Re: [R] Test for equality of coefficients in multivariate multipleregression
Dear Berwin, Simply stacking the problems and treating the resulting observations as independent will give you the correct coefficients, but incorrect coefficient variances and artificially zero covariances. The approach that I suggested originally -- testing a linear hypothesis using the coefficient estimates and covariances from the multivariate linear model -- seems simple enough. For example, to test that all three coefficients are the same across the two equations, b - as.vector(coef(x.mlm)) V - vcov(x.mlm) L - c(1, 0, 0,-1, 0, 0, 0, 1, 0, 0,-1, 0, 0, 0, 1, 0, 0,-1) L - matrix(L, nrow=3, byrow=TRUE) t(L %*% b) %*% (L %*% V %*% t(L)) %*% (L %*% b) The test statistic is chi-square with 3 df under the null hypothesis. (Note: not checked carefully.) (BTW, it's a bit unclear to me how much of this exchange was on r-help, but I'm copying to r-help since at least one of Ulrich's messages referring to alternative approaches appeared there. I hope that's OK.) Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: Berwin A Turlach [mailto:[EMAIL PROTECTED] On Behalf Of Berwin A Turlach Sent: Tuesday, July 18, 2006 9:28 PM To: Andrew Robinson Cc: Ulrich Keller; John Fox Subject: Re: [R] Test for equality of coefficients in multivariate multipleregression G'day all, AR == Andrew Robinson [EMAIL PROTECTED] writes: AR I suggest that you try to rewrite the model system into a AR single mixed-effects model, [...] Why a mixed-effect model, wouldn't a fixed effect be o.k. too? Something like: DF-data.frame(x1=rep(c(0,1),each=50),x2=rep(c(0,1),50)) tmp-rnorm(100) DF$y1-tmp+DF$x1*.5+DF$x2*.3+rnorm(100,0,.5) DF$y2-tmp+DF$x1*.5+DF$x2*.7+rnorm(100,0,.5) x.mlm-lm(cbind(y1,y2)~x1+x2,data=DF) coef(x.mlm) y1 y2 (Intercept) -0.08885266 -0.05749196 x1 0.33749086 0.60395258 x2 0.72017894 1.11932077 DF2 - with(DF, data.frame(y=c(y1,y2))) DF2$x11 - with(DF, c(x1, rep(0,100))) DF2$x21 - with(DF, c(x2, rep(0,100))) DF2$x12 - with(DF, c(rep(0,100), x1)) DF2$x22 - with(DF, c(rep(0,100), x2)) DF2$x1 - with(DF, c(x1, x1)) DF2$wh - rep(c(0,1), each=100) fm1 - lm(y~wh + x11 + x21 + x12 + x22, DF2) fm1 Call: lm(formula = y ~ wh + x11 + x21 + x12 + x22, data = DF2) Coefficients: (Intercept) wh x11 x21 x12 x22 -0.08885 0.03136 0.33749 0.72018 0.60395 1.11932 fm2 - lm(y~wh + x1 + x21 + x22, DF2) anova(fm2,fm1) Analysis of Variance Table Model 1: y ~ wh + x1 + x21 + x22 Model 2: y ~ wh + x11 + x21 + x12 + x22 Res.Df RSS Df Sum of Sq F Pr(F) 1195 246.919 2194 246.031 1 0.888 0.6998 0.4039 Cheers, Berwin == Full address Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr) School of Mathematics and Statistics+61 (8) 6488 3383 (self) The University of Western Australia FAX : +61 (8) 6488 1028 35 Stirling Highway Crawley WA 6009e-mail: [EMAIL PROTECTED] Australiahttp://www.maths.uwa.edu.au/~berwin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Test for equality of coefficients in multivariate multipleregression
G'day John, JF == John Fox [EMAIL PROTECTED] writes: JF Simply stacking the problems and treating the resulting JF observations as independent will give you the correct JF coefficients, but incorrect coefficient variances Yes, after Andrew's (off-list) answer I realised this too. If I am not mistaken, all variances/covariances should be off by a factor of 1/2 or something like that. JF and artificially zero covariances. Well, I must admit that I misread Ulrich's code for most of the day. I hadn't realised that the variable `tmp' introduces a correlation between `y1' and `y2' in his code: DF-data.frame(x1=rep(c(0,1),each=50),x2=rep(c(0,1),50)) tmp-rnorm(100) DF$y1-tmp+DF$x1*.5+DF$x2*.3+rnorm(100,0,.5) DF$y2-tmp+DF$x1*.5+DF$x2*.7+rnorm(100,0,.5) for some reason, my brain kept parsing this as generate *one* random intercept for y1 and *one* random intercept for y2, not that each individual observation has a random intercept. Under the model that my brain kept parsing, one would have zero covariances. :) Now I understand why Andrew suggested the use of mixed models and would go down that way too. But I believe your approach is valid too. JF (BTW, it's a bit unclear to me how much of this exchange was JF on r-help, Easy, all those that have r-help either in the TO: or CC: field. Those were Ulrich's original message and the answer by you and Andrew, I kept all my mails so far off-list. JF but I'm copying to r-help since at least one of Ulrich's JF messages referring to alternative approaches appeared there. Yes, I noticed that and answered off-list. In that message, if I read it correctly, he had confused Andrew and me. JF I hope that's OK.) Sure, why not? :) Cheers, Berwin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How would you export a 3-dimensional array to an SQL database?
Hello,
How would you export a 3-dimensional array to an SQL database?
a-array(1:24, 2:4)
Is there an open source DB that would be more adequate for this type of
operation?
Is there a way to reshape/flatten a 3-dimensional array?
Regards,
Pierre Lapointe
**
AVIS DE NON-RESPONSABILITE: Ce document transmis par courrie...{{dropped}}
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Re: [R] Fitting a distribution to peaks in histogram
Hi
There are some packages for mass spectra processing (spectrino,
caMassClass). I did not use them so I do not know how they suit your
needs.
However you can compute area (integrate) by these functions
# uses information interactively from plot(x,y)
# first it replots data between corners *replot(x,y)*
# then it computes sum between x axis and y values - osum -
# and between baseline and y values - cista - based
# on locator positions
integ-function (x,y)
{
replot(x,y)
meze-locator(2)
dm-meze$x[1]
hm-meze$x[2]
abline(v=c(dm,hm),col=2)
vyber-x=hmx=dm
f3 - splinefun(x, y)
osum-integrate(f3, dm, hm)$value
o1-(y[x==min(x[vyber])]+y[x==max(x[vyber])])*(max(x[vyber])-
min(x[vyber]))/2
cista-osum-o1
return(c(osum,cista))
}
# similar as integ but you has to supply upper and lower limits (dm,
# hm) manually if you do not want to perform integration of whole #
area under the curve.
integ1-function (x,y,dm=-Inf,hm=+Inf)
{
ifelse(dm==-Inf, dm-min(x), dm-dm)
ifelse(hm==+Inf, hm-max(x), hm-hm)
vyber-x=hmx=dm
f3 - splinefun(x, y)
osum-integrate(f3, dm, hm)$value
o1-(y[x==min(x[vyber])]+y[x==max(x[vyber])])*(max(x[vyber])-
min(x[vyber]))/2
cista-osum-o1
return(c(osum,cista))
}
On 19 Jul 2006 at 11:58, Ulrik Stervbo wrote:
Date sent: Wed, 19 Jul 2006 11:58:38 +0200
From: Ulrik Stervbo [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject:[R] Fitting a distribution to peaks in histogram
Hello list!
I would like to fit a distribution to each of the peaks in a
histogram, such as this:
http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.pn
g .
The peaks are identified using Petr Pikal peaks function (
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/33097.html), but after
that I am quite stuck.
Any idea as to how I can:
Fit a distribution to each peak
Integrate the area between each two peaks, using the means and widths
of the distributions fitted to the two peaks. I will be using the
integrate function
The histogram is based on approximately 15000 events, which makes
Mclust and pam (which both delivers the information I need) less
useful.
The whole point of this exercise is to find the percentage of cells in
peak 1, 2, 3, and so on, and between peak 1-2, peak 2-3, peak 3-4 and
so on. Having more that 6 peaks does not appears likely.
I am quite new to R and apologise if the solution is fairly basic.
Thank you in advance for any help and suggestions
Sincerely,
Ulrik
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Petr Pikal
[EMAIL PROTECTED]
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[R] Stirling numbers
Hi anyone coded up Stirling numbers in R? [I need unsigned Stirling numbers of the first kind] cheers Robin -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Output and Word
On page 2 of the manual, Section 2 (Requirements) has
The package also requires a utility to zip and unzip compressed
files,
such as unzip, Winzip or jar.
With a footnote that unzip can be found at
http://www.info-zip.org/
for free. You can use any utility that can zip/unzip pkzip formatted
files.
If you want to use something else, you can. See ?odfWeaveControl.
I didn't use utils::zip.unpack since there did not appear to be an
analogous
utility for re-zipping the file. Is this incorrect?
I will put an automatic check on package startup for the above utilities
and print a warning if nothing is found.
Max
0n Wed, 19 Jul 2006, David Hajage wrote:
thank you Greg Snow for this information !
But I have this message :
odfWeave(c:/simple.odt, c:/essai.odt)
Setting wd
Copying c:/simple.odt
Decompressing ODF file using unzip -o
C:\DOCUME~1\Maud\LOCALS~1\Temp\RtmpF0hdqb/simple.odt
Erreur dans odfWeave(c:/simple.odt, c:/essai.odt) :
Error unzipping file
De plus : Warning message:
unzip introuvable
R says that it doesn't find unzip... What is this program ?
It is in the Rtools.zip bundle used to build source packages for R
under
Windows (your unstated OS, it seems).
However, you should take this up with the package maintainer, as R has
the
capability to unzip files builtin (utils::zip.unpack) on Windows.
2006/7/18, Greg Snow Greg.Snow at intermountainmail.org:
--
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Re: [R] R and DDE (Dynamic Data Exchange)
On 7/19/06, Philippe Grosjean [EMAIL PROTECTED] wrote: Richard M. Heiberger wrote: I am thrilled to learn tcltk2 has DDE capability. It is the piece I have been needing to make ESS work directly with the RGUI on Windows. GNU emacs on Windows has a ddeclient, but no access to COM. So if R, or tcltk2 talking in both directions to R, has a ddeserver, all should be possible. I will be reading the documentation closely in a few weeks to tie it together and then intend to make it happen. Do you, or any other list member, have a sense of the size, complexity, ease, magnitude of the task I just defined? Any advice as I get started on it? Rich Well, to be honest, DDE is an old exchange protocol (the first one proposed by M$ in Windows version 1 or 2). It is not that reliable. In practice, when the communication is working fine, you have no problems with it. But if something fails in either the server or the client, you got a very bad behaviour sometimes. There is a good discussion in this DDE FAQ of when DDE would be preferred and when COM would be: http://www.angelfire.com/biz/rhaminisys/ddeinfo.html#DDEpreferred __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Progress in a loop
Hi, I have to use a loop to perform a quite computer intensive estimation and I would like to know the progress of the loop during the process. I tried to include something like print(paste(k,date(),sep= : )) where k is the number of the iteration, but the result appears only at the end of the loop. Can someone help me please ? ___ Découvrez un nouveau moyen de poser toutes vos questions quelque soit le sujet ! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stirling numbers
Robin == Robin Hankin [EMAIL PROTECTED]
on Wed, 19 Jul 2006 14:25:21 +0100 writes:
Robin Hi anyone coded up Stirling numbers in R?
Sure ;-)
Robin [I need unsigned Stirling numbers of the first kind]
but with my quick search, I can only see those for which I had
2nd kind :
-o--o---
##-- Stirling numbers of the 2nd kind
##-- (Abramowitz/Stegun: 24,1,4 (p. 824-5 ; Table 24.4, p.835)
## S^{(m)}_n = number of ways of partitioning a set of $n$ elements into $m$
## non-empty subsets
Stirling2 - function(n,m)
{
## Purpose: Stirling Numbers of the 2-nd kind
## S^{(m)}_n = number of ways of partitioning a set of
## $n$ elements into $m$ non-empty subsets
## Author: Martin Maechler, Date: May 28 1992, 23:42
##
## Abramowitz/Stegun: 24,1,4 (p. 824-5 ; Table 24.4, p.835)
## Closed Form : p.824 C.
##
if (0 m || m n) stop('m' must be in 0..n !)
k - 0:m
sig - rep(c(1,-1)*(-1)^m, length= m+1)# 1 for m=0; -1 1 (m=1)
## The following gives rounding errors for (25,5) :
## r - sum( sig * k^n /(gamma(k+1)*gamma(m+1-k)) )
ga - gamma(k+1)
round(sum( sig * k^n /(ga * rev(ga
}
options(digits=15)
for (n in 11:31) cat(n =, n, S_n(5) =, Stirling2(n,5), \n)
n - 25
for(k in c(3,5,10))
cat( S_,n,^(,formatC(k,wid=2),) = , Stirling2(n,k),\n,sep = )
for (n in 1:15)
cat(formatC(n,w=2),:, sapply(1:n, Stirling2, n = n),\n)
## 1 : 1
## 2 : 1 1
## 3 : 1 3 1
## 4 : 1 7 6 1
## 5 : 1 15 25 10 1
## 6 : 1 31 90 65 15 1
## 7 : 1 63 301 350 140 21 1
## 8 : 1 127 966 1701 1050 266 28 1
## 9 : 1 255 3025 7770 6951 2646 462 36 1
## 10 : 1 511 9330 34105 42525 22827 5880 750 45 1
## 11 : 1 1023 28501 145750 246730 179487 63987 11880 1155 55 1
## 12 : 1 2047 86526 611501 1379400 1323652 627396 159027 22275 1705 66 1
## 13 : 1 4095 261625 2532530 7508501 9321312 5715424 1899612 359502 39325 2431
78 1
## 14 : 1 8191 788970 10391745 40075035 63436373 49329280 20912320 5135130
752752 66066 3367 91 1
## 15 : 1 16383 2375101 42355950 210766920 420693273 408741333 216627840
67128490 12662650 1479478 106470 4550 105 1
plot(6:30, sapply(6:30, Stirling2, m=5), log = y, type = l)
## Abramowitz says something like S2(n,m) ~ m^n / m!
## --
nn - 6:30; sapply(nn, Stirling2, m=5) / (5^nn / gamma(5+1))
## 0.114 0.21 .. 0.99033 0.992266 0.993812
-o--o---
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[R] WLS ins systemfit question
How does one specify the weights for WLS in the systemfit command ? That is, there is a weight option in lm(), but there doesn't seem to be weight option for systemfit(WLS) Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Progress in a loop
Florent Bresson wrote: Hi, I have to use a loop to perform a quite computer intensive estimation and I would like to know the progress of the loop during the process. I tried to include something like print(paste(k,date(),sep= : )) where k is the number of the iteration, but the result appears only at the end of the loop. Can someone help me please ? Please read the R for Windows FAQ: When using Rgui the output to the console seems to be delayed. Uwe Ligges ___ Découvrez un nouveau moyen de poser toutes vos questions quelque soit le sujet ! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Progress in a loop
Look for progress() in the svMisc package -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Florent Bresson Sent: Wednesday, July 19, 2006 10:13 AM To: r-help@stat.math.ethz.ch Subject: [R] Progress in a loop Hi, I have to use a loop to perform a quite computer intensive estimation and I would like to know the progress of the loop during the process. I tried to include something like print(paste(k,date(),sep= : )) where k is the number of the iteration, but the result appears only at the end of the loop. Can someone help me please ? __ _ Découvrez un nouveau moyen de poser toutes vos questions quelque soit le sujet ! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Progress in a loop
On Wed, 2006-07-19 at 16:12 +0200, Florent Bresson wrote:
Hi, I have to use a loop to perform a quite computer
intensive estimation and I would like to know the
progress of the loop during the process. I tried to
include something like
print(paste(k,date(),sep= : ))
where k is the number of the iteration, but the result
appears only at the end of the loop. Can someone help
me please ?
Windows I assume - you are asked to provide some rudimentary information
about your system when asking for help as the posting guide states.
You need to use flush.console() on Windows, as in:
dat - matrix(runif(20), ncol = 2)
res - numeric(length = 10)
for(i in 1:10) {
res[i] - sum(dat[i, ])
cat(paste(Iteration #:, i, -, date(), \n))
flush.console()
}
Depending on how you want the printed statements to appear on the
screen, you'd be better off with cat not print, e.g.:
cat(paste(k,date(),sep= : ))
If this isn't the solution, post a reply containing information about
your R version, OS, and a reproducible example (simple code data as I
did) to show us the problem.
HTH
G
--
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Gavin Simpson [t] +44 (0)20 7679 0522
ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/cv/
UK. WC1E 6BT. [w] http://www.ucl.ac.uk/~ucfagls/
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[R] plain shading (not residuals) in mosaic plot
Hello. I've been using R for a couple of months and enjoying it a lot. This is my first post to R-help. I'm using the vcd package to make mosaic plots with labels on the tiles indicating the number of items in each cell. For example, I've made this plot: allmorph-structure(c(10, 26, 17, 100, 70, 97, 253, 430, 185, 177, 25, 1), .Dim = as.integer(c(6, 2)), .Dimnames = structure(list(Stem.initial.obstruent = c(p, t,s, k,b,d,g),Subst.behavior=c(unsubstituted,substituted)), .Names = c(Stem-initial obstruent,Behavior according to dictionary)), class = table) mosaic(allmorph,direction=v,pop=FALSE) labeling_cells(text=allmorphs,margin=0)(allmorph) So far so good. What I can't figure out how to do--after searching through the vcd documentation (http://cran.r-project.org/doc/packages/vcd.pdf), Googling, and checking the r-help archive--is how to shade the tiles according to their values for the variables rather than to reflect residuals. That is, I want all the tiles at the bottom, whose value for the x-axis variable is substituted, to be dark grey, and those at the top, in the unsubstituted category, to be light grey. I know how to do it with mosaicplot(): mosaicplot(morphs3,color=c(grey(0.8),grey(0.4))) ...but this doesn't work with mosaic(): the command mosaic(morphs3,color=c(grey(0.8),grey(0.4))) yields a plot with all tiles the same color. And conversely, I can't find a way to use mosaicplot() and add numeric labels to the tiles--without much hope of success, I tried combining mosaicplot() with labeling_cells(), but, unsurprisingly, it didn't work: mosaicplot(morphs3,color=c(grey(0.8),grey(0.4)),pop=FALSE) Warning message: extra argument(s) 'pop' will be disregarded in: mosaicplot.default(morphs3, color = c(grey(0.8), grey(0.4)), labeling_cells(text=morphs3,margin=0)(morphs3) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) :Viewport 'cell:Stem-initial obstruent=p,Behavior according to dictionary=unsubstituted' was not found Does anyone know how to get both the shading I want and the labels I want, whether with mosaic(), with mosaicplot(), or in some other way? Thanks for your attention. -Kie Zuraw __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and DDE (Dynamic Data Exchange)
Gabor, Thank you for that information. The reason for choosing DDE is that GNU emacs doesn't speak COM. Every year or so I ask on the emacs-for-windows list, and every year I get the answer no. DDE is the technology that I have been using in ESS for sending information to the S-Plus Commands window in the S-Plus GUI on Windows. I want to send information to the Rgui window on Windows in the same way. The Rterm window runs on Windows emacs in an *R* buffer exactly the way R runs on Unix. But it doesn't interact smoothly with other Windows programs. The specific difficulty that I want to solve now is the interaction with RExcel. RExcel and RGui work together smoothly. RExcel and Rterm in an emacs *R* buffer do not work smoothly (emacs buffers freeze requiring ^G to get control back). Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with ordered logistic regression using polr function.
On Wed, 19 Jul 2006, Debarchana Ghosh wrote: Hi, I'm trying to fit a ordered logistic regression. The response variable (y) has three levels (0,1,2). The command I've used is: /ordlog-polr(y~x1+x2+x3+x4, data=finalbase, subset=heard, weight=wt, na.action=na.omit) / (There are no NA's in y but there are NA's in X's) The error I'm getting is: /Warning messages: 1: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) 2: design appears to be rank-deficient, so dropping some coefs in: polr(right.ans ~ S107 + children + work + rel + media + V013 + / Those are not errors. They are warnings (and I told you yesterday that the first one would happen and would be harmless with probability weights). The second warning may indicate a real problem or not: you can tell by looking at which coefficients have been dropped. Also, if that is the warning message then the polr() call you used is not the one you said you were using. Also, if I write /summary(ordlog)/ I'm getting the following error: /Re-fitting to get Hessian Error in if (all(pr 0)) -sum(wt * log(pr)) else Inf : missing value where TRUE/FALSE needed /Could anybody point out the problem? You can specify Hess=TRUE in the original polr() call so that refitting would not be necessary. This is sensible anyway if you know you are going to be computing standard errors. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RE : Re: Progress in a loop
Thanks, it is exactly what I was looking for.
Florent Bresson
--- Gavin Simpson [EMAIL PROTECTED] a écrit :
On Wed, 2006-07-19 at 16:12 +0200, Florent Bresson
wrote:
Hi, I have to use a loop to perform a quite
computer
intensive estimation and I would like to know the
progress of the loop during the process. I tried
to
include something like
print(paste(k,date(),sep= : ))
where k is the number of the iteration, but the
result
appears only at the end of the loop. Can someone
help
me please ?
Windows I assume - you are asked to provide some
rudimentary information
about your system when asking for help as the
posting guide states.
You need to use flush.console() on Windows, as in:
dat - matrix(runif(20), ncol = 2)
res - numeric(length = 10)
for(i in 1:10) {
res[i] - sum(dat[i, ])
cat(paste(Iteration #:, i, -, date(), \n))
flush.console()
}
Depending on how you want the printed statements to
appear on the
screen, you'd be better off with cat not print,
e.g.:
cat(paste(k,date(),sep= : ))
If this isn't the solution, post a reply containing
information about
your R version, OS, and a reproducible example
(simple code data as I
did) to show us the problem.
HTH
G
--
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Gavin Simpson [t] +44 (0)20 7679
0522
ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679
0565
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gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w]
http://www.ucl.ac.uk/~ucfagls/cv/
UK. WC1E 6BT. [w]
http://www.ucl.ac.uk/~ucfagls/
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Re: [R] How would you export a 3-dimensional array to an SQL database?
Here's a way to flatten and unflatten your array.
a -array(1:24, 2:4)
d -dim(a)
flattened -cbind(expand.grid(1:d[1],1:d[2],1:d[3]),as.vector(a))
unflattened -array(flattened[,4],d)
identical(a,unflattened)
a==unflattened
NeuroRox
From: Lapointe, Pierre [EMAIL PROTECTED]
To: 'r-help@stat.math.ethz.ch' r-help@stat.math.ethz.ch
Subject: [R] How would you export a 3-dimensional array to an SQL database?
Date: Wed, 19 Jul 2006 08:45:42 -0400
Hello,
How would you export a 3-dimensional array to an SQL database?
a-array(1:24, 2:4)
Is there an open source DB that would be more adequate for this type of
operation?
Is there a way to reshape/flatten a 3-dimensional array?
Regards,
Pierre Lapointe
**
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[R] connection network - influence of site
Dear R users, I'm trying to construct a distance matrix based on a nb object created by spdep where sites must have a larger influence in one direction then in the other. Here is an example to better illustrate what I need: Let say I have the following Gabriel connection network library(spdep) library(ade4) data(orbatid) nbgab-graph2nb(gabrielneigh(as.matrix(oribatid$xy))) plot(nbgab,oribatid$xy) text(oribatid$xy,as.character(1:70),pos=1) # site number arrows(-0.3,0,-0.3,10) # gradient direction In that example, site 1 shouldn't influence site 2 (so it should have a distance if 0 in the distance matrix). However site 1 should influence site 7 (1 in the distance matrix), it should also influence site 12 and 10 (2 in the distance matrix), and site 13,14,17 and 20 (3 in the distance matrix) and so on for every site. Also, the smallest number of jumps from one site to the other has to be considered (e.g. 1 to 20 can be connected through 3 links (1 - 7 - 10 - 20) or through 4 links (1 - 7 - 12 - 13 - 20)). Considering the gradient, it has to be noted that the distance matrix will be asymmetric (e.g. site 7 doesn't influence site 1). This needs to be done for various connection network, going from regular grid (rook connections) to networks such as the one presented above. Can it be done ? If it can, I would be very happy for some one to give me a hand. And if it has already been done I would be glad to be pointed in the right direction. Thanks in advance !! Guillaume Blanchet __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] trellis.focus with postscript device
Hello.
First: R 2.3.1 on Windows XP.
I am trying to add information (sample size) to the Trellis strips which
I am successful using the trellis.focus function with the default
Windows device. However, I typically use the postscript device as I use
LaTeX and \includegraphic for incorporating graphs into stat reviews.
Here's some example code (apologies for the lack of creativity and
resemblance to a real example)
yy - c(rnorm(20,2),rnorm(35,3), rnorm(30,2),rnorm(20,3),rnorm(4,2),
rnorm(10,3))
xx - c(1:20,1:35,1:30,1:20,1:4,1:10)
gg - rep(c('A','B','A','B','A','B'), c(20,35,30,20,4,10))
pp - rep(c('Cond 1','Cond 2','Cond 3'), c(55, 50, 14))
xyplot(yy ~ xx | pp, groups=gg)
trellis.focus('strip', 1, 1)
ltext(0,.5,'20',col='red', pos=4)
ltext(1,.5,'35',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 2, 1)
ltext(0,.5,'30',col='red', pos=4)
ltext(1,.5,'20',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 1, 2)
ltext(0,.5,'4',col='red', pos=4)
ltext(1,.5,'10',col='black', pos=2)
trellis.unfocus()
This works. But if I do,
postscript('C:/TEMP/example.eps')
# All code as above
dev.off()
I notice a problem with the graphic. When looking at the EPS figure, the
only strip with added data is the first one (bottom left) with the strip
still highlighted in red (i.e. it doesn't appear that trellis.unfocus()
was executed). Work arounds that I can think of are to simply save the
Windows device as postscript and save to the correct directory or better
yet, write my own strip function. However, I was curious if there was
another way using the strategy of postscript(), graph code,
trellis.focus() code, dev.off().
Thanks,
Mat
***
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Re: [R] plain shading (not residuals) in mosaic plot
If you look at ?mosaic the ... argument says it gets passed to strucplot and looking at ?strucplot we see it accepts a gp= arg so try this (same as your plus gp= arg): cols - c(grey(0.8),grey(0.4)) mosaic(allmorph, direction = v, pop = FALSE, gp = list(col = cols)) On 7/19/06, Kie Zuraw [EMAIL PROTECTED] wrote: Hello. I've been using R for a couple of months and enjoying it a lot. This is my first post to R-help. I'm using the vcd package to make mosaic plots with labels on the tiles indicating the number of items in each cell. For example, I've made this plot: allmorph-structure(c(10, 26, 17, 100, 70, 97, 253, 430, 185, 177, 25, 1), .Dim = as.integer(c(6, 2)), .Dimnames = structure(list(Stem.initial.obstruent = c(p, t,s, k,b,d,g),Subst.behavior=c(unsubstituted,substituted)), .Names = c(Stem-initial obstruent,Behavior according to dictionary)), class = table) mosaic(allmorph,direction=v,pop=FALSE) labeling_cells(text=allmorphs,margin=0)(allmorph) So far so good. What I can't figure out how to do--after searching through the vcd documentation (http://cran.r-project.org/doc/packages/vcd.pdf), Googling, and checking the r-help archive--is how to shade the tiles according to their values for the variables rather than to reflect residuals. That is, I want all the tiles at the bottom, whose value for the x-axis variable is substituted, to be dark grey, and those at the top, in the unsubstituted category, to be light grey. I know how to do it with mosaicplot(): mosaicplot(morphs3,color=c(grey(0.8),grey(0.4))) ...but this doesn't work with mosaic(): the command mosaic(morphs3,color=c(grey(0.8),grey(0.4))) yields a plot with all tiles the same color. And conversely, I can't find a way to use mosaicplot() and add numeric labels to the tiles--without much hope of success, I tried combining mosaicplot() with labeling_cells(), but, unsurprisingly, it didn't work: mosaicplot(morphs3,color=c(grey(0.8),grey(0.4)),pop=FALSE) Warning message: extra argument(s) 'pop' will be disregarded in: mosaicplot.default(morphs3, color = c(grey(0.8), grey(0.4)), labeling_cells(text=morphs3,margin=0)(morphs3) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) :Viewport 'cell:Stem-initial obstruent=p,Behavior according to dictionary=unsubstituted' was not found Does anyone know how to get both the shading I want and the labels I want, whether with mosaic(), with mosaicplot(), or in some other way? Thanks for your attention. -Kie Zuraw __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: Classification error rate increased by bagging - any ideas?
Hi, I'm analysing some anthropometric data on fifty odd skull bases. We know the gender of each skull, and we are trying to develop a predictor to identify the sex of unknown skulls. Rpart with cross-validation produces two models - one of which predicts gender for Males well, and Females poorly, and the other does the opposite (Females well, and Males poorly). In both cases the error rate for the worse predicted gender is close to 50%, and for the better predicted gender about 15%. Bagging tree models produces a model which classifies both males and females equally well (or equally poorly), but has an overall error rate (just over 30%) higher than either of the rpart models (about 25%). My instinct is to go for the bagging results, as they seem more reasonable, but my colleagues really like the lower overall error rate. Any thoughts? Ta, Anthony Staines-- Dr. Anthony Staines, Senior Lecturer in Epidemiology. School of Public Health and Population Sciences, UCD, Earlsfort Terrace, Dublin 2, Ireland. Tel:- +353 1 716 7345. Fax:- +353 1 716 7407 Mobile:- +353 86 606 9713 Web:- http://phm.ucd.ie __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to use large data set ?
Hello R users, Sorry for my English, i'm French. I want to use a large dataset (3 millions of rows and 70 var) but I don't know how to do because my computer crash quickly (P4 2.8Ghz, 1Go ). I have also a bi Xeon with 2Go so I want to do computation on this computer and show the results on mine. Both of them are on Windows XP... To do shortly I have: 1 server with a MySQL database 1computer and I want to use them with a large dataset. I'm trying to use RDCOM to connect the database and installing (but it's hard for me..) Rpad. Is there another solutions ? Thanks in advance Yohan C. -- Ce message est confidentiel. Son contenu ne represente en aucun cas un engagement de la part du Groupe Soft Computing sous reserve de tout accord conclu par ecrit entre vous et le Groupe Soft Computing. Toute publication, utilisation ou diffusion, meme partielle, doit etre autorisee prealablement. Si vous n'etes pas destinataire de ce message, merci d'en avertir immediatement l'expediteur. This message is confidential. Its content does not constitute a commitment by Soft Computing Group except where provided for in a written agreement between you and Soft Computing Group. Any unauthorised disclosure, use or dissemination, either whole or partial, is prohibited. If you are not the intended recipient of this message, please notify the sender immediately. -- [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trellis.focus with postscript device
On 7/19/06, Soukup, Mat [EMAIL PROTECTED] wrote:
Hello.
First: R 2.3.1 on Windows XP.
I am trying to add information (sample size) to the Trellis strips which
I am successful using the trellis.focus function with the default
Windows device. However, I typically use the postscript device as I use
LaTeX and \includegraphic for incorporating graphs into stat reviews.
Here's some example code (apologies for the lack of creativity and
resemblance to a real example)
yy - c(rnorm(20,2),rnorm(35,3), rnorm(30,2),rnorm(20,3),rnorm(4,2),
rnorm(10,3))
xx - c(1:20,1:35,1:30,1:20,1:4,1:10)
gg - rep(c('A','B','A','B','A','B'), c(20,35,30,20,4,10))
pp - rep(c('Cond 1','Cond 2','Cond 3'), c(55, 50, 14))
xyplot(yy ~ xx | pp, groups=gg)
trellis.focus('strip', 1, 1)
ltext(0,.5,'20',col='red', pos=4)
ltext(1,.5,'35',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 2, 1)
ltext(0,.5,'30',col='red', pos=4)
ltext(1,.5,'20',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 1, 2)
ltext(0,.5,'4',col='red', pos=4)
ltext(1,.5,'10',col='black', pos=2)
trellis.unfocus()
This works. But if I do,
postscript('C:/TEMP/example.eps')
# All code as above
dev.off()
I notice a problem with the graphic. When looking at the EPS figure, the
only strip with added data is the first one (bottom left) with the strip
still highlighted in red (i.e. it doesn't appear that trellis.unfocus()
was executed).
Actually, you have produced a multiple-page postscript file, with what
you really want in the last page. If you highlight the strips when
calling trelis.focus, they have to be un-highlighted by
trellis.unfocus. In theory, this is just a removal of a rectangle
object. In practice, grid achieves this by drawing a new page. You
need to avoid this.
Your options are:
(1) add 'highlight = FALSE' to all trellis.focus() calls
(2) run the script in batch mode, where the default highlight =
interactive() is FALSE
I'll think about adding an option to control the default.
Deepayan
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Re: [R] Random structure of nested design in lme
Although I know it's not correct, this is what I tried in lme: anova(lme(NA.1~soiltype*habitat,random=~1|destination/habitat/origin/soiltype)) # numDF denDF F-value p-value #(Intercept) 1 130 12.136195 0.0007 #soiltype 1 130 15.099792 0.0002 #habitat 110 0.699045 0.4226 #soiltype:habitat 1 130 2.123408 0.1475 René. -Original Message- From: Doran, Harold [mailto:[EMAIL PROTECTED] Sent: Wed 2006-07-19 13:53 To: ESCHEN Rene; r-help@stat.math.ethz.ch Subject: RE: [R] Random structure of nested design in lme Can you provide an example of what you have done with lme so we might be able to evaluate the issue? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ESCHEN Rene Sent: Wednesday, July 19, 2006 7:37 AM To: r-help@stat.math.ethz.ch Subject: [R] Random structure of nested design in lme All, I'm trying to analyze the results of a reciprocal transplant experiment using lme(). While I get the error-term right in aov(), in lme() it appears impossible to get as expected. I would be greatful for any help. My experiment aimed to identify whether two fixed factors (habitat type and soil type) affect the development of plants. I took soil from six random sites each of two types (arable and grassland) and transplanted them back into the sites of origin in such way that in each of the sites there were six pots containing arable soil and six pots of grassland soil, each containing a seedling. With aov(), I got the analysis as I expected, with habitat type tested against destination site, and soil type tested against origin site: summary(aov(response~soiltype*habitat+Error(destination+origin))) # #Error: destination # Df Sum Sq Mean Sq F value Pr(F) #habitat1 1. 1. 0.699 0.4226 #Residuals 10 14.3056 1.4306 # #Error: origin # Df Sum Sq Mean Sq F value Pr(F) #soiltype 1 1.8 1.8 11.636 0.006645 ** #Residuals 10 1.52778 0.15278 #--- #Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 # #Error: Within # Df Sum Sq Mean Sq F value Pr(F) #soiltype:habitat 1 0.2500 0.2500 2.1774 0.1427 #Residuals120 13.7778 0.1148 However, when I try to replicate this analysis in lme, I am unable to get the structure of the random factors (origin and destination) correct. Does anyone have a suggestion how to resolve this problem? Thanks in advance. René Eschen CABI Bioscience Centre Switzerland Rue des Grillons 1 2800 Delémont Switzerland [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave and multipage lattice
Dieter Menne wrote:
Dear R-Listeners,
as the Sweave faq says:
http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html
creating several figures from one figure chunk does not work, and for
standard graphics, a workaround is given. Now I have a multipage trellis
plot with an a-priori unknown number of pages, and I don't see an elegant
way of dividing it up into multiple pdf-files.
I noted there is a page event handler in the ... parameters, which would
provide a handle to open/close the file.
Any good idea would be appreciated.
Dieter
Hi, Dieter,
I haven't seen a reply to this and I don't know Sweave. However, will
the following example work? It does require you know the layout for one
page.
--sundar
library(lattice)
trellis.device(postscript, file = barley%02d.eps,
width = 5, height = 3, onefile = FALSE,
paper = special)
## from ?xyplot
dotplot(variety ~ yield | site, data = barley, groups = year,
key = simpleKey(levels(barley$year), space = right),
xlab = Barley Yield (bushels/acre) ,
aspect=0.5, layout = c(1, 1), ylab=NULL)
dev.off()
files - list.files(pattern = glob2rx(barley*.eps))
for(file in files)
cat(\\includegraphics{, file, }\n\n, sep=)
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Re: [R] trellis.focus with postscript device
It works fine as long as you give it the layout. I used xyplot(yy ~ xx | pp, groups=gg, layout=c(2,2)) This is needed to make sure that the rows and columns of the trellis that you reference are consistent with the layout that xyplot has chosen. Another way to handle this is to change the factor labels pp - factor(pp) levels(pp) - c(20 Cond 1 35, 30 Cond 2 20, 4 Cond 3 10) xyplot(yy ~ xx | pp, groups=gg) Rich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting a distribution to peaks in histogram
I would like to fit a distribution to each of the peaks in a histogram, such as this: http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png As a first shot, I'd try fitting a mixture of gamma distributions (say 3), plus a constant term for the highest bin. You could do this using ML. If the number of peaks is truly unknown, this will be a little trickier but still possible and you could use the LRT to chose between them. Integrate the area between each two peaks, using the means and widths of the distributions fitted to the two peaks. I will be using the integrate function Why do you want to do this? The histogram is based on approximately 15000 events, which makes Mclust and pam (which both delivers the information I need) less useful. If you have unbinned data, it would be better (more precise/powerful) to use that. Regards, Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] WLS ins systemfit question
On Wednesday 19 July 2006 16:22, Benn Fine wrote: How does one specify the weights for WLS in the systemfit command ? That is, there is a weight option in lm(), but there doesn't seem to be weight option for systemfit(WLS) WLS in systemfit means that the different _equations_ (not the observations) are weighted differently. The weights of the equations are taken from a first-step OLS regression by taking the (inverse of the) residual variances of each equation. Of course, this can be iterated. The WLS estimation is similar to SUR but in WLS all off-diagonal elements of the residual covariance matrix are constrained to be zero. Best regards, Arne Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trellis.focus with postscript device
Thanks Deepayan.
Adding the argument highlight=FALSE to each trellis.focus() call worked
marvelously.
Cheers,
Mat
-Original Message-
From: Deepayan Sarkar [mailto:[EMAIL PROTECTED]
Sent: Wednesday, July 19, 2006 11:58 AM
To: Soukup, Mat
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] trellis.focus with postscript device
On 7/19/06, Soukup, Mat [EMAIL PROTECTED] wrote:
Hello.
First: R 2.3.1 on Windows XP.
I am trying to add information (sample size) to the Trellis strips
which
I am successful using the trellis.focus function with the default
Windows device. However, I typically use the postscript device as I
use
LaTeX and \includegraphic for incorporating graphs into stat reviews.
Here's some example code (apologies for the lack of creativity and
resemblance to a real example)
yy - c(rnorm(20,2),rnorm(35,3), rnorm(30,2),rnorm(20,3),rnorm(4,2),
rnorm(10,3))
xx - c(1:20,1:35,1:30,1:20,1:4,1:10)
gg - rep(c('A','B','A','B','A','B'), c(20,35,30,20,4,10))
pp - rep(c('Cond 1','Cond 2','Cond 3'), c(55, 50, 14))
xyplot(yy ~ xx | pp, groups=gg)
trellis.focus('strip', 1, 1)
ltext(0,.5,'20',col='red', pos=4)
ltext(1,.5,'35',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 2, 1)
ltext(0,.5,'30',col='red', pos=4)
ltext(1,.5,'20',col='black', pos=2)
trellis.unfocus()
trellis.focus('strip', 1, 2)
ltext(0,.5,'4',col='red', pos=4)
ltext(1,.5,'10',col='black', pos=2)
trellis.unfocus()
This works. But if I do,
postscript('C:/TEMP/example.eps')
# All code as above
dev.off()
I notice a problem with the graphic. When looking at the EPS figure,
the
only strip with added data is the first one (bottom left) with the
strip
still highlighted in red (i.e. it doesn't appear that
trellis.unfocus()
was executed).
Actually, you have produced a multiple-page postscript file, with what
you really want in the last page. If you highlight the strips when
calling trelis.focus, they have to be un-highlighted by
trellis.unfocus. In theory, this is just a removal of a rectangle
object. In practice, grid achieves this by drawing a new page. You
need to avoid this.
Your options are:
(1) add 'highlight = FALSE' to all trellis.focus() calls
(2) run the script in batch mode, where the default highlight =
interactive() is FALSE
I'll think about adding an option to control the default.
Deepayan
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Re: [R] Fitting a distribution to peaks in histogram
On 7/19/06, hadley wickham [EMAIL PROTECTED] wrote: I would like to fit a distribution to each of the peaks in a histogram, such as this: http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png As a first shot, I'd try fitting a mixture of gamma distributions (say 3), plus a constant term for the highest bin. You could do this using ML. If the number of peaks is truly unknown, this will be a little trickier but still possible and you could use the LRT to chose between them. Can you be a bit more excact? I a biologist and relatively new to R Integrate the area between each two peaks, using the means and widths of the distributions fitted to the two peaks. I will be using the integrate function Why do you want to do this? I am measureing the amount of DNA in cells, and I need to know the percentage of cells in a part of the cell cycle; that the percentage of cells in the first peak, in the second peak and so on. I want to integrate the area between to two cells, because that apparently is how its none (as far as I can tell from the literature) The histogram is based on approximately 15000 events, which makes Mclust and pam (which both delivers the information I need) less useful. If you have unbinned data, it would be better (more precise/powerful) to use that. It very probably is better, but mclust had no result after running for at least 2 hours (I terminated the function after two hours), and as I generate 50-100 datasets, such as the one used for the histogram, as week, I would like to find a faster solution Regards, Hadley Thanks Ulrik -- Blog: http://ulrikstervbo.blogspot.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stirling numbers
Well, given Martin's 2nd kind function and the fact that the 1st and 2nd
kind matrices are inverses, you can get at least some of what you want
by:
... # fill a matrix S2 with second kind numbers and zeros
S2
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]1000000
[2,]1100000
[3,]1310000
[4,]1761000
[5,]1 15 25 10100
[6,]1 31 90 65 1510
[7,]1 63 301 350 140 211
abs(round(solve(S2)))
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]1000000
[2,]1100000
[3,]2310000
[4,]6 1161000
[5,] 24 50 35 10100
[6,] 120 274 225 85 1510
[7,] 720 1764 1624 735 175 211
Not sure how big arguments you need.
HTH,
David L. Reiner
Rho Trading Securities, LLC
Chicago IL 60605
312-362-4963
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler
Sent: Wednesday, July 19, 2006 9:19 AM
To: Robin Hankin
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Stirling numbers
Robin == Robin Hankin [EMAIL PROTECTED]
on Wed, 19 Jul 2006 14:25:21 +0100 writes:
Robin Hi anyone coded up Stirling numbers in R?
Sure ;-)
Robin [I need unsigned Stirling numbers of the first kind]
but with my quick search, I can only see those for which I had
2nd kind :
-o--o-
--
##-- Stirling numbers of the 2nd kind
##-- (Abramowitz/Stegun: 24,1,4 (p. 824-5 ; Table 24.4, p.835)
## S^{(m)}_n = number of ways of partitioning a set of $n$ elements
into $m$
## non-empty subsets
Stirling2 - function(n,m)
{
## Purpose: Stirling Numbers of the 2-nd kind
## S^{(m)}_n = number of ways of partitioning a set of
## $n$ elements into $m$ non-empty subsets
## Author: Martin Maechler, Date: May 28 1992, 23:42
##
## Abramowitz/Stegun: 24,1,4 (p. 824-5 ; Table 24.4, p.835)
## Closed Form : p.824 C.
##
if (0 m || m n) stop('m' must be in 0..n !)
k - 0:m
sig - rep(c(1,-1)*(-1)^m, length= m+1)# 1 for m=0; -1 1 (m=1)
## The following gives rounding errors for (25,5) :
## r - sum( sig * k^n /(gamma(k+1)*gamma(m+1-k)) )
ga - gamma(k+1)
round(sum( sig * k^n /(ga * rev(ga
}
options(digits=15)
for (n in 11:31) cat(n =, n, S_n(5) =, Stirling2(n,5), \n)
n - 25
for(k in c(3,5,10))
cat( S_,n,^(,formatC(k,wid=2),) = , Stirling2(n,k),\n,sep =
)
for (n in 1:15)
cat(formatC(n,w=2),:, sapply(1:n, Stirling2, n = n),\n)
## 1 : 1
## 2 : 1 1
## 3 : 1 3 1
## 4 : 1 7 6 1
## 5 : 1 15 25 10 1
## 6 : 1 31 90 65 15 1
## 7 : 1 63 301 350 140 21 1
## 8 : 1 127 966 1701 1050 266 28 1
## 9 : 1 255 3025 7770 6951 2646 462 36 1
## 10 : 1 511 9330 34105 42525 22827 5880 750 45 1
## 11 : 1 1023 28501 145750 246730 179487 63987 11880 1155 55 1
## 12 : 1 2047 86526 611501 1379400 1323652 627396 159027 22275 1705 66
1
## 13 : 1 4095 261625 2532530 7508501 9321312 5715424 1899612 359502
39325 2431 78 1
## 14 : 1 8191 788970 10391745 40075035 63436373 49329280 20912320
5135130 752752 66066 3367 91 1
## 15 : 1 16383 2375101 42355950 210766920 420693273 408741333 216627840
67128490 12662650 1479478 106470 4550 105 1
plot(6:30, sapply(6:30, Stirling2, m=5), log = y, type = l)
## Abramowitz says something like S2(n,m) ~ m^n / m!
## --
nn - 6:30; sapply(nn, Stirling2, m=5) / (5^nn / gamma(5+1))
## 0.114 0.21 .. 0.99033 0.992266 0.993812
-o--o-
--
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[R] Answer found: Re: How to write a function in a graph
Dear Thomas and Simon, Thank you for your messages. I have found the best solution based on your advice. FAQ 7.13 does provide an effective way to answer my question. Kind regards, Junguo Thomas Lumley [EMAIL PROTECTED] wrote: On Tue, 18 Jul 2006, junguo liu wrote: Dear R-ers, I conducted a regression analysis, and then intended to add the regression function (y=4.33+1.07x) in a graph. But the following code can only give me a text like y=a+bx. Who can help me out? Thank you very much in advance. This is FAQ 7.13. -thomas CODE # Read data x - c(1, 2, 3, 4, 5, 6, 7, 8, 9) y - c(6, 5, 8, 9, 11, 10, 11, 12, 15) data01 - data.frame(x, y) # Regression analysis res.lm.y - nls(y~a+b*x, start=list(a=1, b=2),data=data01) # Obtain parameters a- coef(res.lm.y)[a] b- coef(res.lm.y)[b] a b #a=4.33 #b=1.07 # Plot the results def.par - par() par(mfrow=c(1,1),xaxs=i,yaxs=i) plot(data01$x,data01$y,main=Fit,xlab=x,ylab=y) lines(data01$x,predict(res.lm.y)) #=== text (6, 13, expression(y==a+b*x)) #=== ## I intended to add text like y=4.33+1.07x ## but the above code added y=a+bx Swiss Federal Institute for Environmental Science and Technology (EAWAG) Ueberlandstrasse 133 P.O.Box 611 CH-8600 Duebendorf Switzerland Phone: 0041-18235012 Fax: 0041-18235375 - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle Swiss Federal Institute for Environmental Science and Technology (EAWAG) Ueberlandstrasse 133 P.O.Box 611 CH-8600 Duebendorf Switzerland Phone: 0041-18235012 Fax: 0041-18235375 - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plain shading (not residuals) in mosaic plot
Maybe like this: mosaic(allmorph, direction = v, pop = FALSE, gp=gpar(fill=c(grey(0.8),grey(0.4 Best, Muhammad Subianto On 7/19/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: If you look at ?mosaic the ... argument says it gets passed to strucplot and looking at ?strucplot we see it accepts a gp= arg so try this (same as your plus gp= arg): cols - c(grey(0.8),grey(0.4)) mosaic(allmorph, direction = v, pop = FALSE, gp = list(col = cols)) On 7/19/06, Kie Zuraw [EMAIL PROTECTED] wrote: Hello. I've been using R for a couple of months and enjoying it a lot. This is my first post to R-help. I'm using the vcd package to make mosaic plots with labels on the tiles indicating the number of items in each cell. For example, I've made this plot: allmorph-structure(c(10, 26, 17, 100, 70, 97, 253, 430, 185, 177, 25, 1), .Dim = as.integer(c(6, 2)), .Dimnames = structure(list(Stem.initial.obstruent = c(p, t,s, k,b,d,g),Subst.behavior=c(unsubstituted,substituted)), .Names = c(Stem-initial obstruent,Behavior according to dictionary)), class = table) mosaic(allmorph,direction=v,pop=FALSE) labeling_cells(text=allmorphs,margin=0)(allmorph) So far so good. What I can't figure out how to do--after searching through the vcd documentation (http://cran.r-project.org/doc/packages/vcd.pdf), Googling, and checking the r-help archive--is how to shade the tiles according to their values for the variables rather than to reflect residuals. That is, I want all the tiles at the bottom, whose value for the x-axis variable is substituted, to be dark grey, and those at the top, in the unsubstituted category, to be light grey. I know how to do it with mosaicplot(): mosaicplot(morphs3,color=c(grey(0.8),grey(0.4))) ...but this doesn't work with mosaic(): the command mosaic(morphs3,color=c(grey(0.8),grey(0.4))) yields a plot with all tiles the same color. And conversely, I can't find a way to use mosaicplot() and add numeric labels to the tiles--without much hope of success, I tried combining mosaicplot() with labeling_cells(), but, unsurprisingly, it didn't work: mosaicplot(morphs3,color=c(grey(0.8),grey(0.4)),pop=FALSE) Warning message: extra argument(s) 'pop' will be disregarded in: mosaicplot.default(morphs3, color = c(grey(0.8), grey(0.4)), labeling_cells(text=morphs3,margin=0)(morphs3) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) :Viewport 'cell:Stem-initial obstruent=p,Behavior according to dictionary=unsubstituted' was not found Does anyone know how to get both the shading I want and the labels I want, whether with mosaic(), with mosaicplot(), or in some other way? Thanks for your attention. -Kie Zuraw __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting a distribution to peaks in histogram
With this much data, I think it makes more sense to fit a nonparametric
density estimate. ?density does this via a kernel density procedure, but
RSiteSearch('nonparametric density') will find many alternatives. The ash
and mclust packages are two that come to mind, but there are certainly
others.
Of course, if you must have a parametric fit, then you'll have to fit a
mixture of some sort. But when both the number of components and individual
distributions are to be estimated, this is a nontrivial problem, as one runs
into identifiability issues and corresponding convergence problems. VR's
discussion of density estimation in MASS has some useful things to say about
these issues, and Ripley's book, PATTERN RECOGNITION AND NEURAL NETWORKS
has even more. As both sources indicate, there's a large literature on this
issue and much software.
Cheers,
Bert Gunter
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of hadley wickham
Sent: Wednesday, July 19, 2006 9:21 AM
To: Ulrik Stervbo
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Fitting a distribution to peaks in histogram
I would like to fit a distribution to each of the peaks in
a histogram, such
as this:
http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-B
cl-xL.png
As a first shot, I'd try fitting a mixture of gamma distributions (say
3), plus a constant term for the highest bin. You could do this using
ML. If the number of peaks is truly unknown, this will be a little
trickier but still possible and you could use the LRT to chose between
them.
Integrate the area between each two peaks, using the means
and widths of the
distributions fitted to the two peaks. I will be using the integrate
function
Why do you want to do this?
The histogram is based on approximately 15000 events, which
makes Mclust and
pam (which both delivers the information I need) less useful.
If you have unbinned data, it would be better (more precise/powerful)
to use that.
Regards,
Hadley
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Re: [R] plain shading (not residuals) in mosaic plot
Maybe like this: mosaic(allmorph, direction = v, pop = FALSE, gp=gpar(fill=c(grey(0.8),grey(0.4 Best, Muhammad Subianto On 7/19/06, Gabor Grothendieck [EMAIL PROTECTED] wrote: If you look at ?mosaic the ... argument says it gets passed to strucplot and looking at ?strucplot we see it accepts a gp= arg so try this (same as your plus gp= arg): cols - c(grey(0.8),grey(0.4)) mosaic(allmorph, direction = v, pop = FALSE, gp = list(col = cols)) On 7/19/06, Kie Zuraw [EMAIL PROTECTED] wrote: Hello. I've been using R for a couple of months and enjoying it a lot. This is my first post to R-help. I'm using the vcd package to make mosaic plots with labels on the tiles indicating the number of items in each cell. For example, I've made this plot: allmorph-structure(c(10, 26, 17, 100, 70, 97, 253, 430, 185, 177, 25, 1), .Dim = as.integer(c(6, 2)), .Dimnames = structure(list(Stem.initial.obstruent = c(p, t,s, k,b,d,g),Subst.behavior=c(unsubstituted,substituted)), .Names = c(Stem-initial obstruent,Behavior according to dictionary)), class = table) mosaic(allmorph,direction=v,pop=FALSE) labeling_cells(text=allmorphs,margin=0)(allmorph) So far so good. What I can't figure out how to do--after searching through the vcd documentation (http://cran.r-project.org/doc/packages/vcd.pdf), Googling, and checking the r-help archive--is how to shade the tiles according to their values for the variables rather than to reflect residuals. That is, I want all the tiles at the bottom, whose value for the x-axis variable is substituted, to be dark grey, and those at the top, in the unsubstituted category, to be light grey. I know how to do it with mosaicplot(): mosaicplot(morphs3,color=c(grey(0.8),grey(0.4))) ...but this doesn't work with mosaic(): the command mosaic(morphs3,color=c(grey(0.8),grey(0.4))) yields a plot with all tiles the same color. And conversely, I can't find a way to use mosaicplot() and add numeric labels to the tiles--without much hope of success, I tried combining mosaicplot() with labeling_cells(), but, unsurprisingly, it didn't work: mosaicplot(morphs3,color=c(grey(0.8),grey(0.4)),pop=FALSE) Warning message: extra argument(s) 'pop' will be disregarded in: mosaicplot.default(morphs3, color = c(grey(0.8), grey(0.4)), labeling_cells(text=morphs3,margin=0)(morphs3) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) :Viewport 'cell:Stem-initial obstruent=p,Behavior according to dictionary=unsubstituted' was not found Does anyone know how to get both the shading I want and the labels I want, whether with mosaic(), with mosaicplot(), or in some other way? Thanks for your attention. -Kie Zuraw __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reproducible Research - Examples
Question: Reproducible research is clearly desirable and feasible. Could anyone provide examples (stand-alone URLs or supplementary material in journals) that you would recommend as a models for reproducible research in R? Here are some attempts based on RWeb, contributed by Jeff Banfield, to allow for the reproduction of research papers: http://biomserv.univ-lyon1.fr/~necsulea/repro/ http://pbil.univ-lyon1.fr/members/lobry/repro/gene06/ http://biomserv.univ-lyon1.fr/~palmeira/repro/ http://pbil.univ-lyon1.fr/members/lobry/repro/toxo/ http://pbil.univ-lyon1.fr/datasets/SemonLobryDuret2005/ http://pbil.univ-lyon1.fr/members/lobry/repro/gene05/ http://pbil.univ-lyon1.fr/members/lobry/repro/bioinfo04/ http://pbil.univ-lyon1.fr/members/lobry/repro/lncs04/ http://pbil.univ-lyon1.fr/members/lobry/repro/jag03/ http://pbil.univ-lyon1.fr/members/lobry/repro/jme97/ http://pbil.univ-lyon1.fr/members/lobry/repro/jme95/ http://pbil.univ-lyon1.fr/members/lobry/repro/cabios95/ http://pbil.univ-lyon1.fr/members/lobry/repro/nar94/ I would not recommend these as a models, but I would like to point out that: 1) If you are already using Sweave (many thanks to Friedrich Leisch) there is virtually no extra-cost for the authors of the paper to write the corresponding web page. 2) There is no way to be more cristal clear with respect to your reviewers during the submission process: data are available online, methods are available online, the parameters of the methods are available and editable online. This is good science, but, problem: what would be the equivalent of JSTOR for this? How people can, say 100 years in the future, reproduce your results? Best, Jean Lobry P.S. If you want to play with the data used by Student (aka William Sealy Gosset) for the experimental validation of the famous t-test (The probable error of a mean. Biometrika, 6:1-25,1908) they are at your R prompt: crim-read.table(file=http://pbil.univ-lyon1.fr/R/donnees/criminals1902.txt;) Can you reproduce Student's results nowadays? -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 12 87 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to find S4 generics?
Dear Prof. Ripley: Thanks very much. Am I correct then that the 'methods' function could, at least theoretically, be revised so methods(class=...) could identify both S3 and S4 methods (ignoring inheritance, as it does now, I believe)? I ask, because it's not always obvious (at least to me) what helper functions are available. Some but not all are mentioned in the documentation, and even if they are, they may not be featured prominently. For the S3 standard, methods(class=...) reports what's available, and it's faster and more reliable than scanning the help files. After I find something with methods(class=...), then I have better ideas for what to look for in the documentation. Best Wishes, Spencer Graves Prof Brian Ripley wrote: On Tue, 18 Jul 2006, Spencer Graves wrote: * * methods * * You have asked an excellent question. I can provide a partial answer below. First, however, I wish to pose a question of my own, which could help answer your question: How can one obtain a simple list of the available generics for a class? For an S3 class, the 'methods' functions provide that. What about an S4 class? That's entirely opaque to me, if I somehow can't find the relevant information in other ways. For example, ?lmer-class lists many but not all of the methods available for objects of class 'lmer'. I think I once found a way to get that, but I'm not able to find documentation on it now. It doesn't work the same way. S3 generics are defined on a single argument and hence have methods for a class, and so it is relevant to ask what generics there are which have methods for a given class - but even then there can be other generics and other methods which dispatch on object from that class by inheritance (e.g. on lm for glm objects). S4 generics dispatch on a signature which can involve two or more classes, and I guess the simplest interpretation of your question is `what S4 generics are there which have methods with signatures mentioning this class'. Given the decentralized way such information is stored, I think the only way to do that is to find all the generics currently available (via getGenerics or its synonym allGenerics) and then call showMethods on each generic. In particular, methods are stored in the S4 generic and not in the package defining the method. However, I suspect inheritance is much more important here, and there is no way to know if methods for class ANY actually work for a specific S4 class. [...] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to find S4 generics?
On Wed, 19 Jul 2006, Spencer Graves wrote: Dear Prof. Ripley: Thanks very much. Am I correct then that the 'methods' function could, at least theoretically, be revised so methods(class=...) could identify both S3 and S4 methods (ignoring inheritance, as it does now, I believe)? It is correct that in principle there could be such a function in the methods package, but not that methods() in utils could be revised to do so. (For efficiency reasons on the stats4 package in the base distribution may depend on methods) I ask, because it's not always obvious (at least to me) what helper functions are available. Some but not all are mentioned in the documentation, and even if they are, they may not be featured prominently. For the S3 standard, methods(class=...) reports what's available, and it's faster and more reliable than scanning the help files. After I find something with methods(class=...), then I have better ideas for what to look for in the documentation. Best Wishes, Spencer Graves Prof Brian Ripley wrote: On Tue, 18 Jul 2006, Spencer Graves wrote: * * methods * * You have asked an excellent question. I can provide a partial answer below. First, however, I wish to pose a question of my own, which could help answer your question: How can one obtain a simple list of the available generics for a class? For an S3 class, the 'methods' functions provide that. What about an S4 class? That's entirely opaque to me, if I somehow can't find the relevant information in other ways. For example, ?lmer-class lists many but not all of the methods available for objects of class 'lmer'. I think I once found a way to get that, but I'm not able to find documentation on it now. It doesn't work the same way. S3 generics are defined on a single argument and hence have methods for a class, and so it is relevant to ask what generics there are which have methods for a given class - but even then there can be other generics and other methods which dispatch on object from that class by inheritance (e.g. on lm for glm objects). S4 generics dispatch on a signature which can involve two or more classes, and I guess the simplest interpretation of your question is `what S4 generics are there which have methods with signatures mentioning this class'. Given the decentralized way such information is stored, I think the only way to do that is to find all the generics currently available (via getGenerics or its synonym allGenerics) and then call showMethods on each generic. In particular, methods are stored in the S4 generic and not in the package defining the method. However, I suspect inheritance is much more important here, and there is no way to know if methods for class ANY actually work for a specific S4 class. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gamm
Sorry for the delay replying: I was on holiday, but have foolishly come back. I am a bit confused about gamm in mgcv. Consulting Wood (2006) or Ruppert et al. (2003) hasn't taken away my confusion. In this code from the gamm help file: b2-gamm(y~s(x0)+s(x1)+s(x2)+s(x3),family=poisson,random=list(fac=~1)) Am I correct in assuming that we have a random intercept herebut that the amount of smoothing is also changing per level of the factor?? Or is it only the intercept that is changing? - the degree of smoothing is the same for each level of `fac' but there is a different intercept for each level of `fac': these intercepts are assumed Normally distributed. i.e. all `s()' terms apply to all data, they are not nested within groups. And where can I find some explanation on the magic output below? mgcv::gamm is basically a wrapper that turns a GAMM into the sort of model that nlme::lme or MASS::glmmPQL expects to see `gamm' returns an object with two parts - the `lme' part is the object that was returned by glmmPQL or lme; the `gam' part is an object with most of the attributes of a `gam' object (all those that can be reconstructed from an lme/glmmPQL fitted model object). So the `lme' object contains a bunch of opaque stuff that results from turning the original GAMM into something that lme/glmmPQL can work with... further detail below. summary(b2$lme) Random effects: - The output starting here relates to the random components of the 4 smooths in the model. Each smooth starts with 10 degrees of freedom, but one of these is lost to the GAM centering constraint that ensures additive identifiability, and one is treated as a fixed effect (see Wood, 2006, for details), so each smooth have 8 random coefficients. Each of these coefficients is treated as having the same variance (after some preparatory reparameterization), but this variance (which plays the role of a smoothing parameter) is unknown and is estimated as part of model estimation. [Note that g.1 to g.4 below are dummy grouping factors, each having only one level - they force the smooths to apply to all the data, rather than being nested within, e.g. the levels of `fac']. Formula: ~Xr.1 - 1 | g.1 Structure: pdIdnot Xr.11Xr.12Xr.13Xr.14Xr.15Xr.16Xr.17Xr.18 StdDev: 1.680679 1.680679 1.680679 1.680679 1.680679 1.680679 1.680679 1.680679 Formula: ~Xr.2 - 1 | g.2 %in% g.1 Structure: pdIdnot Xr.21 Xr.22 Xr.23 Xr.24 Xr.25 Xr.26 Xr.27 Xr.28 StdDev: 1.57598 1.57598 1.57598 1.57598 1.57598 1.57598 1.57598 1.57598 Formula: ~Xr.3 - 1 | g.3 %in% g.2 %in% g.1 Structure: pdIdnot Xr.31Xr.32Xr.33Xr.34Xr.35Xr.36Xr.37Xr.38 StdDev: 20.06377 20.06377 20.06377 20.06377 20.06377 20.06377 20.06377 20.06377 Formula: ~Xr.4 - 1 | g.4 %in% g.3 %in% g.2 %in% g.1 Structure: pdIdnot Xr.41Xr.42Xr.43Xr.44Xr.45 StdDev: 0.0001063304 0.0001063304 0.0001063304 0.0001063304 0.0001063304 Xr.46Xr.47Xr.48 StdDev: 0.0001063304 0.0001063304 0.0001063304 - that's the random component information relating to the smooths done with. What follows is the information realting to the random intercept. Note that the rather complicated Formula is really equivalent to ~1|fac since the g.j are degenerate. Formula: ~1 | fac %in% g.4 %in% g.3 %in% g.2 %in% g.1 (Intercept) Residual StdDev: 0.6621173 1.007227 Variance function: Structure: fixed weights Formula: ~invwt - What follows is information about the fixed effects. In this case there is one fixed effect for each smooth, and an overall intercept: `X(Intercept)'. Fixed effects: y.0 ~ X - 1 Value Std.Error DF t-value p-value X(Intercept) 2.0870364 0.3337787 392 6.252755 0. Xs(x0)Fx1-0.325 0.1028794 392 -0.000316 0.9997 Xs(x1)Fx1 0.3831694 0.0957323 392 4.002509 0.0001 Xs(x2)Fx1 1.4584330 0.3909237 392 3.730736 0.0002 Xs(x3)Fx1-0.0123951 0.0143162 392 -0.865809 0.3871 Correlation: Hope that's some use. Simon - Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY - +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mgcv::gam error message
Could anyone please tell me what to do to resolve this error message? - Any chance you could send me some code (and associated data) that I can cut and paste in order to chase this up? Whatever's wrong here, `gam' should probably pick it up before things get this far, but I can't tell what's happening without a reproducible example. Thanks, Simon I tried to run a gam with the mgcv package and got the following error: Error in qr.qty(qrc, sm$S[[1]]): NA/NaN/Inf in foreign function call (arg 5) (I have 116 covariates, I'm using the cr basis to speed things up, the binomial family and, where necessary, have set the required k to lower than the number of distinct values for a given covarate when less than the default) Thank you, Savrina [EMAIL PROTECTED] School of Information Technologies Univeristy of Sydney __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fitting a distribution to peaks in histogram
Can you be a bit more excact? I a biologist and relatively new to R In that case, I would _strongly_ advise that you get advice from a local statistician. I am measureing the amount of DNA in cells, and I need to know the percentage of cells in a part of the cell cycle; that the percentage of cells in the first peak, in the second peak and so on. I want to integrate the area between to two cells, because that apparently is how its none (as far as I can tell from the literature) That doesn't sound quite right to me, because you also need to take into account the fact that some cells between peak 1 and 2 belong to peak 1, and some to peak 2. This is something that will come out immediately from a mixture based approach. If you know that peaks correspond to certain parts of the cell cycle, then this is important information that should be included in the analysis. It very probably is better, but mclust had no result after running for at least 2 hours (I terminated the function after two hours), and as I generate 50-100 datasets, such as the one used for the histogram, as week, I would like to find a faster solution I doubt that mclust is appropriate for this task, so letting it run longer wouldn't help anyway. Again I would suggest that you seek local statistical help. Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] fracdiff
Hi, I'm using the function fracdiff and can not figure out how to get the estimated values for sigma2 or confidence intervals for the parameter estimates. Does anyone know how to obtain these values? Thanks, Melissa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to use large data set ?
You did not say what analysis you want to do, but many common analyses
can be done as special cases of regression models and you can use the
biglm package to do regression models.
Here is an example that worked for me to get the mean and standard
deviation by day from an oracle database with over 23 million rows (I
had previously set up 'edw' as an odbc connection to the database under
widows, any of the database connections packages should work for you
though):
library(RODBC)
library(biglm)
con - odbcConnect('edw',uid='glsnow',pwd=pass)
odbcQuery(con, select ADMSN_WEEKDAY_CD, LOS_DYS from CM.CASEMIX_SMRY)
t1 - Sys.time()
tmp - sqlGetResults(con, max=10)
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
ff - log(LoS) ~ Day
fit - biglm(ff, tmp)
i - nrow(tmp)
while( !is.null(nrow( tmp - sqlGetResults(con, max=10) ) ) ){
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
fit - update(fit,tmp)
i - i + nrow(tmp)
cat(format(i,big.mark=','), rows processed\n)
}
summary(fit)
t2 - Sys.time()
t2-t1
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Yohan CHOUKROUN
Sent: Wednesday, July 19, 2006 9:42 AM
To: 'r-help@stat.math.ethz.ch'
Subject: [R] how to use large data set ?
Hello R users,
Sorry for my English, i'm French.
I want to use a large dataset (3 millions of rows and 70 var) but I
don't know how to do because my computer crash quickly (P4 2.8Ghz, 1Go
).
I have also a bi Xeon with 2Go so I want to do computation on this
computer and show the results on mine. Both of them are on Windows XP...
To do shortly I have:
1 server with a MySQL database
1computer
and I want to use them with a large dataset.
I'm trying to use RDCOM to connect the database and installing (but it's
hard for me..) Rpad.
Is there another solutions ?
Thanks in advance
Yohan C.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Wrap a loop inside a function
I need to wrap a loop inside a function and am having a small bit of
difficulty getting the results I need. Below is a replicable example.
# define functions
pcm - function(theta,d,score){
exp(rowSums(outer(theta,d[1:score],'-')))/
apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)
}
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)), ncol =
length(theta))
for(i in 1:length(items)) like.mat[i, ] - pcm(theta, items[[i]],
score[[i]])
}
# begin example
theta - c(-1,-.5,0,.5,1)
items - list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1))
score - c(2,1,3,1)
(foo(theta, items, score))
# R output from function foo
[1] 0.8807971 0.8175745 0.7310586 0.6224593 0.500
However, what I am expecting from the function foo is
like.mat
[,1] [,2] [,3] [,4] [,5]
[1,] 0.118499655 0.17973411 0.25949646 0.34820743 0.4223188
[2,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
[3,] 0.005899109 0.01474683 0.03505661 0.07718843 0.1520072
[4,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
I cannot seem to track down why the function foo is only keeping the
last row of the full matrix I need. Can anyone see where my error is?
Thanks,
Harold
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.0
year 2006
month 04
day24
svn rev37909
language R
version.string Version 2.3.0 (2006-04-24)
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wrap a loop inside a function
Doran, Harold wrote:
I need to wrap a loop inside a function and am having a small bit of
difficulty getting the results I need. Below is a replicable example.
# define functions
pcm - function(theta,d,score){
exp(rowSums(outer(theta,d[1:score],'-')))/
apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)
}
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)), ncol =
length(theta))
for(i in 1:length(items)) like.mat[i, ] - pcm(theta, items[[i]],
score[[i]])
}
# begin example
theta - c(-1,-.5,0,.5,1)
items - list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1))
score - c(2,1,3,1)
(foo(theta, items, score))
# R output from function foo
[1] 0.8807971 0.8175745 0.7310586 0.6224593 0.500
However, what I am expecting from the function foo is
like.mat
[,1] [,2] [,3] [,4] [,5]
[1,] 0.118499655 0.17973411 0.25949646 0.34820743 0.4223188
[2,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
[3,] 0.005899109 0.01474683 0.03505661 0.07718843 0.1520072
[4,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
I cannot seem to track down why the function foo is only keeping the
last row of the full matrix I need. Can anyone see where my error is?
Thanks,
Harold
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.0
year 2006
month 04
day24
svn rev37909
language R
version.string Version 2.3.0 (2006-04-24)
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hi, Harold,
Your function foo is only returning the last call from for. Try:
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)),
ncol = length(theta))
for(i in 1:length(items))
like.mat[i, ] - pcm(theta, items[[i]], score[[i]])
## return like.mat, not just the last line from for
like.mat
}
HTH,
--sundar
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] voronoi tessellations
Okay, been working with tripack, seems the most mature package for this. Got it to work well with their test data set - data(tritest). When i tried random numbers to explore further, i am getting some results that don't reconcile. example run this: library(tripack) y - runif(100) x - runif(100) vm - voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') when you look at the plot of the mosaic overlayed with the raw data, the mosaic should have each data point in 1 cell, however that is not the case - any help would be appreciated. However if you run data(tritest) x - tritest$x y - tritest$y vm - voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') it looks at it should. -zubin From: Prof Brian Ripley [EMAIL PROTECTED] Date: 2006/07/19 Wed AM 03:15:51 EDT To: Don MacQueen [EMAIL PROTECTED] CC: zubin [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] voronoi tessellations On Tue, 18 Jul 2006, Don MacQueen wrote: I'll suggest going to the CRAN packages page and doing a search for voronoi. The problem here is that `Voronoi tessellation' is a secondary name. The concept has many names, including Dirichlet tessellation and Thiessen polygons, and Dirichlet has priority over Voronoi. Also, search for 'triangulation', since that is one of the uses of them. I know of packages deldir, tripack and perhaps geometry. -Don At 11:46 PM -0400 7/18/06, zubin wrote: Hello, looking to draw a voronoi tessellations in R - can anyone recommend a package that has tackled this? some background: i have a economic data set and created a sammons projection, like to now overlay a voronoi tessellation over the sammons 2-D solution for a slick visual, and potentially color each tessellation element based on a metric. home.u - unique(home1) home.dist - dist(home.u) home.sam - sammon(home.dist,k=2) plot(home.sam$points) Wait a minute. If this is sammon() from MASS (uncredited), it is not a projection, and there is no relevant concept of distance between points in the mapped space apart from between the supplied points. I suggest Zubin reads carefully the reference whose support software he appears to be using. (It would also have answered his question.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wrap a loop inside a function
I'm sure when you read this there will be the sound of a palm slapping
a forehead. :-)
The value of a function is the value of the last expression evaluated
in the function. If you rewrite foo as
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)),
ncol = length(theta))
for(i in 1:length(items))
like.mat[i, ] - pcm(theta, items[[i]], score[[i]])
like.mat
}
you will get the result that you want.
On 7/19/06, Doran, Harold [EMAIL PROTECTED] wrote:
I need to wrap a loop inside a function and am having a small bit of
difficulty getting the results I need. Below is a replicable example.
# define functions
pcm - function(theta,d,score){
exp(rowSums(outer(theta,d[1:score],'-')))/
apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)
}
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)), ncol =
length(theta))
for(i in 1:length(items)) like.mat[i, ] - pcm(theta, items[[i]],
score[[i]])
}
# begin example
theta - c(-1,-.5,0,.5,1)
items - list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1))
score - c(2,1,3,1)
(foo(theta, items, score))
# R output from function foo
[1] 0.8807971 0.8175745 0.7310586 0.6224593 0.500
However, what I am expecting from the function foo is
like.mat
[,1] [,2] [,3] [,4] [,5]
[1,] 0.118499655 0.17973411 0.25949646 0.34820743 0.4223188
[2,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
[3,] 0.005899109 0.01474683 0.03505661 0.07718843 0.1520072
[4,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
I cannot seem to track down why the function foo is only keeping the
last row of the full matrix I need. Can anyone see where my error is?
Thanks,
Harold
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.0
year 2006
month 04
day24
svn rev37909
language R
version.string Version 2.3.0 (2006-04-24)
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Correlation Mapping
Thank you for the advice. This is what I was looking for. If I would like to label the axes, how can I do that? Specifically I would like to label the x axis (AAA, AA, A, BBB) and same with the y axis. jdr On 7/17/06, Jim Lemon [EMAIL PROTECTED] wrote: justin rapp wrote: On the cover of Zivot and Wang's Modeling Financial Time Series with S Plus, there is a correlation plot that seems to indicate the strength of correlation with color-coded squares, so that more highly correlated stocks appear darker red. If anybody out there is familiar with the book or understands what I am talking about, I am curious as to whether or not there is a similar function in R and how I can call it up. Hi justin, I think that color2D.matplot in the plotrix package will do exactly what you want. Jim [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] voronoi tessellations
On Wed, 19 Jul 2006, [EMAIL PROTECTED] wrote: Okay, been working with tripack, seems the most mature package for this. Got it to work well with their test data set - data(tritest). When i tried random numbers to explore further, i am getting some results that don't reconcile. example run this: library(tripack) y - runif(100) x - runif(100) vm - voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') plot() changes the axis scales. Use points(x,y) -thomas when you look at the plot of the mosaic overlayed with the raw data, the mosaic should have each data point in 1 cell, however that is not the case - any help would be appreciated. However if you run data(tritest) x - tritest$x y - tritest$y vm - voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') it looks at it should. -zubin From: Prof Brian Ripley [EMAIL PROTECTED] Date: 2006/07/19 Wed AM 03:15:51 EDT To: Don MacQueen [EMAIL PROTECTED] CC: zubin [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] voronoi tessellations On Tue, 18 Jul 2006, Don MacQueen wrote: I'll suggest going to the CRAN packages page and doing a search for voronoi. The problem here is that `Voronoi tessellation' is a secondary name. The concept has many names, including Dirichlet tessellation and Thiessen polygons, and Dirichlet has priority over Voronoi. Also, search for 'triangulation', since that is one of the uses of them. I know of packages deldir, tripack and perhaps geometry. -Don At 11:46 PM -0400 7/18/06, zubin wrote: Hello, looking to draw a voronoi tessellations in R - can anyone recommend a package that has tackled this? some background: i have a economic data set and created a sammons projection, like to now overlay a voronoi tessellation over the sammons 2-D solution for a slick visual, and potentially color each tessellation element based on a metric. home.u - unique(home1) home.dist - dist(home.u) home.sam - sammon(home.dist,k=2) plot(home.sam$points) Wait a minute. If this is sammon() from MASS (uncredited), it is not a projection, and there is no relevant concept of distance between points in the mapped space apart from between the supplied points. I suggest Zubin reads carefully the reference whose support software he appears to be using. (It would also have answered his question.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to use large data set ?
Hi,
I would like to extend to the query posted earlier on using large data
bases. I am trying to use Rgdal to mine within the remote sensing imageries.
I dont have problems bring the images within the R environment. But when I
try to convert the images to a data.frame I receive an warning message from
R saying 1: Reached total allocation of 510Mb: see help(memory.size) and
the process terminates. Due to project constarints I am given a very
old 2.4Ghz computer with only 512 MB RAM. I think what R is currently
doing is
trying to store the results in the RAM and since the image size is very big
(some 9 million pixels), I think it gets out of memory.
My question is
1. Is there any possibility to dump the temporary variables in a temp folder
within the hard disk (as many softwares do) instead of leting R store them
in RAM
2. Could this be possible without creating a connection to a any back hand
database like Oracle.
Thanks,
Mahesh
On 7/19/06, Greg Snow [EMAIL PROTECTED] wrote:
You did not say what analysis you want to do, but many common analyses
can be done as special cases of regression models and you can use the
biglm package to do regression models.
Here is an example that worked for me to get the mean and standard
deviation by day from an oracle database with over 23 million rows (I
had previously set up 'edw' as an odbc connection to the database under
widows, any of the database connections packages should work for you
though):
library(RODBC)
library(biglm)
con - odbcConnect('edw',uid='glsnow',pwd=pass)
odbcQuery(con, select ADMSN_WEEKDAY_CD, LOS_DYS from CM.CASEMIX_SMRY)
t1 - Sys.time()
tmp - sqlGetResults(con, max=10)
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
ff - log(LoS) ~ Day
fit - biglm(ff, tmp)
i - nrow(tmp)
while( !is.null(nrow( tmp - sqlGetResults(con, max=10) ) ) ){
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
fit - update(fit,tmp)
i - i + nrow(tmp)
cat(format(i,big.mark=','), rows processed\n)
}
summary(fit)
t2 - Sys.time()
t2-t1
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Yohan CHOUKROUN
Sent: Wednesday, July 19, 2006 9:42 AM
To: 'r-help@stat.math.ethz.ch'
Subject: [R] how to use large data set ?
Hello R users,
Sorry for my English, i'm French.
I want to use a large dataset (3 millions of rows and 70 var) but I
don't know how to do because my computer crash quickly (P4 2.8Ghz, 1Go
).
I have also a bi Xeon with 2Go so I want to do computation on this
computer and show the results on mine. Both of them are on Windows XP...
To do shortly I have:
1 server with a MySQL database
1computer
and I want to use them with a large dataset.
I'm trying to use RDCOM to connect the database and installing (but it's
hard for me..) Rpad.
Is there another solutions ?
Thanks in advance
Yohan C.
--
Ce message est confidentiel. Son contenu ne represente en aucun cas un
engagement de la part du Groupe Soft Computing sous reserve de tout
accord conclu par ecrit entre vous et le Groupe Soft Computing. Toute
publication, utilisation ou diffusion, meme partielle, doit etre
autorisee prealablement.
Si vous n'etes pas destinataire de ce message, merci d'en avertir
immediatement l'expediteur.
This message is confidential. Its content does not constitute a
commitment by Soft Computing Group except where provided for in a
written agreement between you and Soft Computing Group. Any unauthorised
disclosure, use or dissemination, either whole or partial, is
prohibited. If you are not the intended recipient of this message,
please notify the sender immediately.
--
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
Re: [R] Wrap a loop inside a function
Very true, the resounding echo was large.
Thanks, Doug.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf
Of Douglas Bates
Sent: Wednesday, July 19, 2006 4:20 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Wrap a loop inside a function
I'm sure when you read this there will be the sound of a palm
slapping a forehead. :-)
The value of a function is the value of the last expression
evaluated in the function. If you rewrite foo as
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)),
ncol = length(theta))
for(i in 1:length(items))
like.mat[i, ] - pcm(theta, items[[i]], score[[i]])
like.mat
}
you will get the result that you want.
On 7/19/06, Doran, Harold [EMAIL PROTECTED] wrote:
I need to wrap a loop inside a function and am having a
small bit of
difficulty getting the results I need. Below is a
replicable example.
# define functions
pcm - function(theta,d,score){
exp(rowSums(outer(theta,d[1:score],'-')))/
apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)
}
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)), ncol =
length(theta))
for(i in 1:length(items)) like.mat[i, ] - pcm(theta, items[[i]],
score[[i]])
}
# begin example
theta - c(-1,-.5,0,.5,1)
items - list(item1 = c(0,1,2), item2 = c(0,1), item3 =
c(0,1,2,3,4),
item4 = c(0,1))
score - c(2,1,3,1)
(foo(theta, items, score))
# R output from function foo
[1] 0.8807971 0.8175745 0.7310586 0.6224593 0.500
However, what I am expecting from the function foo is
like.mat
[,1] [,2] [,3] [,4] [,5]
[1,] 0.118499655 0.17973411 0.25949646 0.34820743 0.4223188 [2,]
0.880797078 0.81757448 0.73105858 0.62245933 0.500 [3,]
0.005899109 0.01474683 0.03505661 0.07718843 0.1520072 [4,]
0.880797078 0.81757448 0.73105858 0.62245933 0.500
I cannot seem to track down why the function foo is only
keeping the
last row of the full matrix I need. Can anyone see where my
error is?
Thanks,
Harold
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.0
year 2006
month 04
day24
svn rev37909
language R
version.string Version 2.3.0 (2006-04-24)
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] voronoi tessellations
On 7/19/2006 4:21 PM, [EMAIL PROTECTED] wrote: Okay, been working with tripack, seems the most mature package for this. Got it to work well with their test data set - data(tritest). When i tried random numbers to explore further, i am getting some results that don't reconcile. example run this: library(tripack) y - runif(100) x - runif(100) vm - voronoi.mosaic(x,y) plot(vm) par(new=T) Don't do that! That throws away the coordinate system that has already been established. Do it this way: library(tripack) y - runif(100) x - runif(100) vm - voronoi.mosaic(x,y) plot(vm) points(x,y,col='blue') and if you want the axes, axis(1) axis(2) box() Duncan Murdoch plot(x,y,col='blue') when you look at the plot of the mosaic overlayed with the raw data, the mosaic should have each data point in 1 cell, however that is not the case - any help would be appreciated. However if you run data(tritest) x - tritest$x y - tritest$y vm - voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') it looks at it should. -zubin From: Prof Brian Ripley [EMAIL PROTECTED] Date: 2006/07/19 Wed AM 03:15:51 EDT To: Don MacQueen [EMAIL PROTECTED] CC: zubin [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] voronoi tessellations On Tue, 18 Jul 2006, Don MacQueen wrote: I'll suggest going to the CRAN packages page and doing a search for voronoi. The problem here is that `Voronoi tessellation' is a secondary name. The concept has many names, including Dirichlet tessellation and Thiessen polygons, and Dirichlet has priority over Voronoi. Also, search for 'triangulation', since that is one of the uses of them. I know of packages deldir, tripack and perhaps geometry. -Don At 11:46 PM -0400 7/18/06, zubin wrote: Hello, looking to draw a voronoi tessellations in R - can anyone recommend a package that has tackled this? some background: i have a economic data set and created a sammons projection, like to now overlay a voronoi tessellation over the sammons 2-D solution for a slick visual, and potentially color each tessellation element based on a metric. home.u - unique(home1) home.dist - dist(home.u) home.sam - sammon(home.dist,k=2) plot(home.sam$points) Wait a minute. If this is sammon() from MASS (uncredited), it is not a projection, and there is no relevant concept of distance between points in the mapped space apart from between the supplied points. I suggest Zubin reads carefully the reference whose support software he appears to be using. (It would also have answered his question.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to use large data set ?
Hi,
While R is generally flexible enough for just about anything you can throw at
it, detailed analysis of imagery might be better accomplished in a
specialized piece of software. One option might be GRASS, which would allow
you to do further processing on a subset of the original data in R.
Cheers,
Dylan
On Wednesday 19 July 2006 13:22, mahesh r wrote:
Hi,
I would like to extend to the query posted earlier on using large data
bases. I am trying to use Rgdal to mine within the remote sensing
imageries. I dont have problems bring the images within the R environment.
But when I try to convert the images to a data.frame I receive an warning
message from R saying 1: Reached total allocation of 510Mb: see
help(memory.size) and the process terminates. Due to project constarints I
am given a very old 2.4Ghz computer with only 512 MB RAM. I think what R is
currently doing is
trying to store the results in the RAM and since the image size is very big
(some 9 million pixels), I think it gets out of memory.
My question is
1. Is there any possibility to dump the temporary variables in a temp
folder within the hard disk (as many softwares do) instead of leting R
store them in RAM
2. Could this be possible without creating a connection to a any back hand
database like Oracle.
Thanks,
Mahesh
On 7/19/06, Greg Snow [EMAIL PROTECTED] wrote:
You did not say what analysis you want to do, but many common analyses
can be done as special cases of regression models and you can use the
biglm package to do regression models.
Here is an example that worked for me to get the mean and standard
deviation by day from an oracle database with over 23 million rows (I
had previously set up 'edw' as an odbc connection to the database under
widows, any of the database connections packages should work for you
though):
library(RODBC)
library(biglm)
con - odbcConnect('edw',uid='glsnow',pwd=pass)
odbcQuery(con, select ADMSN_WEEKDAY_CD, LOS_DYS from CM.CASEMIX_SMRY)
t1 - Sys.time()
tmp - sqlGetResults(con, max=10)
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
ff - log(LoS) ~ Day
fit - biglm(ff, tmp)
i - nrow(tmp)
while( !is.null(nrow( tmp - sqlGetResults(con, max=10) ) ) ){
names(tmp) - c(Day,LoS)
tmp$Day - factor(tmp$Day, levels=as.character(1:7))
tmp - na.omit(tmp)
tmp - subset(tmp, LoS 0)
fit - update(fit,tmp)
i - i + nrow(tmp)
cat(format(i,big.mark=','), rows processed\n)
}
summary(fit)
t2 - Sys.time()
t2-t1
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Yohan CHOUKROUN
Sent: Wednesday, July 19, 2006 9:42 AM
To: 'r-help@stat.math.ethz.ch'
Subject: [R] how to use large data set ?
Hello R users,
Sorry for my English, i'm French.
I want to use a large dataset (3 millions of rows and 70 var) but I
don't know how to do because my computer crash quickly (P4 2.8Ghz, 1Go
).
I have also a bi Xeon with 2Go so I want to do computation on this
computer and show the results on mine. Both of them are on Windows XP...
To do shortly I have:
1 server with a MySQL database
1computer
and I want to use them with a large dataset.
I'm trying to use RDCOM to connect the database and installing (but it's
hard for me..) Rpad.
Is there another solutions ?
Thanks in advance
Yohan C.
--
Ce message est confidentiel. Son contenu ne represente en aucun cas un
engagement de la part du Groupe Soft Computing sous reserve de tout
accord conclu par ecrit entre vous et le Groupe Soft Computing. Toute
publication, utilisation ou diffusion, meme partielle, doit etre
autorisee prealablement.
Si vous n'etes pas destinataire de ce message, merci d'en avertir
immediatement l'expediteur.
This message is confidential. Its content does not constitute a
commitment by Soft Computing Group except where provided for in a
written agreement between you and Soft Computing Group. Any unauthorised
disclosure, use or dissemination, either whole or partial, is
prohibited. If you are not the intended recipient of this message,
please notify the sender immediately.
--
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal,
[R] error when compiling stats library in R-2.3.1 on Solaris x86
Hello, I tried to compile v2.3.1 on Solaris x86 with SUN Pro compilers. I had an error while stats libarary was being compiled and I notice that -xtarget=generic64 was not passed to f95 while cc used it. Could you tell me how to fix this problem? f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o -xlic_lib=sunperf -lsunmath -Rreg -R/mounts/devel/SUNWspro/lib/amd64:/opt/SUNWspro/lib/amd64 -L/mounts/devel/SUNWspro/prod/lib/amd64 -L/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu -lsunmath -lmtsk -lm ld: fatal: file bsplvd.o: wrong ELF class: ELFCLASS32 ld: fatal: File processing errors. No output written to stats.so *** Error code 1 make: Fatal error: Command failed for target `stats.so' I did not have any problem when I compiled v2.2.1 as below: cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c family.c -o family.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bsplvd.f -o bsplvd.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalue.f -o bvalue.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalus.f -o bvalus.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c loessf.f -o loessf.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c ppr.f -o ppr.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c qsbart.f -o qsbart.o cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c sbart.c -o sbart.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o carray.o filter.o mburg.o myw.o pacf.o qr.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o -xlic_lib=sunperf -lsunmath -Rreg -R/mounts/devel/SUNWspro/lib/amd64:/opt/SUNWspro/lib/amd64 -L/mounts/devel/SUNWspro/prod/lib/amd64 -L/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu -lsunmath -lmtsk -lm mkdir ../../../../library/stats/libs Thank you very much!! Dongseok Choi, Ph.D. Assistant Professor Division of Biostatistics Department of Public Health Preventive Medicine Oregon Health Science University 3181 SW Sam Jackson Park Road, CB-669 Portland, OR 97239-3098 TEL) 503-494-5336 FAX) 503-494-4981 [EMAIL
Re: [R] error when compiling stats library in R-2.3.1 on Solaris x86
How did 'cc -xtarget=generic64' get there? AFAIK R does not know about it, so presumably you specified it for CC. You need to do the same thing for *all* the compilers, that is CC, CXX, F77 and FC. The INSTALL file asked you to read the R-admin manual: there you will find a very similar example for 64-bit Sparc Solaris. That uses -xarch, which seems preferred to -xtarget (or at least to generic targets). On Wed, 19 Jul 2006, Dongseok Choi wrote: Hello, I tried to compile v2.3.1 on Solaris x86 with SUN Pro compilers. I had an error while stats libarary was being compiled and I notice that -xtarget=generic64 was not passed to f95 while cc used it. Could you tell me how to fix this problem? f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o -xlic_lib=sunperf -lsunmath -Rreg -R/mounts/devel/SUNWspro/lib/amd64:/opt/SUNWspro/lib/amd64 -L/mounts/devel/SUNWspro/prod/lib/amd64 -L/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu -lsunmath -lmtsk -lm ld: fatal: file bsplvd.o: wrong ELF class: ELFCLASS32 ld: fatal: File processing errors. No output written to stats.so *** Error code 1 make: Fatal error: Command failed for target `stats.so' I did not have any problem when I compiled v2.2.1 as below: cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c family.c -o family.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bsplvd.f -o bsplvd.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalue.f -o bvalue.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalus.f -o bvalus.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c loessf.f -o loessf.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c ppr.f -o ppr.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c qsbart.f -o qsbart.o cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c sbart.c -o sbart.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o carray.o filter.o mburg.o myw.o pacf.o qr.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o
Re: [R] error when compiling stats library in R-2.3.1 on Solaris x86
It was given iin the config.site. CC=cc -xtarget=generic64 CFLAGS=-O -I/mounts/devel/SUNWspro/prod/include F77=f95 -xtarget=generic64 FFLAGS=-O -I/mounts/devel/SUNWspro/prod/include CXX=CC -xtarget=generic64 CXXFLAGS=-O -I/mounts/devel/SUNWspro/prod/include CPPFLAGS=-I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include I am not sure why it was not passed to f95 while it was OK with cc. I did not have any problem with R2.2.1. Please let me know if you need any other info. Thanks again, Dongseok Prof Brian Ripley [EMAIL PROTECTED] 7/19/2006 2:39 PM How did 'cc -xtarget=generic64' get there? AFAIK R does not know about it, so presumably you specified it for CC. You need to do the same thing for *all* the compilers, that is CC, CXX, F77 and FC. The INSTALL file asked you to read the R-admin manual: there you will find a very similar example for 64-bit Sparc Solaris. That uses -xarch, which seems preferred to -xtarget (or at least to generic targets). On Wed, 19 Jul 2006, Dongseok Choi wrote: Hello, I tried to compile v2.3.1 on Solaris x86 with SUN Pro compilers. I had an error while stats libarary was being compiled and I notice that -xtarget=generic64 was not passed to f95 while cc used it. Could you tell me how to fix this problem? f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o -xlic_lib=sunperf -lsunmath -Rreg -R/mounts/devel/SUNWspro/lib/amd64:/opt/SUNWspro/lib/amd64 -L/mounts/devel/SUNWspro/prod/lib/amd64 -L/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu -lsunmath -lmtsk -lm ld: fatal: file bsplvd.o: wrong ELF class: ELFCLASS32 ld: fatal: File processing errors. No output written to stats.so *** Error code 1 make: Fatal error: Command failed for target `stats.so' I did not have any problem when I compiled v2.2.1 as below: cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c family.c -o family.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bsplvd.f -o bsplvd.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalue.f -o bvalue.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalus.f -o bvalus.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c loessf.f -o loessf.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c ppr.f -o ppr.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c qsbart.f -o qsbart.o cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c sbart.c -o sbart.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc
Re: [R] How to find S4 generics?
On Wed, 19 Jul 2006, Spencer Graves wrote:
Am I correct then that the 'methods' function could, at least
theoretically, be revised so methods(class=...) could identify both S3
and S4 methods (ignoring inheritance, as it does now, I believe)?
Here is a function to find methods for a formal class. It returns a list
with elements corresponding to a generic, and each element is a list of
strings showing all the signatures that contain any of the specified
classes.
If super=TRUE it looks at all superclasses, if ANY=TRUE it also returns
methods for ANY class.
If you have lme4 loaded, try
methods4(lmer
methods4(ddiMatrix)
methods4(ddiMatrix,super=TRUE)
-thomas
methods4-function(classes, super=FALSE, ANY=FALSE){
if (super) classes-unlist(sapply(classes, function(cl)
getAllSuperClasses(getClass(cl
if (ANY) classes-c(classes,ANY)
gens-allGenerics()@.Data
sigs-lapply(gens, function(g) linearizeMlist(getMethods(g))@classes)
names(sigs)[EMAIL PROTECTED]
sigs-lapply(sigs, function(gen){ gen[unlist(sapply(gen, function(sig)
any(sig %in% classes)))]})
sigs[sapply(sigs,length)0]
}
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Data from Ying, Jung and Wei (1995)
Dear all,
I am looking for the Small Cell Lung Cancer
data from the paper
Ying, Z., Jung, S. H., and Wei, L. J. (1995),
Survival Analysis with Median Regression Models,
Journal of the American Statistical Association} {\bf 90}, 178--184.
Do any one know if it exist in an R readable format somewhere?
Thanks!
Mai Zhou
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to find S4 generics?
Hi, Thomas: Thanks very much. I haven't tried it yet, but it looks
very useful. Best Wishes, Spencer Graves
Thomas Lumley wrote:
On Wed, 19 Jul 2006, Spencer Graves wrote:
Am I correct then that the 'methods' function could, at least
theoretically, be revised so methods(class=...) could identify both S3
and S4 methods (ignoring inheritance, as it does now, I believe)?
Here is a function to find methods for a formal class. It returns a list
with elements corresponding to a generic, and each element is a list of
strings showing all the signatures that contain any of the specified
classes.
If super=TRUE it looks at all superclasses, if ANY=TRUE it also returns
methods for ANY class.
If you have lme4 loaded, try
methods4(lmer
methods4(ddiMatrix)
methods4(ddiMatrix,super=TRUE)
-thomas
methods4-function(classes, super=FALSE, ANY=FALSE){
if (super) classes-unlist(sapply(classes, function(cl)
getAllSuperClasses(getClass(cl
if (ANY) classes-c(classes,ANY)
gens-allGenerics()@.Data
sigs-lapply(gens, function(g) linearizeMlist(getMethods(g))@classes)
names(sigs)[EMAIL PROTECTED]
sigs-lapply(sigs, function(gen){ gen[unlist(sapply(gen, function(sig)
any(sig %in% classes)))]})
sigs[sapply(sigs,length)0]
}
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wrap a loop inside a function
foo can be written as a mapply:
t(mapply(pcm, items, score, MoreArgs = list(theta = theta)))
On 7/19/06, Doran, Harold [EMAIL PROTECTED] wrote:
I need to wrap a loop inside a function and am having a small bit of
difficulty getting the results I need. Below is a replicable example.
# define functions
pcm - function(theta,d,score){
exp(rowSums(outer(theta,d[1:score],'-')))/
apply(exp(apply(outer(theta,d, '-'), 1, cumsum)), 2, sum)
}
foo - function(theta,items, score){
like.mat - matrix(numeric(length(items) * length(theta)), ncol =
length(theta))
for(i in 1:length(items)) like.mat[i, ] - pcm(theta, items[[i]],
score[[i]])
}
# begin example
theta - c(-1,-.5,0,.5,1)
items - list(item1 = c(0,1,2), item2 = c(0,1), item3 = c(0,1,2,3,4),
item4 = c(0,1))
score - c(2,1,3,1)
(foo(theta, items, score))
# R output from function foo
[1] 0.8807971 0.8175745 0.7310586 0.6224593 0.500
However, what I am expecting from the function foo is
like.mat
[,1] [,2] [,3] [,4] [,5]
[1,] 0.118499655 0.17973411 0.25949646 0.34820743 0.4223188
[2,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
[3,] 0.005899109 0.01474683 0.03505661 0.07718843 0.1520072
[4,] 0.880797078 0.81757448 0.73105858 0.62245933 0.500
I cannot seem to track down why the function foo is only keeping the
last row of the full matrix I need. Can anyone see where my error is?
Thanks,
Harold
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 3.0
year 2006
month 04
day24
svn rev37909
language R
version.string Version 2.3.0 (2006-04-24)
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Re: [R] error when compiling stats library in R-2.3.1 on Solaris x86
Dear Prof. Ripley, Following your advice, I read the manual and I realized that I missed two lines in my config.site. FC=f95 -xtarget=generic64 FCFLAGS=-O -I/mounts/devel/SUNWspro/prod/include This solved my problem. It seemed that these two lines are new since R-2.3.0. I am updating from R-2.2.1. I am very sorry about not reading the manual carefully. ;) Thanks for your help! Dongseok Prof Brian Ripley [EMAIL PROTECTED] 7/19/2006 2:39 PM How did 'cc -xtarget=generic64' get there? AFAIK R does not know about it, so presumably you specified it for CC. You need to do the same thing for *all* the compilers, that is CC, CXX, F77 and FC. The INSTALL file asked you to read the R-admin manual: there you will find a very similar example for 64-bit Sparc Solaris. That uses -xarch, which seems preferred to -xtarget (or at least to generic targets). On Wed, 19 Jul 2006, Dongseok Choi wrote: Hello, I tried to compile v2.3.1 on Solaris x86 with SUN Pro compilers. I had an error while stats libarary was being compiled and I notice that -xtarget=generic64 was not passed to f95 while cc used it. Could you tell me how to fix this problem? f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o -xlic_lib=sunperf -lsunmath -Rreg -R/mounts/devel/SUNWspro/lib/amd64:/opt/SUNWspro/lib/amd64 -L/mounts/devel/SUNWspro/prod/lib/amd64 -L/lib/amd64 -L/usr/lib/amd64 -lfui -lfai -lfsu -lsunmath -lmtsk -lm ld: fatal: file bsplvd.o: wrong ELF class: ELFCLASS32 ld: fatal: File processing errors. No output written to stats.so *** Error code 1 make: Fatal error: Command failed for target `stats.so' I did not have any problem when I compiled v2.2.1 as below: cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c family.c -o family.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bsplvd.f -o bsplvd.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalue.f -o bvalue.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c bvalus.f -o bvalus.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c loessf.f -o loessf.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c ppr.f -o ppr.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c qsbart.f -o qsbart.o cc -xtarget=generic64 -I../../../../include -I/mounts/devel/SUNWspro/prod/include -I/mounts/devel/GNU/repoz/readline43/include -D__NO_MATH_INLINES -KPIC -O -I/mounts/devel/SUNWspro/prod/include -c sbart.c -o sbart.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sgram.f -o sgram.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sinerp.f -o sinerp.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c sslvrg.f -o sslvrg.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stxwx.f -o stxwx.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c hclust.f -o hclust.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c kmns.f -o kmns.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c eureka.f -o eureka.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c stl.f -o stl.o f95 -xtarget=generic64 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o
[R] Automating package building packages and repository uploading
Dear Rusers, I have developed two packages for a client of mine. After new features are added or bugs corrected, I upload them to my own web repository. I create both source and binary versions. In fact, I made an script that checks, builds, and uploads them via ftp. However, I am facing two nuisances that do make it difficult to automate: 1) Even if I build the binary version with the command R CMD build --use-zip --binary $package within my script, the output package still gets tarballed and gzipped instead than simply zipped. I come around this automatically extracting and compressing back the files but, am I missing something some other option that would make all this simpler? 2) I expect my packages to be named something like mypackage_1.3.12.tar.gz or mypackage_1.3.12.zip. However, sometimes --I haven't looked at the code that decides the name to give to the packages, so it looks quite random to me-- they get renamed into something like mypackage_1.3.12_R_i486-pc-linux-gnu.tar.gz or mypackage_1.3.12_R_i486-pc-linux-gnu.zip. The problem is that, then, the update.packages() function cannot find them. Is there a way to prevent this trailing string from appearing in the file name? Or else, is there a way to have update.packages() find the package regardless of it? I am running platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 3.1 year 2006 month 06 day01 svn rev38247 language R version.string Version 2.3.1 (2006-06-01) on Debian Etch with kernel 2.6.15-1-k7. Thank you very much. Carlos J. Gil Bellosta http://www.datanalytics.com http://www.data-mining-blog.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] get rid of error in Factor Analysis
Robert,
try try().
Andrew.
On Wed, Jul 19, 2006 at 10:27:07AM +0200, Robert Mcfadden wrote:
Dear All,
I wrote a program and there is a loop. At each iteration I use maximum
likelihood factor analysis (?factanal). Output of factor analysis I use
later (in this loop). Unfortunately from time to time I get an error message
(I paste it below) and everything is stopped. Is it possible to write a
condition that if error appears in factor analysis (FA), change input data
for FA and do it again? Example
for (i in 1:1000){
FA-factanal(data,factor=3)
If error appears change data to data2 and do factor analysis again
#rest of the program
}
Best,
Robert
Error in optim(start, FAfn, FAgr, method = L-BFGS-B, lower = lower, :
L-BFGS-B needs finite values of 'fn'
In addition: Warning message:
NaNs produced in: log(x)
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--
Andrew Robinson
Department of Mathematics and StatisticsTel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
Email: [EMAIL PROTECTED] http://www.ms.unimelb.edu.au
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Re: [R] Sweave and multipage lattice
On 7/18/06, Dieter Menne [EMAIL PROTECTED] wrote: Dear R-Listeners, as the Sweave faq says: http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html creating several figures from one figure chunk does not work, and for standard graphics, a workaround is given. Now I have a multipage trellis plot with an a-priori unknown number of pages, and I don't see an elegant way of dividing it up into multiple pdf-files. try searching the listserv for the following message title (no quotes): Sweave and Printing Lattice Figures From Loop In that message I report code and give a snw file that you can try out. Its very long and not well written, but it got the job done for megood luck -- Joel F. Kincaid Associate Professor of Economics School of Business and Economics Winston Salem State University Winston-Salem, NC 27110 Telephone: (336) 750-2348 Fax: (336) 750-2335 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rearrange data.
Hi,
I am trying to rearrange the following data
d.f - data.frame(x=c(1,1,2,2), y=c(1,2,1,2), vals=c(a11, a12,
a21, a22))
to look like a table with x as the rows and y as the columns, something like
y 1 2
x
1a11 a12
2a21 a22
I tried doing this
funny - function(x,y){d.f[d.f$x==x d.f$y==y,3]}
outer(1:2,1:2, FUN=funny)
But get the error
Error in outer(1:2, 1:2, FUN = funny) : dim- : dims [product 4] do
not match the length of object [2]
What am I doing wrong? I am sure there are a hundred different ways of
doing this.
version
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
http://darwin.cwru.edu/~rsinha
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Rearrange data.
This is FAQ 7.17:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-does-outer_0028_0029-behave-strangely-with-my-function_003f
On 7/19/06, Ritwik Sinha [EMAIL PROTECTED] wrote:
Hi,
I am trying to rearrange the following data
d.f - data.frame(x=c(1,1,2,2), y=c(1,2,1,2), vals=c(a11, a12,
a21, a22))
to look like a table with x as the rows and y as the columns, something like
y 1 2
x
1a11 a12
2a21 a22
I tried doing this
funny - function(x,y){d.f[d.f$x==x d.f$y==y,3]}
outer(1:2,1:2, FUN=funny)
But get the error
Error in outer(1:2, 1:2, FUN = funny) : dim- : dims [product 4] do
not match the length of object [2]
What am I doing wrong? I am sure there are a hundred different ways of
doing this.
version
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major2
minor2.1
year 2005
month12
day 20
svn rev 36812
language R
--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
http://darwin.cwru.edu/~rsinha
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Re: [R] Confirmação de pedido para entrar no grup o python-brasil
On 20 Jul 2006 02:05:32 - Yahoo! Grupos [EMAIL PROTECTED] wrote: Olá [EMAIL PROTECTED], Recebemos sua solicitação para entrar no grupo python-brasil do Yahoo! Grupos, um serviço de comunidades online gratuito e super fácil de usar. Este pedido expirará em 7 dias. PARA ENTRAR NESTE GRUPO: 1) Vá para o site do Yahoo! Grupos clicando neste link: http://br.groups.yahoo.com/i?i=pywddWlXNxf-67g6yNq6a5yrLpQe=savio%2Eoutros%40oi%2Ecom%2Ebr (Se não funcionar, use os comandos para cortar e colar o link acima na barra de endereço do seu navegador.) -OU- 2) RESPONDA a este e-mail clicando em Responder e depois em Enviar, no seu programa de e-mail. Se você não fez esta solicitação ou se não tem interesse em entrar no grupo python-brasil, por favor, ignore esta mensagem. Saudações, Atendimento ao usuário do Yahoo! Grupos O uso que você faz do Yahoo! Grupos está sujeito aos http://br.yahoo.com/info/utos.html -- Sávio Martins Ramos - Arquiteto Rio de Janeiro ICQ 174972645 Pirataria não! Seja livre: Linux http://www.debian.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot fit of a generic function
Yes, that will do.
Thank you Gabor!
Gabor Grothendieck wrote:
You could plot y vs. fitted(y.lm) where y.lm is the output of lm or
plot both y and fitted(y.lm) against x on the same chart.
On 7/18/06, Gregor Gorjanc [EMAIL PROTECTED] wrote:
Hello!
Say I have a function, which creates a design matrix i.e.
myFunc - function(x)
{
ret - cbind(x, x*x, x*x*x)
colnames(ret) - 1:ncol(ret)
return(ret)
}
n - 200
x - runif(n=n, min=0, max=100)
y - myFunc(x) %*% c(1, 0.2, -0.0002) + rnorm(n=n, sd=100)
then I can use this in formulae as here
(fit - lm(y ~ myFunc(x)))
Now I would like to plot data and fitted function on the plot, but I do
not want to access each parameter estimate from object fit i.e. I
would like to use something similar to abline for linear regression but
in a generic way. Is there anything similar to my case?
plot(y=y, x=x)
???plotMyFunc???
Thanks!
--
Lep pozdrav / With regards,
Gregor Gorjanc
--
University of Ljubljana PhD student
Biotechnical Faculty
Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan
Groblje 3 mail: gregor.gorjanc at bfro.uni-lj.si
SI-1230 Domzale tel: +386 (0)1 72 17 861
Slovenia, Europefax: +386 (0)1 72 17 888
--
One must learn by doing the thing; for though you think you know it,
you have no certainty until you try. Sophocles ~ 450 B.C.
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PLEASE do read the posting guide!
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and provide commented, minimal, self-contained, reproducible code.
--
Lep pozdrav / With regards,
Gregor Gorjanc
--
University of Ljubljana PhD student
Biotechnical Faculty
Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan
Groblje 3 mail: gregor.gorjanc at bfro.uni-lj.si
SI-1230 Domzale tel: +386 (0)1 72 17 861
Slovenia, Europefax: +386 (0)1 72 17 888
--
One must learn by doing the thing; for though you think you know it,
you have no certainty until you try. Sophocles ~ 450 B.C.
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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[R] R Visual Basic
Der R-UserRs, I need a little help, I wish to know if exists a way to use R in Visual Basic environment, in creation of VB applications, embedding R in VB. Is it possible? Can anyone help me? Is there something such as books, articles, other available on the web? Thanks in advance. Regards. Vito Se non ora, quando? Se non qui, dove? Se non tu, chi? Personal Web Space: http://vr71.spaces.msn.com/ Chiacchiera con i tuoi amici in tempo reale! http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to find S4 generics? (was: inames() function and lmer())
On Tue, 18 Jul 2006, Spencer Graves wrote: * * methods * * You have asked an excellent question. I can provide a partial answer below. First, however, I wish to pose a question of my own, which could help answer your question: How can one obtain a simple list of the available generics for a class? For an S3 class, the 'methods' functions provide that. What about an S4 class? That's entirely opaque to me, if I somehow can't find the relevant information in other ways. For example, ?lmer-class lists many but not all of the methods available for objects of class 'lmer'. I think I once found a way to get that, but I'm not able to find documentation on it now. It doesn't work the same way. S3 generics are defined on a single argument and hence have methods for a class, and so it is relevant to ask what generics there are which have methods for a given class - but even then there can be other generics and other methods which dispatch on object from that class by inheritance (e.g. on lm for glm objects). S4 generics dispatch on a signature which can involve two or more classes, and I guess the simplest interpretation of your question is `what S4 generics are there which have methods with signatures mentioning this class'. Given the decentralized way such information is stored, I think the only way to do that is to find all the generics currently available (via getGenerics or its synonym allGenerics) and then call showMethods on each generic. In particular, methods are stored in the S4 generic and not in the package defining the method. However, I suspect inheritance is much more important here, and there is no way to know if methods for class ANY actually work for a specific S4 class. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how can I delete rows?
Hello, I am very new in R so I am so sorry for this question. I have the Barro-Lee data set which contains 98 countries and I want to run the regressions only for the Latin America countries, so what do you recomend? How can I delete all the other countries or how can I select the countries of Lat. Am. thank you this is the list of countries SHCODE COUNTRY NAME WBCTRY (1) (2) _ 1Algeria DZA + + 2Angola AGO - - 3BeninBEN - + 4Botswana BWA + + 5Burkina Faso HVO - - 6Burundi BDI + - 7Cameroon CMR + + 8Cape verde CPV - - 9Central African Rep. CAF + + 10Chad TCD - - 11Comoros COM - - 12CongoCOG - + 13EgyptEGY + + 14Ethiopia ETH + - 15GabonGAB + - 16Gambia GMB - + 17GhanaGHA + + 18Guinea GIN - - 19Guinea-BissauGNB - - 20Cote d'IvoireCIV + - 21KenyaKEN + + 22Lesotho LSO - + 23Liberia LBR + + 24Madagascar MDG + - 25Malawi MWI + + 26Mali MLI - + 27Mauritania MRT - - 28MauritiusMUS + + 29Morocco MAR + - 30Mozambique MOZ - - 31NigerNER - + 32Nigeria NGA + - 33Rwanda RWA + + 34Senegal SEN + + 35Seychelles SYC - - 36Sierra Leone SLE + + 37Somalia SOM - - 38South africa ZAF + + 39SudanSDN + + 40SwazilandSWZ + + 41Tanzania TZA + + 42Togo TGO + + 43Tunisia TUN + + 44Uganda UGA + + 45ZaireZAR + + 46Zambia ZMB + + 47Zimbabwe ZWE + + 48Bahamas, The BHS - - 49Barbados BRB + + 50Canada CAN + + 51Costa Rica CRI + + 52Dominica DMA - - 53Dominican Rep. DOM + + 54El Salvador SLV + + 55Grenada GRD - - 56GuatemalaGTM + + 57HaitiHTI + + 58Honduras HND + + 59Jamaica JAM + + 60Mexico MEX + + 61NicaraguaNIC + + 62Panama PAN + + 63St.Lucia LCA - - 64St.Vincent Grens. VCT - - 65Trinidad TobagoTTO + + 66United StatesUSA + + 67ArgentinaARG + + 68Bolivia BOL + + 69Brazil BRA + + 70ChileCHL + + 71Colombia COL + + 72Ecuador ECU + + 73Guyana GUY + + 74Paraguay PRY + +
[R] Classification error rate increased by bagging - any ideas?
Hi, I'm analysing some anthropometric data on fifty odd skull bases. We know the gender of each skull, and we are trying to develop a predictor to identify the sex of unknown skulls. Rpart with cross-validation produces two models - one of which predicts gender for Males well, and Females poorly, and the other does the opposite (Females well, and Males poorly). In both cases the error rate for the worse predicted gender is close to 50%, and for the better predicted gender about 15%. Bagging tree models produces a model which classifies both males and females equally well (or equally poorly), but has an overall error rate (just over 30%) higher than either of the rpart models (about 25%). My instinct is to go for the bagging results, as they seem more reasonable, but my colleagues really like the lower overall error rate. Any thoughts? Ta, Anthony Staines -- Dr. Anthony Staines, Senior Lecturer in Epidemiology. School of Public Health and Population Sciences, UCD, Earlsfort Terrace, Dublin 2, Ireland. Tel:- +353 1 716 7345. Fax:- +353 1 716 7407 Mobile:- +353 86 606 9713 Web:- http://phm.ucd.ie [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Visual Basic
On Wed, 19 Jul 2006, Vito Ricci wrote: Der R-UserRs, I need a little help, I wish to know if exists a way to use R in Visual Basic environment, in creation of VB applications, embedding R in VB. Is it possible? Can anyone help me? Is there something such as books, articles, other available on the web? See the rw-FAQ Q2.18 and the projects it points you to. Thanks in advance. Regards. Vito -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] voronoi tessellations
On Tue, 18 Jul 2006, Don MacQueen wrote: I'll suggest going to the CRAN packages page and doing a search for voronoi. The problem here is that `Voronoi tessellation' is a secondary name. The concept has many names, including Dirichlet tessellation and Thiessen polygons, and Dirichlet has priority over Voronoi. Also, search for 'triangulation', since that is one of the uses of them. I know of packages deldir, tripack and perhaps geometry. -Don At 11:46 PM -0400 7/18/06, zubin wrote: Hello, looking to draw a voronoi tessellations in R - can anyone recommend a package that has tackled this? some background: i have a economic data set and created a sammons projection, like to now overlay a voronoi tessellation over the sammons 2-D solution for a slick visual, and potentially color each tessellation element based on a metric. home.u - unique(home1) home.dist - dist(home.u) home.sam - sammon(home.dist,k=2) plot(home.sam$points) Wait a minute. If this is sammon() from MASS (uncredited), it is not a projection, and there is no relevant concept of distance between points in the mapped space apart from between the supplied points. I suggest Zubin reads carefully the reference whose support software he appears to be using. (It would also have answered his question.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] odfWeave Package
The odfWeave package is now available on CRAN at
http://lib.stat.cmu.edu/R/CRAN/src/contrib/Descriptions/odfWeave.html
and your local mirror.
The package extends Sweave to Open Document Format (ODF) text document
files. Latex-style code chunks and in-line Sexpr commands can be used
to embed R output into ODF file, which can then be exported to doc,
rtf, html, pdf and other formats.
Other functions in the package facilitate ODF formatted tables, text
and lists.
The current limitations of the package are:
O tangling is not yet implement (but will be)
O testing has been done on text documents generated by OpenOffice.
Other formats/editors may work, but are not (yet) supported.
Please send comments, suggestions and/or contributions.
Max Kuhn
Research Statistics
Pfizer Global RD
Max.Kuhn at pfizer.com
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Re: [R] how can I delete rows?
On Tue, Jul 18, 2006 at 12:25:47PM -0300, raul sanchez wrote:
I have the Barro-Lee data set which contains 98 countries and I want
to run the regressions only for the Latin America countries, so what
do you recomend? How can I delete all the other countries or how can
I select the countries of Lat. Am. thank you
this is the list of countries
SHCODE COUNTRY NAME WBCTRY (1) (2)
_
1Algeria DZA + +
2Angola AGO - -
3BeninBEN - +
4Botswana BWA + +
5Burkina Faso HVO - -
6Burundi BDI + -
7Cameroon CMR + +
[...]
Assuming the data is stored in a data frame called bl you could do
something like this:
First you generate a list of all countries you are interested in - e.g.
set = c('Benin', 'Congo', 'Mali')
And then you subset the data frame with it
bl[bl$COUNTRY %in% set, ]
SHCODE COUNTRY NAME WBCTRY X.1. X.2.
3 3 Benin BEN -+ NA
12 12 Congo COG -+ NA
26 26Mali MLI -+ NA
cu
Philipp
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Dept. of Genome Oriented Bioinformatics Fax. +49-8161-71 2186
Technical University of Munich
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85350 Freising, Germany
and
Institute for Bioinformatics / MIPS Tel. +49-89-3187 3675
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Re: [R] R and DDE (Dynamic Data Exchange)
Richard M. Heiberger wrote: I am thrilled to learn tcltk2 has DDE capability. It is the piece I have been needing to make ESS work directly with the RGUI on Windows. GNU emacs on Windows has a ddeclient, but no access to COM. So if R, or tcltk2 talking in both directions to R, has a ddeserver, all should be possible. I will be reading the documentation closely in a few weeks to tie it together and then intend to make it happen. Do you, or any other list member, have a sense of the size, complexity, ease, magnitude of the task I just defined? Any advice as I get started on it? Rich Well, to be honest, DDE is an old exchange protocol (the first one proposed by M$ in Windows version 1 or 2). It is not that reliable. In practice, when the communication is working fine, you have no problems with it. But if something fails in either the server or the client, you got a very bad behaviour sometimes. I think there is some interest to have DDE available for R (WinEdt uses DDE, I think... Uwe???), together with (D)COM, and socket server. Currently, I am improving the socket server build in svSocket (SciViews bundle) because it is the communication protocol we decided to push forward in Tinn-R, but there are other implementations out there. I think that using a socket server is more reliable and it is also a cross-platform solution. So, I would personnally prefer that solution. Best, Philippe Grosjean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and DDE (Dynamic Data Exchange)
Gabor Grothendieck wrote: You can access DDE via COM as in this example which uses DDE to open an Excel file. Note that Excel also supports COM directly and normally one would use COM with Excel, not DDE, so you might check if your application also supports COM. # opens an excel spreadsheet c:\test.xls using dde library(RDCOMClient) sh - COMCreate(Shell.Application) sh$Namespace(C:\\)$ParseName(test.xls)$InvokeVerb(Open) Well, I think you are really using COM here, not DDE. M$ implemented the same DDE commands in Excel and Word in COM to ease upgrading from DDE to COM... but the internal is completelly different! Best, Philippe Grosjean Also if you are going to access DDE via COM or just COM also check out the rcom package which is similar to RDCOMClient. On 7/17/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: R and DDE (Dynamic Data Exchange) Dear Rusers, I run an application (not mine) which acts as a DDE server. I would like to use R to get data from this application, say once per minute, and do some processing on it. I didn't find much info on the R DDE abilities, apart the tcltk2 package in which I will try to go deeper. I would be very thankful for any info, pointer or advice about the good ways to make R program get online data from a DDE server. Thanks Vincent __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A contingency table of counts by case
sorry, answered to quickly... actually it's easier using paste(): df - df[order(df$case),] apply(combinations(9,2), 1, function(y) table(factor(do.call(paste, c(with(df[df$id %in% y, ], split(x, id)), sep=)), levels=c(00,01,10,11 --- Jacques VESLOT CNRS UMR 8090 I.B.L (2ème étage) 1 rue du Professeur Calmette B.P. 245 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 http://www-good.ibl.fr --- Serguei Kaniovski a écrit : Here is an example of the data.frame that I have, df-data.frame(case=rep(1:5,each=9),id=rep(1:9,times=5),x=round(runif(length(rep(1:5,each=9) case represents the cases, id the persons, and x is the binary state. I would like to know in how many cases any two persons a. both have 1, b. the first has 0 - the second has 1, c. the first has 0 - the second has 0, d. both have 0. There will be choose(9,2) sums, denoted s_ij for 1=ij=9, where i and j are running indices for an id-pair. Please help, this is way beyond my knowledge of R! Thank you, Serguei Kaniovski __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] get rid of error in Factor Analysis
Dear All,
I wrote a program and there is a loop. At each iteration I use maximum
likelihood factor analysis (?factanal). Output of factor analysis I use
later (in this loop). Unfortunately from time to time I get an error message
(I paste it below) and everything is stopped. Is it possible to write a
condition that if error appears in factor analysis (FA), change input data
for FA and do it again? Example
for (i in 1:1000){
FA-factanal(data,factor=3)
If error appears change data to data2 and do factor analysis again
#rest of the program
}
Best,
Robert
Error in optim(start, FAfn, FAgr, method = L-BFGS-B, lower = lower, :
L-BFGS-B needs finite values of 'fn'
In addition: Warning message:
NaNs produced in: log(x)
[[alternative HTML version deleted]]
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Re: [R] get rid of error in Factor Analysis
?try
On Wed, 19 Jul 2006, Robert Mcfadden wrote:
Dear All,
I wrote a program and there is a loop. At each iteration I use maximum
likelihood factor analysis (?factanal). Output of factor analysis I use
later (in this loop). Unfortunately from time to time I get an error message
(I paste it below) and everything is stopped. Is it possible to write a
condition that if error appears in factor analysis (FA), change input data
for FA and do it again? Example
for (i in 1:1000){
FA-factanal(data,factor=3)
If error appears change data to data2 and do factor analysis again
#rest of the program
}
Best,
Robert
Error in optim(start, FAfn, FAgr, method = L-BFGS-B, lower = lower, :
L-BFGS-B needs finite values of 'fn'
In addition: Warning message:
NaNs produced in: log(x)
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
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] Output and Word
thank you Greg Snow for this information ! But I have this message : odfWeave(c:/simple.odt, c:/essai.odt) Setting wd Copying c:/simple.odt Decompressing ODF file using unzip -o C:\DOCUME~1\Maud\LOCALS~1\Temp\RtmpF0hdqb/simple.odt Erreur dans odfWeave(c:/simple.odt, c:/essai.odt) : Error unzipping file De plus : Warning message: unzip introuvable R says that it doesn't find unzip... What is this program ? 2006/7/18, Greg Snow [EMAIL PROTECTED]: Others have suggested using R2HTML (which is a good option). Another option is to use Sweave and specifically the new odfWeave package for R. This works on OpenOffice files rather than word files (but OpenOffice http://www.openoffice.org/ can inport and export word documents). The basic idea is to write your report in OpenOffice (or LaTeX or HTML), but anywhere that you want statisticial output (graphs, tables) you include instead the R code to produce the table, graph, or whatever. Run this file through R (using Sweave or odfWeave) and the resulting file has replaced all the code segments with their output. The documentation with odfWeave has examples. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sharon snowdon Sent: Monday, July 17, 2006 2:36 PM To: r-help@stat.math.ethz.ch Subject: [R] Output and Word Hi I have just started to have a look at R. I have used most stats software packages and can use perl, visual basic etc. I am interested in how well it handles lots of output e.g. tables or charts. How would you get lots of output most easily and quickly into a Word document? Sharon Snowdon - -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- David [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Aligning ragged text columns
Can anyone please suggest how I can print: a - matrix(c( Heading 1, This is some info\nabout heading 1, Heading 2, This is some info\nabout heading 2, ), byrow=T, nrow=2) to look like: Heading 1 This is some info about heading 1 Heading 2 This is some info about heading 2 (if you're not using a fixed width font, I want the text in the second column to line up) I've looked at encodeString and format, but neither seems to quite be the right tool Thanks! Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] conditional plot
Manoj wrote: Hi, Can anyone pls help me in plotting the following data? The data-set contains company name, specification-1, specification-2. The graph would basically plot company name with specification-1 on x-axis, specification-2 on y-axis. Simply put - company name should get classified into one of the four quardrants created by specification 1 specification2. You could do something along these lines, replacing LETTERS with your company names: df - data.frame(SPEC1 = runif(26), SPEC2 = runif(26), COMPANY = LETTERS) par(lab=c(10,10,7), las=1) plot(df$SPEC1, df$SPEC2, type=n, xlab=Specification 1, ylab=Specification 2, ylim=c(0,1), xlim=c(0,1)) text(df$SPEC1, df$SPEC2, df$COMPANY) axis(side=1, at = .5, tck=1, col=grey, lty=2) axis(side=2, at = .5, tck=1, col=grey, lty=2) Thanks. Manoj __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Aligning ragged text columns
Am Mittwoch, den 19.07.2006, 10:03 +0100 schrieb hadley wickham: Can anyone please suggest how I can print: a - matrix(c( Heading 1, This is some info\nabout heading 1, Heading 2, This is some info\nabout heading 2, ), byrow=T, nrow=2) to look like: Heading 1 This is some info about heading 1 Heading 2 This is some info about heading 2 Guess its heading1 - Heading1 heading2 - Heading2 a - matrix(c( Heading 1, paste(This is some info\nabout, heading1, sep=), Heading 2, paste(This is some info\nabout, heading2, sep=), ), byrow=T, nrow=2) Cheers, John __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Aligning ragged text columns
heading1 - Heading1 heading2 - Heading2 a - matrix(c( Heading 1, paste(This is some info\nabout, heading1, sep=), Heading 2, paste(This is some info\nabout, heading2, sep=), ), byrow=T, nrow=2) I wasn't so concerned about the redundancy in my example, but how it looks - eg. somefunction(h) Heading 1 This is some info about heading 1 Heading 2 This is some info about heading 2 Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Aligning ragged text columns
Hi Hadley, I find that things line up better in data.frames data.frame(c1 = c(Heading 1, , Heading 2, ), + c2 = c(This is some info, about heading 1, This is some info, about heading )) c1c2 1 Heading 1 This is some info 2 about heading 1 3 Heading 2 This is some info 4 about heading although, this looks better in my console window than pasted here. Then the question is what to so with the row and column names. HTH, ken heading1 - Heading1 heading2 - Heading2 a - matrix(c( Heading 1, paste(This is some info\nabout, heading1, sep=), Heading 2, paste(This is some info\nabout, heading2, sep=), ), byrow=T, nrow=2) I wasn't so concerned about the redundancy in my example, but how it looks - eg. somefunction(h) Heading 1 This is some info about heading 1 Heading 2 This is some info about heading 2 Hadley [[alternative text/enriched version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Aligning ragged text columns
Just a follow-up, by giving names with variable amounts of white space, I could make the column and rownames invisible (although this is probably abusing the mechanisms, however, this is only for display purposes, I suppose). dd - data.frame(c1 = c(Heading 1, , Heading 2, ), c2 = c(This is some info, about heading 1, This is some info, about heading )) names(dd) - c( , ) rownames(dd) - c( ,, , ) dd Heading 1 This is some info about heading 1 Heading 2 This is some info about heading On Jul 19, 2006, at 11:40 AM, ken knoblauch wrote: Hi Hadley, I find that things line up better in data.frames data.frame(c1 = c(Heading 1, , Heading 2, ), + c2 = c(This is some info, about heading 1, This is some info, about heading )) c1c2 1 Heading 1 This is some info 2 about heading 1 3 Heading 2 This is some info 4 about heading although, this looks better in my console window than pasted here. Then the question is what to so with the row and column names. HTH, ken heading1 - Heading1 heading2 - Heading2 a - matrix(c( Heading 1, paste(This is some info\nabout, heading1, sep=), Heading 2, paste(This is some info\nabout, heading2, sep=), ), byrow=T, nrow=2) I wasn't so concerned about the redundancy in my example, but how it looks - eg. somefunction(h) Heading 1 This is some info about heading 1 Heading 2 This is some info about heading 2 Hadley [[alternative text/enriched version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Output and Word
On Wed, 19 Jul 2006, David Hajage wrote: thank you Greg Snow for this information ! But I have this message : odfWeave(c:/simple.odt, c:/essai.odt) Setting wd Copying c:/simple.odt Decompressing ODF file using unzip -o C:\DOCUME~1\Maud\LOCALS~1\Temp\RtmpF0hdqb/simple.odt Erreur dans odfWeave(c:/simple.odt, c:/essai.odt) : Error unzipping file De plus : Warning message: unzip introuvable R says that it doesn't find unzip... What is this program ? It is in the Rtools.zip bundle used to build source packages for R under Windows (your unstated OS, it seems). However, you should take this up with the package maintainer, as R has the capability to unzip files builtin (utils::zip.unpack) on Windows. 2006/7/18, Greg Snow [EMAIL PROTECTED]: Others have suggested using R2HTML (which is a good option). Another option is to use Sweave and specifically the new odfWeave package for R. This works on OpenOffice files rather than word files (but OpenOffice http://www.openoffice.org/ can inport and export word documents). The basic idea is to write your report in OpenOffice (or LaTeX or HTML), but anywhere that you want statisticial output (graphs, tables) you include instead the R code to produce the table, graph, or whatever. Run this file through R (using Sweave or odfWeave) and the resulting file has replaced all the code segments with their output. The documentation with odfWeave has examples. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sharon snowdon Sent: Monday, July 17, 2006 2:36 PM To: r-help@stat.math.ethz.ch Subject: [R] Output and Word Hi I have just started to have a look at R. I have used most stats software packages and can use perl, visual basic etc. I am interested in how well it handles lots of output e.g. tables or charts. How would you get lots of output most easily and quickly into a Word document? Sharon Snowdon - -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fitting a distribution to peaks in histogram
Hello list! I would like to fit a distribution to each of the peaks in a histogram, such as this: http://photos1.blogger.com/blogger/7029/2724/1600/DU145-Bax3-Bcl-xL.png . The peaks are identified using Petr Pikal peaks function ( http://finzi.psych.upenn.edu/R/Rhelp02a/archive/33097.html), but after that I am quite stuck. Any idea as to how I can: Fit a distribution to each peak Integrate the area between each two peaks, using the means and widths of the distributions fitted to the two peaks. I will be using the integrate function The histogram is based on approximately 15000 events, which makes Mclust and pam (which both delivers the information I need) less useful. The whole point of this exercise is to find the percentage of cells in peak 1, 2, 3, and so on, and between peak 1-2, peak 2-3, peak 3-4 and so on. Having more that 6 peaks does not appears likely. I am quite new to R and apologise if the solution is fairly basic. Thank you in advance for any help and suggestions Sincerely, Ulrik [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Test for equality of coefficients in multivariate multiple regression
Hello and thank you for your answers, Andrew and Berwin. If I'm not mistaken, the mixed-model version of Berwin's approach would be: #My stuff: DF-data.frame(x1=rep(c(0,1),each=50),x2=rep(c(0,1),50)) tmp-rnorm(100) DF$y1-tmp+DF$x1*.5+DF$x2*.3+rnorm(100,0,.5) DF$y2-tmp+DF$x1*.5+DF$x2*.7+rnorm(100,0,.5) x.mlm-lm(cbind(y1,y2)~x1+x2,data=DF) #1st part of Andrew's suggestion: DF2 - with(DF, data.frame(y=c(y1,y2))) DF2$x11 - with(DF, c(x1, rep(0,100))) DF2$x21 - with(DF, c(x2, rep(0,100))) DF2$x12 - with(DF, c(rep(0,100), x1)) DF2$x22 - with(DF, c(rep(0,100), x2)) DF2$x1 - with(DF, c(x1, x1)) DF2$wh - rep(c(0,1), each=100) #Mixed version of models: DF2$unit - rep(c(1:100), 2) library(nlme) mm1 - lme(y~wh + x11 + x21 + x12 + x22, random= ~1 | unit, DF2, method=ML) fixef(mm1) (Intercept) wh x11 x21 x12 x22 0.07800993 0.15234579 0.52936947 0.13853332 0.37285132 0.46048418 coef(x.mlm) y1y2 (Intercept) 0.07800993 0.2303557 x1 0.52936947 0.3728513 x2 0.13853332 0.4604842 mm2 - update(mm1, y~wh + x1 + x12 + x22) anova(mm1, mm2) Model df AIC BIClogLik Test L.Ratio p-value mm1 1 8 523.6284 550.0149 -253.8142 mm2 2 7 522.0173 545.1055 -254.0086 1 vs 2 0.388908 0.5329 This seems to be correct. What anova() tells me is that the effect of x1 is the same for y1 and y2. What I don't understand then is why the coefficients for x12 and x22 differ so much between mm1 and mm2: fixef(mm2) (Intercept) wh x1 x12 x22 0.1472766 0.1384474 0.5293695 -0.1565182 0.3497476 fixef(mm1) (Intercept) wh x11 x21 x12 x22 0.07800993 0.15234579 0.52936947 0.13853332 0.37285132 0.46048418 Sorry for being a bit slow here, I'm (obviously) not a statistician. Thanks again, Uli Andrew Robinson wrote: G'day Berwin, my major reason for preferring the mixed-effect approach is that, as you can see below, the residual df for your models are 195 and 194, respectively. The 100 units are each contributing two degrees of freedom to your inference, and presumably to your estimate of the variance. I feel a little sqeueamish about that, because it's not clear to me that they can be assumed to be independent. I worry about the effects on the size of the test. With a mixed-effects model each unit could be a cluster of two observations, and I would guess the size would be closer to nominal, if not nominal. Cheers Andrew __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] conditional plot
does this do what you want? x - data.frame(company=LETTERS, spec1=runif(26), spec2=runif(26)) plot(range(x$spec1), range(x$spec2), type='n') abline(v=.5, h=.5) text(x$spec1, x$spec2, labels=x$company) On 7/19/06, Manoj [EMAIL PROTECTED] wrote: Hi, Can anyone pls help me in plotting the following data? The data-set contains company name, specification-1, specification-2. The graph would basically plot company name with specification-1 on x-axis, specification-2 on y-axis. Simply put - company name should get classified into one of the four quardrants created by specification 1 specification2. Thanks. Manoj __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Aligning ragged text columns
I find that things line up better in data.frames
That's a good idea, although I was hoping there would be something in
R to do it for me.
I have ended up with:
fwidth - max(nchar(x[,1]))
descs - strwrap(x[,2], width=width - fwidth - 5, simplify=FALSE)
output - do.call(rbind, mapply(function(name, desc) {
cbind(c(name, rep(, length=length(desc)-1)), desc)
}, x[,1], descs))
cat(paste(format(output[,1]), output[,2], collapse=\n), \n)
Thanks,
Hadley
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[R] Plotting lines and points on the second plot when using gap.plot in plotrix
Hi My question is simple - the gap.plot function in the plotrix package allows users to draw graphs that have a broken axis. However, I want to then add a line to the second plot, but can't. Eg: twogrp-c(rnorm(10)+4,rnorm(10)+20) gap.plot(twogrp,rnorm(20),gap.bounds=c(8,16),gap.axis=x,xlab=X values, xtics=c(4,7,17,20),ylab=Y values,main=Plot gap on X axis) # this doesn't work points(17,0,col=red) # this does work points(4,0,col=green) I somehow need to set the focus to the second plot so that I can draw lines and points on it. Any help? Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting lines and points on the second plot when usinggap.plot in plotrix
I've answered my own question, the x-values of the line/points I want to plot must be adjusted by the gap size Thanks Mick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 19 July 2006 11:58 To: r-help@stat.math.ethz.ch Subject: [R] Plotting lines and points on the second plot when usinggap.plot in plotrix Hi My question is simple - the gap.plot function in the plotrix package allows users to draw graphs that have a broken axis. However, I want to then add a line to the second plot, but can't. Eg: twogrp-c(rnorm(10)+4,rnorm(10)+20) gap.plot(twogrp,rnorm(20),gap.bounds=c(8,16),gap.axis=x,xlab=X values, xtics=c(4,7,17,20),ylab=Y values,main=Plot gap on X axis) # this doesn't work points(17,0,col=red) # this does work points(4,0,col=green) I somehow need to set the focus to the second plot so that I can draw lines and points on it. Any help? Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Random structure of nested design in lme
All, I'm trying to analyze the results of a reciprocal transplant experiment using lme(). While I get the error-term right in aov(), in lme() it appears impossible to get as expected. I would be greatful for any help. My experiment aimed to identify whether two fixed factors (habitat type and soil type) affect the development of plants. I took soil from six random sites each of two types (arable and grassland) and transplanted them back into the sites of origin in such way that in each of the sites there were six pots containing arable soil and six pots of grassland soil, each containing a seedling. With aov(), I got the analysis as I expected, with habitat type tested against destination site, and soil type tested against origin site: summary(aov(response~soiltype*habitat+Error(destination+origin))) # #Error: destination # Df Sum Sq Mean Sq F value Pr(F) #habitat1 1. 1. 0.699 0.4226 #Residuals 10 14.3056 1.4306 # #Error: origin # Df Sum Sq Mean Sq F value Pr(F) #soiltype 1 1.8 1.8 11.636 0.006645 ** #Residuals 10 1.52778 0.15278 #--- #Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 # #Error: Within # Df Sum Sq Mean Sq F value Pr(F) #soiltype:habitat 1 0.2500 0.2500 2.1774 0.1427 #Residuals120 13.7778 0.1148 However, when I try to replicate this analysis in lme, I am unable to get the structure of the random factors (origin and destination) correct. Does anyone have a suggestion how to resolve this problem? Thanks in advance. René Eschen CABI Bioscience Centre Switzerland Rue des Grillons 1 2800 Delémont Switzerland [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Random structure of nested design in lme
Can you provide an example of what you have done with lme so we might be able to evaluate the issue? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ESCHEN Rene Sent: Wednesday, July 19, 2006 7:37 AM To: r-help@stat.math.ethz.ch Subject: [R] Random structure of nested design in lme All, I'm trying to analyze the results of a reciprocal transplant experiment using lme(). While I get the error-term right in aov(), in lme() it appears impossible to get as expected. I would be greatful for any help. My experiment aimed to identify whether two fixed factors (habitat type and soil type) affect the development of plants. I took soil from six random sites each of two types (arable and grassland) and transplanted them back into the sites of origin in such way that in each of the sites there were six pots containing arable soil and six pots of grassland soil, each containing a seedling. With aov(), I got the analysis as I expected, with habitat type tested against destination site, and soil type tested against origin site: summary(aov(response~soiltype*habitat+Error(destination+origin))) # #Error: destination # Df Sum Sq Mean Sq F value Pr(F) #habitat1 1. 1. 0.699 0.4226 #Residuals 10 14.3056 1.4306 # #Error: origin # Df Sum Sq Mean Sq F value Pr(F) #soiltype 1 1.8 1.8 11.636 0.006645 ** #Residuals 10 1.52778 0.15278 #--- #Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 # #Error: Within # Df Sum Sq Mean Sq F value Pr(F) #soiltype:habitat 1 0.2500 0.2500 2.1774 0.1427 #Residuals120 13.7778 0.1148 However, when I try to replicate this analysis in lme, I am unable to get the structure of the random factors (origin and destination) correct. Does anyone have a suggestion how to resolve this problem? Thanks in advance. René Eschen CABI Bioscience Centre Switzerland Rue des Grillons 1 2800 Delémont Switzerland [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
