs, Lucent Technologies Fax:(908) 582-3340
Murray Hill, NJ 09794-0636
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[R] Acces violation ???
Dear R-listers, I have created a dll and I call it from a R function. However R stops and shows the message: Unhandled exception in Rgui.exe (R.DLL): 0xC005: Access Violation I get this error in other situations and I solved it verifying that all parameters are called fine. (e.g., double precision - as.double, integer - as.integer,...). I have verify this. Then, I have tried to debug Fortran program in order to verify why (or where) function doesn't work. Surprisingly the subroutine arrives until the end. What is happening? Thank you in advance Juan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Solving a tridiagonal system
SparseM is really intended for arbitrary sparse structure, for banded structural there are much more efficient methods, some of which are, if I'm not mistaken, now available in lapack. url:www.econ.uiuc.edu/~roger/my.htmlRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 On Wed, 1 Oct 2003, Thomas W Blackwell wrote: Will - Take a look at Roger Koenker's package SparseMatrix, available from CRAN. Look also for some other package from Roger which depends on SparseMatrix, but has a different name. It's a place to look. I don't recall whether it will answer your need or not. - tom blackwell - u michigan medical school - ann arbor - On Wed, 1 Oct 2003, Will Harvey wrote: I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/01pa/hyb74/node24.html. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Solving a tridiagonal system
The following will create a matrix x with given sub diagonal, diagonal and super diagonal. # define test vectors for a, b and c va - -(1:4); vb - 11:15; vc - 1:4 # diag.num is a matrix whose ith super diagonal equals i and # sub diagonal equals -i diag.num - -outer(seq(vb),seq(vb),-) x - diag(vb) x[diag.num == 1] - va x[diag.num == -1] - vc --- Date: Wed, 1 Oct 2003 05:56:34 -0700 (PDT) From: Will Harvey [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] Solving a tridiagonal system I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/01pa/hyb74/node24.html;. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help message or move to Select a Folder- Folders --InboxDraftsSentTrashBulk Mail My Folders R Back to Inbox | Prev Next As AttachmentAs Inline Text Make My Way Your Home Page | Spread the Word My Settings: Overview | Search | Email | Chat | Portfolio | Calendar | Groups | Profile IMPORTANT: We do not present our users with pop-ups, banners or any other non-text advertising. Nor do we send email to our users. If you see or receive one of these items, it is coming from an outside source, either as a result of something you have previously downloaded or as an exit pop-up from the site you just visited. It is not coming from our site. Privacy Policy Terms of Service Partner with Us Our Mission Advertise with Us Sign In Sign Out Help Center © 2002-2003 My Way ___ No banners. No pop-ups. No kidding. Introducing My Way - http://www.myway.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Solving a tridiagonal system
I just noticed that you defined a to be the lower diagonal whereas I had it as the upper diagonal so the previous email should be as follows to correspond to your notation: # define test vectors for a, b and c va - -(1:4); vb - 11:15; vc - 1:4 # diag.num is a matrix whose ith diagonal equals i diag.num - -outer(seq(vb),seq(vb),-) x - diag(vb) x[diag.num == -1] - va x[diag.num == 1] - vc From: Gabor Grothendieck [EMAIL PROTECTED] To: [EMAIL PROTECTED], [EMAIL PROTECTED] Subject: RE: [R] Solving a tridiagonal system The following will create a matrix x with given sub diagonal, diagonal and super diagonal. # define test vectors for a, b and c va - -(1:4); vb - 11:15; vc - 1:4 # diag.num is a matrix whose ith super diagonal equals i and # sub diagonal equals -i diag.num - -outer(seq(vb),seq(vb),-) x - diag(vb) x[diag.num == 1] - va x[diag.num == -1] - vc --- Date: Wed, 1 Oct 2003 05:56:34 -0700 (PDT) From: Will Harvey [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] Solving a tridiagonal system I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/01pa/hyb74/node24.html;;. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help message or move to Select a Folder- Folders --InboxDraftsSentTrashBulk Mail My Folders R Back to Inbox | Prev Next As AttachmentAs Inline Text Make My Way Your Home Page | Spread the Word My Settings: Overview | Search | Email | Chat | Portfolio | Calendar | Groups | Profile IMPORTANT: We do not present our users with pop-ups, banners or any other non-text advertising. Nor do we send email to our users. If you see or receive one of these items, it is coming from an outside source, either as a result of something you have previously downloaded or as an exit pop-up from the site you just visited. It is not coming from our site. Privacy Policy Terms of Service Partner with Us Our Mission Advertise with Us Sign In Sign Out Help Center © 2002-2003 My Way ___ No banners. No pop-ups. No kidding. Introducing My Way - http://www.myway.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help message or move to Select a Folder- Folders --InboxDraftsSentTrashBulk Mail My Folders R Back to Inbox | Prev Next As AttachmentAs Inline Text Make My Way Your Home Page | Spread the Word My Settings: Overview | Search | Email | Chat | Portfolio | Calendar | Groups | Profile IMPORTANT: We do not present our users with pop-ups, banners or any other non-text advertising. Nor do we send email to our users. If you see or receive one of these items, it is coming from an outside source, either as a result of something you have previously downloaded or as an exit pop-up from the site you just visited. It is not coming from our site. Privacy Policy Terms of Service Partner with Us Our Mission Advertise with Us Sign In Sign Out Help Center © 2002-2003 My Way ___ No banners. No pop-ups. No kidding. Introducing My Way - http://www.myway.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Solving a tridiagonal system
I see that the LAPACK routine DGTSV is in the R source, and defined in R_ext/lapack.h, but I don't know how to get to it from R. Andy -Original Message- From: Roger Koenker [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 01, 2003 10:33 AM To: Thomas W Blackwell Cc: [EMAIL PROTECTED] Subject: Re: [R] Solving a tridiagonal system SparseM is really intended for arbitrary sparse structure, for banded structural there are much more efficient methods, some of which are, if I'm not mistaken, now available in lapack. url: www.econ.uiuc.edu/~roger/my.htmlRoger Koenker email [EMAIL PROTECTED] Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678 Champaign, IL 61820 On Wed, 1 Oct 2003, Thomas W Blackwell wrote: Will - Take a look at Roger Koenker's package SparseMatrix, available from CRAN. Look also for some other package from Roger which depends on SparseMatrix, but has a different name. It's a place to look. I don't recall whether it will answer your need or not. - tom blackwell - u michigan medical school - ann arbor - On Wed, 1 Oct 2003, Will Harvey wrote: I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/0 1pa/hyb74/node24.html. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Solving a tridiagonal system
Thanks. This works, but still seems too slow for my application. It looks like my best option is to figure out how to interface the LAPACK routine DGTSV to R. The inputs to DGTSV are four vectors: the three diagonals and the RHS vector. Will --- Gabor Grothendieck [EMAIL PROTECTED] wrote: I just noticed that you defined a to be the lower diagonal whereas I had it as the upper diagonal so the previous email should be as follows to correspond to your notation: # define test vectors for a, b and c va - -(1:4); vb - 11:15; vc - 1:4 # diag.num is a matrix whose ith diagonal equals i diag.num - -outer(seq(vb),seq(vb),-) x - diag(vb) x[diag.num == -1] - va x[diag.num == 1] - vc From: Gabor Grothendieck [EMAIL PROTECTED] To: [EMAIL PROTECTED], [EMAIL PROTECTED] Subject: RE: [R] Solving a tridiagonal system The following will create a matrix x with given sub diagonal, diagonal and super diagonal. # define test vectors for a, b and c va - -(1:4); vb - 11:15; vc - 1:4 # diag.num is a matrix whose ith super diagonal equals i and # sub diagonal equals -i diag.num - -outer(seq(vb),seq(vb),-) x - diag(vb) x[diag.num == 1] - va x[diag.num == -1] - vc --- Date: Wed, 1 Oct 2003 05:56:34 -0700 (PDT) From: Will Harvey [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] Solving a tridiagonal system I need to find solutions to a tridiagonal system. By this I mean a set of linear equations Ax = d where A is a square matrix containing elements A[i,i-1], A[i,i] and A[i,i+1] for i in 1:nrow, and zero elsewhere. R is probably not the ideal way to do this, but this is part of a larger problem that requires R. In my application it is much easier (and much faster) to generate the diagonal and off-diagonal elements of A as vectors, i.e. a = A[i,i-1], b = A[i,i] and c = A[i,i+1]. So I have three vectors that define A, along with a solution vector d. The conventional method of solving such systems is to use the so-called Thomas algorithm, see e.g. http://www.enseeiht.fr/hmf/travaux/CD0001/travaux/optmfn/hi/01pa/hyb74/node24.html;;. This is very easy to code, but much more difficult to vectorize. Is anyone aware of a library that contains a fast implementation of this algorithm? Another alternative is to use backsolve. I can easily eliminate the lower diagonal a, but I'm still left with b and c, whereas backsolve requires a matrix. Again, I can write a function to read b and c into a matrix, but this requires loops, and is too slow. Is there a vectorized way of doing it? Of course, the diag command works for b, but what about c? In Octave, diag allows for an offset, but R apparently does not. I would appreciate any and all assistance you experts can offer. Thanks in advance. Will Harvey __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help message or move to Select a Folder- Folders --InboxDraftsSentTrashBulk Mail My Folders R Back to Inbox | Prev Next As AttachmentAs Inline Text Make My Way Your Home Page | Spread the Word My Settings: Overview | Search | Email | Chat | Portfolio | Calendar | Groups | Profile IMPORTANT: We do not present our users with pop-ups, banners or any other non-text advertising. Nor do we send email to our users. If you see or receive one of these items, it is coming from an outside source, either as a result of something you have previously downloaded or as an exit pop-up from the site you just visited. It is not coming from our site. Privacy Policy Terms of Service Partner with Us Our Mission Advertise with Us Sign In Sign Out Help Center © 2002-2003 My Way ___ No banners. No pop-ups. No kidding. Introducing My Way - http://www.myway.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help message or move to Select a Folder- Folders --InboxDraftsSentTrashBulk Mail My Folders R Back to Inbox | Prev Next As AttachmentAs Inline Text Make My Way Your Home Page | Spread the Word My Settings: Overview | Search | Email | Chat | Portfolio | Calendar | Groups | Profile IMPORTANT: We do not present our users with pop-ups, banners or any other non-text advertising. Nor do we send email to our users. If you see or receive one of these items, it is coming from an outside source, either as a result of something you have previously downloaded or as an exit pop-up from the site you just visited. It is not coming from our site. Privacy Policy Terms of Service Partner with Us Our Mission Advertise with Us Sign In Sign Out Help Center © 2002-2003 My Way === message
[R] fitting Markov chains
I need to find a computationally simple process for the movement of interest rates. In this simplified model, an interest rate can have 3--5 possible values, and its movement is characterized by a matrix of transition probabilities (ie, it is a Markov process). I would like to estimate this process from a given set of data. For example, let the interest rate time series be: 7 3 8 2 5 9 6 Assume that the discretized variable can take the following values: (3, 5, 8), then we find the nearest discrete point and give its index: 3 1 3 1 2 3 2 Then estimate the transition probabilities. I have the following questions: - how should I select the discrete set of values that the variable can assume? Eg simply get the maximum and minimum, and divide this interval into, say, three pieces? Or estimate the mean, and make the other two values mean plus-minus one standard deviation? - once the variable is discretized, how do I transform each data point to its discretized value (its index)? - the most important: how should I estimate the transition probabilities? References to introductory literature on estimating Markov chains like this would be welcome. Most importantly, I need to know how robust an estimation is to selecting the discrete points, or is there a simple goodness of fit estimation. Thanks, Tamas Papp -- Tamás K. Papp E-mail: [EMAIL PROTECTED] (preferred, especially for large messages) [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
[R] SOS Cor
Ho iniziato ad utilizzare R da pochi giorni e onestamente ho delle difficoltà. Devo correlare una variabile con il resto del dataframe (quindi una variabile con tutte), ma sbaglio nella sintassi e onestamente non so dove. Le singole correlazioni riesco a farle, ma è un lavoro un pò dispersivo. Mi hanno consigliato di utilizzare cbind oppure as.matrix, ma non so continuare. Il problema seguente è cercare di correlare una variabile con altre che sono io a scegliere per motivi di ricerca, ma anche qui non so come selezionare le colonne che a me interessano (non sono intervalli, ma sono disposte a salti). Qualcuno mi può aiutare? GRAZIE CARLA. _ Nuovo MSN Messenger 6.0: con sfondi, foto e giochi. [1]Provalo subito! References 1. http://g.msn.com/8HMAITIT/2728??PS= __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Macintosh binaries; was: Rcmdr and Macintosh
I am a Windows user and trying to make life easier for my Mac-using students. After
investigating the Mac situation more, it appears that the key to easy use is having
precompiled binaries. However the packages I am interested in (Rcmdr and its required
package, car) do not have one. I do not have easy access to a Mac, so I have a plea to
Macintosh users: could someone please create them if it is not too difficult? I am
planning to use R 1.7.1. Please forgive me if my request is inappropriate.
Aniko
This e-mail may contain confidential and/or privileged infor...{{dropped}}
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RE: [R] fitting Markov chains
On 01-Oct-03 Tamas Papp wrote: I need to find a computationally simple process for the movement of interest rates. In this simplified model, an interest rate can have 3--5 possible values, and its movement is characterized by a matrix of transition probabilities (ie, it is a Markov process). I would like to estimate this process from a given set of data. For example, let the interest rate time series be: 7 3 8 2 5 9 6 Assume that the discretized variable can take the following values: (3, 5, 8), then we find the nearest discrete point and give its index: 3 1 3 1 2 3 2 Then estimate the transition probabilities. I have the following questions: - how should I select the discrete set of values that the variable can assume? Eg simply get the maximum and minimum, and divide this interval into, say, three pieces? Or estimate the mean, and make the other two values mean plus-minus one standard deviation? I would suggest dividing the interval, trying to get equal numbers in each interval. If (e.g. because the originals are discrete) this can't quite be done, try to find an similar arrangement which maximises the minimum count. - once the variable is discretized, how do I transform each data point to its discretized value (its index)? ? Something like a-c(0,1,2,3,4);b-c(1,2,3,4,5) x-3.5;which((ax)(x=b)) [1] 4 x-1.5;which((ax)(x=b)) [1] 2 - the most important: how should I estimate the transition probabilities? Most simply as Nij/Ni. where Ni. is the number of times the system has been in state i, and Nij is the number of transitions from i to j. Statistical properties of even this estimator can be a bit elusive because the sample sizes Ni. are random; the above recommendation about how to select intervals will probably help on this front. Also, after grouping the system is no longer a Markov Chain (even assuming it really was in the first place) since the probability of transition from i to j will depend somewhat on which member within i was arrived at, and this will depend (though hopefullly not much) on where it was before. By refining your grouping you can diminish this effect, though you will also reduce the Ni. and hence the quality of estimation. To discuss such issues one really need to know more about your data, in particular how long the series are, what groupings are you thinking of, and how the series behave. Also, you don't seem to be thinking about trends, cycles etc. ... Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 167 1972 Date: 01-Oct-03 Time: 17:49:21 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] question about predictions with linear models
Hi, this question is probably very obvious but I just cant see where I might be going wrong. I'm using the lm() function to generate a linear model and then make predictions using a different set of data. To generate the model I do (tdata pdata are matrices of observations and parameters, tdepv, pdepv are response vectors) x - as.data.frame(tdata) x$tdepv - tdepv lnegth(tdepv) = 140 model - lm(x$tdepv ~ x$V1 + x$V2 + x$V3 + x$V4, x) pred - predict(model, x) length(pred) = 140 y - as.data.frame(pdata) y$pdepv - pdepv length(pdepv) = 16 pred - predict(model, y) length(pred) = 140 But I expect that length(pred) = 16 Why do I get a different length? Furthermore, the original formula specified the variable tdepv which is not in the dataframe that I send to predict() - should I also make a variable called tdepv in the dataframe y? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- The way to love anything is to realize that it might be lost. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] hypergeometric population estimates
help We want to estimate the number of caribou in Jasper. We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. We want to estimate the number of caribou in this population with 95% confidence limits. Gary White uses the hypergeometric distribution and determines the population estimates using maximum likelihood and 95%CL as -2LogLikelihoods. Below, I determined the population estimate using dhyper(x,m,n,k) and maximizing the density value as a function of n, but do not know how I should calculate MLE with this distribution. x - 8 # number resighted caribou (white balls drawn) m -11 # number collared caribou (white balls total) k - 70# number caribou seen (# balls drawn) n - 1:500 # ?? unknown number of uncollared caribou (# black balls) d - unlist(lapply(n, function(i) dhyper(x,m,i,k))) # density estimate for each value of n data - data.frame(estimate = n+m, d) data - data[is.finite(data$d), ] # filter out NA's max.d - max(data$d) pop.estimate - data[data$d == max.d, 1] Thank-you for your assistance, Jesse __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] sas.get problem
On Wed, 01 Oct 2003 14:02:15 -0400, Peter Flom [EMAIL PROTECTED] wrote
:
When I try
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
I get the following errors and warnings:
'sas' is not recognized as an internal or external command,
operable program or batch file.
That's an S-PLUS function rather than an R function, isn't it? Does
some R package supply sas.get?
I believe the S-PLUS implementation requires that you have SAS
installed, and it looks like the error message is saying that you
don't. But if you're using S-PLUS, you'd be better asking on the
s-news mailing list.
Duncan Murdoch
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RE: [R] hypergeometric population estimates
I'm not sure I understand your notation: (1) We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. (2) k - 70# number caribou seen (# balls drawn) It's the number of balls drawn parenthetical remark that bothers me - I think the total number of balls drawn should be 78 and the number of non-white balls drawn is 70. If x - 8 # number resighted caribou (white balls drawn) m -11 # number collared caribou (white balls total) totaldrawn - 78# number caribou seen (total # balls drawn) I believe that the maximum likelihood estimator you are looking for is given by MLE - floor(m * totaldrawn / x) #floor(11 * 78 / 8) = 107 I believe the trick is to look at f(n) = P(x|m,totaldrawn,n) as a function of n and consider the ratio f(n) / f(n-1). If this ratio is greater than 1 the function is increasing and if the ratio is less than 1 the function is decreasing. Then algebraically show that the maximum occurs at floor(m * totaldrawn / x). Bytheway, this MLE includes both collared and uncollared balls so it may be that you are looking for 107 - 11 as your estimate?? hth Bob Usual disclaimers... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 01, 2003 12:56 PM To: [EMAIL PROTECTED] Subject: [R] hypergeometric population estimates help We want to estimate the number of caribou in Jasper. We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. We want to estimate the number of caribou in this population with 95% confidence limits. Gary White uses the hypergeometric distribution and determines the population estimates using maximum likelihood and 95%CL as -2LogLikelihoods. Below, I determined the population estimate using dhyper(x,m,n,k) and maximizing the density value as a function of n, but do not know how I should calculate MLE with this distribution. x - 8 # number resighted caribou (white balls drawn) m -11 # number collared caribou (white balls total) k - 70# number caribou seen (# balls drawn) n - 1:500 # ?? unknown number of uncollared caribou (# black balls) d - unlist(lapply(n, function(i) dhyper(x,m,i,k))) # density estimate for each value of n data - data.frame(estimate = n+m, d) data - data[is.finite(data$d), ] # filter out NA's max.d - max(data$d) pop.estimate - data[data$d == max.d, 1] Thank-you for your assistance, Jesse __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] sas.get problem
On Wed, 2003-10-01 at 13:23, Duncan Murdoch wrote:
On Wed, 01 Oct 2003 14:02:15 -0400, Peter Flom [EMAIL PROTECTED] wrote
:
When I try
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
I get the following errors and warnings:
'sas' is not recognized as an internal or external command,
operable program or batch file.
That's an S-PLUS function rather than an R function, isn't it? Does
some R package supply sas.get?
I believe the S-PLUS implementation requires that you have SAS
installed, and it looks like the error message is saying that you
don't. But if you're using S-PLUS, you'd be better asking on the
s-news mailing list.
Duncan Murdoch
Duncan,
sas.get() is in Frank Harrell's Hmisc package on CRAN (recently
available there) for R.
I would defer to Frank's comments here, but reading the .PDF file that
is on CRAN, it does confirm that one must be able to run SAS in order to
use sas.get():
Note
You must be able to run SAS (by typing sas) on your system. If the S
command !sas does not start SAS, then this function cannot work.
HTH,
Marc Schwartz
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Re: [R] sas.get problem
It's actually in the Hmisc package. The error looks like Hmisc hasn't
been attached yet, so you might try library(Hmisc) first.
In addition, it does appear from the help file that you need SAS
installed to output the ASCII files that are required to import the
data.
HTH,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Duncan Murdoch [EMAIL PROTECTED] 10/01/03 02:23PM
On Wed, 01 Oct 2003 14:02:15 -0400, Peter Flom [EMAIL PROTECTED] wrote
:
When I try
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
I get the following errors and warnings:
'sas' is not recognized as an internal or external command,
operable program or batch file.
That's an S-PLUS function rather than an R function, isn't it? Does
some R package supply sas.get?
I believe the S-PLUS implementation requires that you have SAS
installed, and it looks like the error message is saying that you
don't. But if you're using S-PLUS, you'd be better asking on the
s-news mailing list.
Duncan Murdoch
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Re: [R] Macintosh binaries; was: Rcmdr and Macintosh
Did you try install.packages()?
I know this is not exactly what you're looking for, but with the
sometimes-called 'Darwin' version of R 1.7.1 for Mac OS X, installed
from source code, not a precompiled binary, and using X Windows,
install.packages('Rcmdr')
install.packages('car')
were successful.
version
_
platform powerpc-apple-darwin6.6
arch powerpc
os darwin6.6
system powerpc, darwin6.6
status
major1
minor7.1
year 2003
month06
day 16
language R
I'm not up to date on whether install.packages() will work from a
precompiled binary for OS X.
I haven't tried it, but I do not expect install.packages() to work if
the Mac OS is 9.x or before, as these are not unix-based. (and
support for R pre-OS X is waning if not completely gone)
-Don
At 10:42 AM -0600 10/1/03, Aniko Szabo wrote:
I am a Windows user and trying to make life easier for my Mac-using
students. After investigating the Mac situation more, it appears
that the key to easy use is having precompiled binaries. However the
packages I am interested in (Rcmdr and its required package, car) do
not have one. I do not have easy access to a Mac, so I have a plea
to Macintosh users: could someone please create them if it is not
too difficult? I am planning to use R 1.7.1. Please forgive me if my
request is inappropriate.
Aniko
This e-mail may contain confidential and/or privileged infor...{{dropped}}
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--
--
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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Re: [R] sas.get problem
Thanks to all who responded
Marc Schwartz wrote
A quick follow up. I installed Frank's Hmisc under R 1.8.0 beta. If
Hmisc is not attached (ie. library(Hmisc)), you get:
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
Error: couldn't find function sas.get
which you would reasonably expect.
Thus, it seems more likely that Dr. Flom either does not have SAS on
his
system or perhaps the SAS executable file (sas.exe? IIRC) is not in
Dr.
Flom's 'PATH' on his system if SAS is installed.
This does seem to be the problem
Thanks again
Peter
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Re: [R] sas.get problem
On Wed, 2003-10-01 at 13:43, Marc Schwartz wrote:
On Wed, 2003-10-01 at 13:23, Duncan Murdoch wrote:
On Wed, 01 Oct 2003 14:02:15 -0400, Peter Flom [EMAIL PROTECTED] wrote
:
When I try
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
I get the following errors and warnings:
'sas' is not recognized as an internal or external command,
operable program or batch file.
That's an S-PLUS function rather than an R function, isn't it? Does
some R package supply sas.get?
I believe the S-PLUS implementation requires that you have SAS
installed, and it looks like the error message is saying that you
don't. But if you're using S-PLUS, you'd be better asking on the
s-news mailing list.
Duncan Murdoch
Duncan,
sas.get() is in Frank Harrell's Hmisc package on CRAN (recently
available there) for R.
I would defer to Frank's comments here, but reading the .PDF file that
is on CRAN, it does confirm that one must be able to run SAS in order to
use sas.get():
Note
You must be able to run SAS (by typing sas) on your system. If the S
command !sas does not start SAS, then this function cannot work.
HTH,
Marc Schwartz
A quick follow up. I installed Frank's Hmisc under R 1.8.0 beta. If
Hmisc is not attached (ie. library(Hmisc)), you get:
citypro - sas.get('c:/ndri/cvar/data', member = 'citypro2')
Error: couldn't find function sas.get
which you would reasonably expect.
Thus, it seems more likely that Dr. Flom either does not have SAS on his
system or perhaps the SAS executable file (sas.exe? IIRC) is not in Dr.
Flom's 'PATH' on his system if SAS is installed.
HTH,
Marc
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[R] curious error with tkcheckbutton
Hello, the following code produces an error when executing it, it is a code
that produces 6 checkbutton that at
the beginning are empty, when selecting the first checkbox he says that
doesn't know the second
variable tcl, he say:
[1] 1
Error in structure(.External(dotTcl, ..., PACKAGE = tcltk), class
= tclObj) :
[tcl] can't read ::RTcl2: no such variable.
when six variables tcl has been created in the array b and they exist:
b
[1] ::RTcl1 ::RTcl2 ::RTcl3 ::RTcl4 ::RTcl5 ::RTcl6
the script is(I'm use R 1.7.1 for win, the fail is in the first execution
of the script):
library(tcltk)
tt-tktoplevel()
f-tkframe(tt)
tkpack(f)
j-6
nbre-c(c1,c2,c3,c4,c5,c6)
b-c()
i-1
while (i=j){
aux-paste(b,i,sep=)
aux-tclVar(init=0)
b-c(b,as.character(aux))
tclvalue(b[i])-0
i-i+1
}
i-1
while (i=j){
t-tkcheckbutton(f,text=nbre[i],variable=eval(b
[i]),relief=raised,command=function()ver())
tkpack(t)
i-i+1
}
ver-function(){
k-1
while (k=j){
print(tclvalue(b[k]))
k-k+1
}
}
any help will be welcome. Thank you Ruben
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Re: [R] Re: Mandelbrot set and C code
[EMAIL PROTECTED] wrote: I decided to take on the 'proper' solution to calculate the Mandelbrot set in R, i.e. to do the raw calculations in C and then link that code with R. This is very cool. I did a slight tweak to your mandelbrot.R code, so that x can be a list with components x and y. This allows you to keep zooming in using your mouse to click on the plot (one of the incredibly nifty features of such sets). Using the tweaked version below, call the function as you suggested: image(mandelbrot(), col = c(heat.colors(49), black)) Then use locator(2) to define your next view: image(mandelbrot(locator(2)), col = c(heat.colors(49), black)) Click the mouse in the corners of the zoom window, and away you go. Lather. Rinse. Repeat. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] hypergeometric population estimates
# another vote for 107 n - 1:500 x - 8 m - 11 totaldrawn - 78 MLE - floor(m * totaldrawn / x) likelihood - choose(m,x)*choose(n-m,totaldrawn-x)/choose(n,totaldrawn) plot(n, likelihood) abline(v=MLE) [EMAIL PROTECTED] wrote: I'm not sure I understand your notation: (1) We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. (2) k - 70# number caribou seen (# balls drawn) It's the number of balls drawn parenthetical remark that bothers me - I think the total number of balls drawn should be 78 and the number of non-white balls drawn is 70. If x - 8 # number resighted caribou (white balls drawn) m -11 # number collared caribou (white balls total) totaldrawn - 78# number caribou seen (total # balls drawn) I believe that the maximum likelihood estimator you are looking for is given by MLE - floor(m * totaldrawn / x) #floor(11 * 78 / 8) = 107 I believe the trick is to look at f(n) = P(x|m,totaldrawn,n) as a function of n and consider the ratio f(n) / f(n-1). If this ratio is greater than 1 the function is increasing and if the ratio is less than 1 the function is decreasing. Then algebraically show that the maximum occurs at floor(m * totaldrawn / x). Bytheway, this MLE includes both collared and uncollared balls so it may be that you are looking for 107 - 11 as your estimate?? hth Bob Usual disclaimers... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 01, 2003 12:56 PM To: [EMAIL PROTECTED] Subject: [R] hypergeometric population estimates help We want to estimate the number of caribou in Jasper. We recently conducted an aerial survey and saw 70 uncollared caribou and 8 of 11 collared caribou. We want to estimate the number of caribou in this population with 95% confidence limits. Gary White uses the hypergeometric distribution and determines the population estimates using maximum likelihood and 95%CL as -2LogLikelihoods. Below, I determined the population estimate using dhyper(x,m,n,k) and maximizing the density value as a function of n, but do not know how I should calculate MLE with this distribution. x - 8 # number resighted caribou (white balls drawn) m -11 # number collared caribou (white balls total) k - 70# number caribou seen (# balls drawn) n - 1:500 # ?? unknown number of uncollared caribou (# black balls) d - unlist(lapply(n, function(i) dhyper(x,m,i,k))) # density estimate for each value of n data - data.frame(estimate = n+m, d) data - data[is.finite(data$d), ] # filter out NA's max.d - max(data$d) pop.estimate - data[data$d == max.d, 1] Thank-you for your assistance, Jesse __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Richard E. Remington III Statistician KERN Statistical Services, Inc. PO Box 1046 Boise, ID 83701 Tel: 208.426.0113 KernStat.com __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R on fairly large machines
Hi, We are considering using R on a large problem that will require four 64 bit cpu's and 64Gb of ram and some flavor of unix. We are just wondering if R is going to be happy in this environment. If have experience with this please let me know. Thanks, Allan Tingey [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] lda source code
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Wei
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Re: [R] lda source code
Wei Geng wrote:
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Here:
http://cran.r-project.org
Hint: MASS is a *package*. You want to view its *source*.
Same with most other R packages. Or just about anything else you want
to know about R.
Cheers
Jason
--
Indigo Industrial Controls Ltd.
http://www.indigoindustrial.co.nz
64-21-343-545
[EMAIL PROTECTED]
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Re: [R] lda source code
Consider the following:
library(MASS)
lda
function (x, ...)
UseMethod(lda)
environment: namespace:MASS
methods(lda)
[1] lda.data.frame lda.defaultlda.formulalda.matrix
Now type lda.data.frame or lda.default, etc., at a command prompt to
see the corresponding R code.
Is this what you want?
spencer graves
Wei Geng wrote:
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Wei
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RE: [R] lda source code
Hi Jason, Spencer, Thanks for the prompt response. The strange thing about MASS is that it's not in Package Sources as most of other R packages are. It seems to come with the binary R installation. I checked out the Rxx/library/MASS on my laptop, there are source code (script) for Venables Ripley's book but no source code for lda(). The lda.data.frame or lda.default at prompt (after loading MASS library(MASS)) has Error: Object lda.data.frame not found Wei __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
Wei Geng,
I asked the same question about six weeks ago, so let me try to answer it.
The source for the entire package 'MASS' is in a single file, I believe (at
least this is true on my Linux setup). The exact location of that file
you'll have to determine by searching the directory/folder where you
installed it. The function 'lda' is implemented entirely in R itself, like
much of its functionality. Look at the functions 'lda' and 'predict.lda' in
this file for details.
Comments are sparse in most R code, from what I gather, but if you look in
Pattern Recognition and Neural Networks by Brian Ripley (one of the
authors of this package), you'll find a discussion in section 2.4
'Predictive classification' that covers much of what's going on, from what
I've been able to glean.
I hope that helps. There are certainly others out there who are more au
fait with this than me.
-Frank Gibbons
At 05:47 PM 10/1/2003, you wrote:
Wei Geng wrote:
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Here:
http://cran.r-project.org
Hint: MASS is a *package*. You want to view its *source*.
Same with most other R packages. Or just about anything else you want to
know about R.
Cheers
Jason
--
Indigo Industrial Controls Ltd.
http://www.indigoindustrial.co.nz
64-21-343-545
[EMAIL PROTECTED]
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PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555 Fax:
617-432-3557 http://llama.med.harvard.edu/~fgibbons
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Re: [R] lda source code
With R 1.7.1 on Windows 2000, I got fine R source code for each of the 4 options. What version of R and what exactly did you do? I can't reproduce your error. hope this helps. spencer graves Wei Geng wrote: Hi Jason, Spencer, Thanks for the prompt response. The strange thing about MASS is that it's not in Package Sources as most of other R packages are. It seems to come with the binary R installation. I checked out the Rxx/library/MASS on my laptop, there are source code (script) for Venables Ripley's book but no source code for lda(). The lda.data.frame or lda.default at prompt (after loading MASS library(MASS)) has Error: Object lda.data.frame not found Wei __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
Wei Geng wrote: Does anyone know where to find out lda source code ? Try typing lda.default at the prompt. That should get you started. Also see: methods(lda) as lda.default isn't the only bit of code used in lda() Alternatively, grab the source from CRAN and read it at your leisure. HTH Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
Wei Geng wrote: Hi Jason, Spencer, Thanks for the prompt response. The strange thing about MASS is that it's not in Package Sources as most of other R packages are. It seems to come with the binary R installation. I checked out the Rxx/library/MASS on my laptop, there are source code (script) for Venables Ripley's book but no source code for lda(). Wei, MASS is actually distributed in a bundle called VR, which is on CRAN. VR as in Venables and Ripley, the authors of MASS (the book). The VR bundle contains MASS, nnet, spatial and class packages. The reason MASS comes with your binary installation is that the VR bundle has Recommended status - and should therefore be available in all binary distributions. HTH, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
Wei Geng wrote: Hi Jason, Spencer, Thanks for the prompt response. The strange thing about MASS is that it's not in Package Sources as most of other R packages are. It seems to come with the binary R installation. I checked out the Rxx/library/MASS on my laptop, there are source code (script) for Venables Ripley's book but no source code for lda(). Ah. On CRAN, the MASS library is part of a bundle called VR. Download the source for that. There are a few bundles on the CRAN source pages - if you encounter this problem again, just follow the Package Sources link, and search the page for MASS (or whatever the package name is). Use Edit-Find, or Ctrl-F, or whatever. In the case of MASS, you find this one: VR: Functions and datasets to support Venables and Ripley, `Modern Applied Statistics with S' (4th edition). Bundle of: MASS class nnet spatial It's the Bundle of part you're looking for. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lda source code
You are using a *beta* version of R 1.8.0 and in that version
lda.default is not visible to the user (hidden in a namespace). You can
access it though by using the ::: (triple colon) operator, as in
library(MASS)
MASS:::lda.default
Actually, the first library() call is not necessary.
-roger
Wei Geng wrote:
I am new to R. Trying to find out how lda() {in MASS R1.8.0 Windows} was
implemented in R. Does anyone know where to find out lda source code ?
Thanks.
Wei
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[R] install from source again
What does Error 255 stand for in the make bitmapdll, please? Thanks, erin [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Re: Mandelbrot set and C code
Jason Turner wrote:
...I did a slight tweak to your mandelbrot.R code, so
that x can be a list with components x and y. This allows you to keep
zooming in using your mouse to click on the plot (one of the incredibly
nifty features of such sets).
Using the tweaked version below, call the function as you suggested:
image(mandelbrot(), col = c(heat.colors(49), black))
Then use locator(2) to define your next view:
image(mandelbrot(locator(2)), col = c(heat.colors(49), black))
Of course, I would've been nice if I'd included the tweaked version. D'ho!
###
# Function to calculate the Mandelbrot set. This function calls a #
# C routine in order to perform the calculations faster. #
# #
# Written by Mario dos Reis. September 2003 #
# Modified: added if(is.list(x)){...} at start to check if co-ords#
# are from locator() or similar - jason turner oct 2 2003 #
###
mandelbrot - function(x = c(-3, 1),# x limits
y = c(-1.8, 1.8),# y limits
nx = 600,# x resolution
ny = 600,# y resolution
iter = 20) # maximun number of iterations
{
if(is.list(x)) {
y - range(x$y)
x - range(x$x)
}
xcoo - seq(x[1], x[2], len = nx) # x coordinates
ycoo - seq(y[1], y[2], len = ny) # y coordinates
set = numeric(nx*ny) # this will store the output of
# the C routine
# This is the call to the C function itself
the.set = .C(mandelbrot,
xcoo = as.double(xcoo),
ycoo = as.double(ycoo),
nx = as.integer(nx),
ny = as.integer(ny),
set = as.integer(set),
iter = as.integer(iter))$set
# Create a list with elements x, y and z,
# suitable for image(), persp(), etc. and return it.
return(list(x = xcoo, y = ycoo, z = matrix(the.set, ncol = ny, byrow
= T)));
}
--
Indigo Industrial Controls Ltd.
http://www.indigoindustrial.co.nz
64-21-343-545
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[R] how calculate mean for each group
Hello, R experts: I got data like this: group duplicate treatment A Y 5 A Y 3 A N 6 B Y 2 B N 4 B Y 1 How to sort the data and calculate the average treatment value for each group in two level of duplicate. Results like this: group duplicate treatment A Y 4 A N 6 B Y 1.5 B N 4 Thank you in advance. Josh __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] how calculate mean for each group
Have you considered aggregate? hope this helps. spencer graves [EMAIL PROTECTED] wrote: Hello, R experts: I got data like this: group duplicate treatment A Y 5 A Y 3 A N 6 B Y 2 B N 4 B Y 1 How to sort the data and calculate the average treatment value for each group in two level of duplicate. Results like this: group duplicate treatment A Y 4 A N 6 B Y 1.5 B N 4 Thank you in advance. Josh __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] how calculate mean for each group
On Wed, 2003-10-01 at 20:15, [EMAIL PROTECTED] wrote: Hello, R experts: I got data like this: group duplicate treatment A Y 5 A Y 3 A N 6 B Y 2 B N 4 B Y 1 How to sort the data and calculate the average treatment value for each group in two level of duplicate. Results like this: group duplicate treatment A Y 4 A N 6 B Y 1.5 B N 4 Thank you in advance. Josh # Create a dataframe df - data.frame(group = c(rep(A, 3), rep(B, 3)), duplicate = c(Y, Y, N, Y, N, Y), treatment = c(5, 3, 6, 2, 4, 1)) # Use aggregate aggregate(df$treatment, list(df$group, df$duplicate), mean) Group.1 Group.2 x 1 A N 6.0 2 B N 4.0 3 A Y 4.0 4 B Y 1.5 Aggregate returns a data frame in this case, so that you can then set the colnames and order the output if you wish. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
