[R] orca binary?
Dear R People: Is there a binary version for rorca, please? Thanks, Laura mailto: [EMAIL PROTECTED] R Windows 1.9.0 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] gauss.hermite?
Dear Spencer,
In Dr. Gray's course notes for Advanced Statistical Computing
(Appendix of Chapter 6) there are some functions for computing
abscissas and corresponding weights for several Gaussian integration
rules:
http://icommons.harvard.edu/~hsph-bio248-01/Lecture_Notes/
I hope this helps.
Best,
Dimitris
Dimitris Rizopoulos
Doctoral Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Spencer Graves [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Friday, May 28, 2004 6:35 AM
Subject: [R] gauss.hermite?
The search at www.r-project.org mentioned a function
gauss.hermite{rmutil}. However, 'install.packages(rmutil)'
produced, 'No package rmutil on CRAN.' How can I find the current
status of gauss.hermite and rmutil?
Thanks,
Spencer Graves
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[R] distance in the function kmeans
Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET Accédez au courrier électronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tél : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Building packages and Rcmd check
Hello yet again! I'm trying to build a package. The Rcmd build works fine. But the Rcmd check produces an error because I don't have latex on my laptop. Any suggestions, please? R Windows 1.9.0 thanks again, Laura _ Learn to simplify your finances and your life in Streamline Your Life from MSN Money. http://special.msn.com/money/0405streamline.armx __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] privileged slots
Martin Maechler schrieb:
Matthias == Matthias Kohl [EMAIL PROTECTED]
on Thu, 27 May 2004 14:01:51 +0100 writes:
Matthias Hi all, in the help for RClassUtils I found the
Matthias expression privileged slots in function
Matthias checkSlotAssignment with the explanation:
Matthias /privileged slots (those that can only be set by
Matthias accesor functions defined along with the class
Matthias itself)/
RClassUtils ???
help.search(RClassUtils)
your right, sorry
but, at least a R Site search in Functions
gives me one match: Utilities for Managing Class Definitions
which hast the title: RClassUtils{methods} R Documentation
No help files found with alias or concept or title matching
'RClassUtils' using fuzzy matching.
-
So I guess that's not something in a standard R document.
You should rather keep to the 'official documentation' ...
I thought this is a official documentation ...
Matthias I thought all slots of a (not private) class can
Matthias be a accessed by a user via the @ Operator.
I tend to agree with your thoughts...
Matthias Is there a way to make a single slot of a class (not
Matthias the whole class) private, so that you can access
Matthias this slot only via an accessor function (not via @)?
I'd rather guess not.
Matthias Thanks, for your help Matthias
Martin
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Re: [R] Building packages and Rcmd check
Laura Holt wrote: Hello yet again! I'm trying to build a package. The Rcmd build works fine. But the Rcmd check produces an error because I don't have latex on my laptop. Any suggestions, please? Rcmd check --help tells you that you can use the option: --no-latexdo not run LaTeX on help files if you don't want LaTeX porcessing to be checked. ... or install LaTeX ... Uwe Ligges R Windows 1.9.0 thanks again, Laura _ Learn to simplify your finances and your life in Streamline Your Life from MSN Money. http://special.msn.com/money/0405streamline.armx __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET As the name says, kmeans() calculates *means* (centres) of clusters. It does not any make sense to do that on distances ... Uwe Ligges Accdez au courrier lectronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tl : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] orca binary?
Laura Holt wrote: Dear R People: Is there a binary version for rorca, please? Given I recall correctly, I tried to build rorca for Windows one or two years ago without success. But maybe Tony (In this context I recall that I'm still owing him a pizza) knows of a binary? Uwe Ligges Thanks, Laura mailto: [EMAIL PROTECTED] R Windows 1.9.0 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
On Fri, 28 May 2004, Uwe Ligges wrote: n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET As the name says, kmeans() calculates *means* (centres) of clusters. It does not any make sense to do that on distances ... Uwe Ligges That's not really true. There is an equivalent to the k-means target criterion in terms of distances, and that uses squared Euklidean distances. However, as far as I know, you cannot compute it directly in R for any other distance. Using pam is the thing which comes closest. Christian Hennig *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] gauss.hermite?
On Fri, May 28, 2004 at 09:04:53AM +0200, Dimitris Rizopoulos wrote:
Dear Spencer,
In Dr. Gray's course notes for Advanced Statistical Computing
(Appendix of Chapter 6) there are some functions for computing
abscissas and corresponding weights for several Gaussian integration
rules:
http://icommons.harvard.edu/~hsph-bio248-01/Lecture_Notes/
Also have a look at
@Book{judd98,
author = {Judd, Kenneth L},
title ={Numerical methods in economics},
publisher ={MIT Press},
year = 1998
}
especially one of the early chapters (integration is in its title,
but I don't have the book at the moment), which covers theory and
practice of numerical integration and quadrature rules.
Implementing these in R has been on my TODO list for a while, so I
would be happy to cooperate on this (but only in July or later).
Best,
Tamas
--
Tamás K. Papp
E-mail: [EMAIL PROTECTED]
Please try to send only (latin-2) plain text, not HTML or other garbage.
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Re: [R] distance in the function kmeans
n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Yes but how can we choose the distance to calculate centers? Thanks in advance, Nicolas BOUGET As the name says, kmeans() calculates *means* (centres) of clusters. It does not any make sense to do that on distances ... Uwe Ligges Accédez au courrier électronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tél : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat. math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Accédez au courrier électronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tél : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sorting Data?
Am 27.05.2004 22:11:04 schrieb(en) Berton Gunter: Your question does not make a lot of sense to me. If you only want to compute distances between mothers and THEIR daughters, you cannot have a matrix, because different mothers have different numbers of daughters. Thats true, but we took only one mother and one daugther in our sample, so in this sample we have only on daugther from one mother. Do you want to define the distance between a mother and someone else's daughter as 0 or INF ? Do you want to show that mothers and their daughters are more similar then mothers and someone else's daughters? Thats my question, yes. ;-) You either need to think about what you wish to do more carefully or express it more carefully. At least for me. Maybe someone else will understand you better. Sorry, its the first time for me to talking about statistics in english and so I have to learn to express it better. Martin -- Bert Martin Klaffenboeck wrote: Hello, Im reading through some manuals, but I cannot find my answer. I have a file containing many data: Vpn CodeFamily Age F1 F2 ... F17 1 1 M 46 1 2 ... 1 2 1 D 18 3 2 ... 4 3 2 M 50 3 3 ... 3 ... and so on. Now I can read it by: F = read.table(file, header=T) but now I want to seperate the mothers (M) and daugthers (D) of the family with all the data in all other fields. How can I do that? The 'Code' Tells me which mother belongs to which dougther. I want to make a matrix where I have the mothers on one and the daugthers on the other axis and compair the distance of every question (F1...F17) and the distance of the sum of this questions. The questions are semantic differencials, 5 values. F4, and F7 must have reverse polarity in this case. Hm. How do I have to do now? Thanks, Martin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Bert Gunter Non-Clinical Biostatistics Genentech MS: 240B Phone: 650-467-7374 The business of the statistician is to catalyze the scientific learning process. -- George E.P. Box __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R CMD check, latex
Hello, I'm trying to build a package and the R CMD build works fine. The R CMD check produces an error, because no latex is found. But I have MikTeX installed and it works fine (only?) in combination with WinEdt. After reinstallation of MikTeX (no errors) I have the same problem. I´m not sure if this is a problem of my latex or a problem of the communication from R to my latex. (I´m running R 1.9.0 on Windows XP) I´m really happy if anybody can help me again. Thanks, Matthias __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sorting Data?
Am 27.05.2004 22:17:04 schrieb(en) Patrick Burns: First comment: F is a bad name to use for an object as it masks the commonly used meaning of FALSE. Oh, thanks, I just took F because 'Fragebogen' is such a long variable. But you are right, I will change that. You'll probably get some better answers, but you can ensure a standard order with: Fsort - Fdf[order(Fdf[, 'Code'], Fdf[, 'Family']), ] And then perhaps use reshape. I will look at this closer. Im now reshaping arround and don't know how I can then create a intercorrelation matrix or a (euklidic) distance matrix. But thanks, Martin Patrick Burns Burns Statistics [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Martin Klaffenboeck wrote: Hello, Im reading through some manuals, but I cannot find my answer. I have a file containing many data: VpnCodeFamilyAgeF1F2...F17 11M4612...1 21D1832...4 32M5033...3 ... and so on. Now I can read it by: F = read.table(file, header=T) but now I want to seperate the mothers (M) and daugthers (D) of the family with all the data in all other fields. How can I do that? The 'Code' Tells me which mother belongs to which dougther. I want to make a matrix where I have the mothers on one and the daugthers on the other axis and compair the distance of every question (F1... F17) and the distance of the sum of this questions. The questions are semantic differencials, 5 values. F4, and F7 must have reverse polarity in this case. Hm. How do I have to do now? Thanks, Martin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R CMD check, latex
It was an (for me not understandable) problem on miktex I´m solving my problem, by copying ..\texmf\miktex\bin\etex.exe to latex.exe I´m wondering that now R CMD check works now. Sorry, for my question to R help. Matthias -Ursprüngliche Nachricht- Von: TEMPL Matthias Gesendet: Freitag, 28. Mai 2004 10:34 An: [EMAIL PROTECTED] Betreff: [R] R CMD check, latex Hello, I'm trying to build a package and the R CMD build works fine. The R CMD check produces an error, because no latex is found. But I have MikTeX installed and it works fine (only?) in combination with WinEdt. After reinstallation of MikTeX (no errors) I have the same problem. I´m not sure if this is a problem of my latex or a problem of the communication from R to my latex. (I´m running R 1.9.0 on Windows XP) I´m really happy if anybody can help me again. Thanks, Matthias __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Pr(|z|) in lme4
Dear List, I am struggling understanding S4 classes. For example, when GLMM summary(glmmML( whatever)) outputs the following line: Estimate Std. Error DF z value Pr(|z|) (Intercept)0.856 0.319 452.68 0.0073 How do I access the Pr column? Dieter __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Statistics Avec R (Vincente Zoonekynd): portuguese translation
On Fri, 2004-05-28 at 00:36, José Cláudio Faria wrote: Dears friends, I have been translating and extended, with educational porposes only, the available material in the www (http://zoonek2.free.fr/UNIX/48_R/all.html) Statistcs avec R for the Portuguese of Brazil. I consider the material very good and would like to share this work with anothers users R. Already I translated and I extended two chapters: Introduction to the R and analysis of variance. I request to the author (Vincente Zoonekynd) an explicit authorization, a time that it authorizes it for the English, but still I did not receive answers. I can disponibilizar the material in HTML for the interested parties. What do you think about it? Best regards, José Cláudio Faria UESC/DCET Brasil 73-634.2779 [EMAIL PROTECTED] [EMAIL PROTECTED] Olá, Under what license is this book ? You have to check if the book is licensed and act in agreement with the license rules. You may not need his authorization. Best regards and hope you finish you're translation. I'll be glad to read it. EJ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
[EMAIL PROTECTED] wrote: n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Yes but how can we choose the distance to calculate centers? Ah, you are going to use different distance measure (e.g. euclidean, manhattan, ...) as in other cluster methods? Well, that's not possible with the kmeans() implementation. See ?kmeans which tells you: The data given by x is clustered by the k-means algorithm. When this terminates, all cluster centres are at the mean of their Voronoi sets (the set of data points which are nearest to the cluster centre). The algorithm of Hartigan and Wong (1979) is used. Of course, you can do some projection based on the calculation of distances, but I don't think there are functions available to do that completely automatical - and interpretation of results won't be that easy ... Uwe Ligges Thanks in advance, Nicolas BOUGET As the name says, kmeans() calculates *means* (centres) of clusters. It does not any make sense to do that on distances ... Uwe Ligges Accdez au courrier lectronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tl : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat. math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Accdez au courrier lectronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tl : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Pr(|z|) in lme4
Dieter == Dieter Menne [EMAIL PROTECTED] on Fri, 28 May 2004 11:04:13 +0200 writes: Dieter Dear List, I am struggling understanding S4 Dieter classes. For example, when GLMM Dieter summary(glmmML( whatever)) Dieter outputs the following line: Dieter Estimate Std. Error DF z value Pr(|z|) Dieter (Intercept) 0.856 0.319 45 2.68 0.0073 Dieter How do I access the Pr column? Did you try s - summary(glmmML( whatever)) s ## to give the above str(s) ## to show the internal structure If 's' itself is an object with a formal class (aka S4 class), str() will give sub-optimal (but still helpful) output in the current version of R [exposing the current implementation of S4 slots, which you should never make use of]. Rather in R Version 2.0.0 Under development (unstable) aka 'R-devel', it gives much nicer output Martin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Pr(|z|) in lme4
Martin Maechler wrote: Dieter == Dieter Menne [EMAIL PROTECTED] on Fri, 28 May 2004 11:04:13 +0200 writes: Dieter Dear List, I am struggling understanding S4 Dieter classes. For example, when GLMM Dieter summary(glmmML( whatever)) Dieter outputs the following line: Dieter Estimate Std. Error DF z value Pr(|z|) Dieter (Intercept) 0.856 0.319 45 2.68 0.0073 Dieter How do I access the Pr column? Did you try s - summary(glmmML( whatever)) s ## to give the above str(s) ## to show the internal structure If 's' itself is an object with a formal class (aka S4 class), str() will give sub-optimal (but still helpful) output in the current version of R [exposing the current implementation of S4 slots, which you should never make use of]. Rather in R Version 2.0.0 Under development (unstable) aka 'R-devel', it gives much nicer output Martin Well, I wonder what Dieter Menne is looking for. GLMM() is in lme4 and uses S4 classes. glmmML() is in glmmML and uses S3 classes. In the latter case, the p-values are calculated within print.glmmML() and the corresponding code is: 1 - pchisq((coef(x)/x$sd)^2, 1) where x is the glmmML object. Uwe Ligges __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Pr(|z|) in lme4
Martin, s - summary(glmmML( whatever)) s ## to give the above str(s) ## to show the internal structure str() is my favorite, it's essentially how I learned R. It was no problem to find my way in nlme, but still lost in lme4. Uwe Liggges wrote: Well, I wonder what Dieter Menne is looking for. GLMM() is in lme4 and uses S4 classes. glmmML() is in glmmML and uses S3 classes. You have reasons to wonder. I meant s - summary(GLMM( whatever)) but had also used Goran's glmmML,which did not handle na.omit as nicely as GLMM does. Dieter __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
n\ == n\ bouget n on Fri, 28 May 2004 09:37:35 +0200 writes: n\ Hi, I want to know which distance is using in the n\ function kmeans and if we can change this distance. n\ Indeed, in the function pam, we can put a distance n\ matrix in parameter (by the line n\ pam-pam(dist(matrixdata),k=7) ) but we can't do it in n\ the function kmeans, we have to put the matrix of data n\ directly ... Thanks in advance, Nicolas BOUGET It might be interesting to look at this from the pam() perspective: What exactly is pam() lacking that kmeans() does for you? Christian, are you suggesting that pam() could do the job if 1) there was a dist(., method=a la kmeans) 2) pam() allowed to be started by a user-specified set of medoids instead of the Kaufman-Rousseeuw-optimal ones ? Regards, Martin Maechler __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
On Fri, 28 May 2004, Martin Maechler wrote:
n\ == n\ bouget n
on Fri, 28 May 2004 09:37:35 +0200 writes:
n\ Hi, I want to know which distance is using in the
n\ function kmeans and if we can change this distance.
n\ Indeed, in the function pam, we can put a distance
n\ matrix in parameter (by the line
n\ pam-pam(dist(matrixdata),k=7) ) but we can't do it in
n\ the function kmeans, we have to put the matrix of data
n\ directly ... Thanks in advance, Nicolas BOUGET
It might be interesting to look at this from the pam()
perspective:
What exactly is pam() lacking that kmeans() does for you?
Christian, are you suggesting that pam() could do the job if
1) there was a dist(., method=a la kmeans)
2) pam() allowed to be started by a user-specified set of
medoids instead of the Kaufman-Rousseeuw-optimal ones
?
The k-means criterion is equivalent to:
Find a partition C=C_1 \cup...\cup C_k such that
\sum_{i=1}^k \sum_{x_j,x_l\in C_i} d(x_j,x_l)/|C_i|=min!
d is squared Euklidean distance (see the Bock book). You may wonder to
what clustering this would lead with another distance.
The difference to pam is that pam minimizes sums of distances to centroid
objects, which have to be part of the dataset. k-means does not need
centroid objects, no mean objects are needed. Thus, pam with squared
Euklidean distances is a kind of approximation to k-means. (In practice,
both are approximations to a global optimum.)
There would also be a further version if other distances would be allowed,
the pam criterion would be optimized, but the cluster centers would be
allowed to lie elsewhere than on an object of the sample.
Of course, pam and the original k-means are more or less easy to compute,
while the suggested alternatives may be computationally complex.
Best,
Christian
Regards,
Martin Maechler
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***
Christian Hennig
Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg
[EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/
###
ich empfehle www.boag-online.de
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Re: [R] Sorting Data?
Am 27.05.2004 22:43:02 schrieb(en) Jonathan Baron: On 05/27/04 21:58, Martin Klaffenboeck wrote: Hello, Im reading through some manuals, but I cannot find my answer. I have a file containing many data: Vpn CodeFamily Age F1 F2 ... F17 1 1 M 46 1 2 ... 1 2 1 D 18 3 2 ... 4 3 2 M 50 3 3 ... 3 ... and so on. Now I can read it by: F = read.table(file, header=T) but now I want to seperate the mothers (M) and daugthers (D) of the family with all the data in all other fields. How can I do that? The 'Code' Tells me which mother belongs to which dougther. I want to make a matrix where I have the mothers on one and the daugthers on the other axis and compair the distance of every question (F1...F17) and the distance of the sum of this questions. The questions are semantic differencials, 5 values. F4, and F7 must have reverse polarity in this case. The following is not tested and probably contains at least one error. Thanks, that helps me much as I am a R newbie. Lets assume that there is one mother per daughter and one daughter per mother, and your file is Myfile, and the Codes are in order. One way is this: Ok, we really have only one daughter per mother in our sample. Im sorting by: Myfile - read.table(Fragebogen.data, header=TRUE) Myfile - Myfile[order(e[, 'Code'], Myfile[, 'Family']), ] Code has one equal code for mother and daugther the same - so I know which mother has which daughter, Family tells me if the person it she mother or the daugther. Myfile$F4 - -Myfile$F4 # reverse polarity Myfile$F7 - -Myfile$F7 Is this also true, if we have a semantic differential with 5 steps? (from 1 to five. I have one missing value (NA), should I set it to 0?) (please tell me also if I use incorrect words). You didn't know that I assume. So now I'm doing: Myfile$F3 - 5-Myfile$F3 that seems to be good for me, please tell me what you think. Mothers - Myfile[Family=M,] Daughters - Myfile[Family=D,] Hm. This seems not to work for me i was testing arround, for me seems to work: Mothers - Myfile[Myfile[[Family]]==M,] Daugthers - ... I hope we have the same results now. ;-) Im really a newbie in R. Itemdiffs - Mothers[,-(1:4)]-Daughters[,-(1:4)] # the -(1:4) # removes cols 1:4 Ok, this seems to work, also but I don't really know what I am doing with it. Also the other things. I have to test the hypothesis: Does a daugther answer the questions (semantic differential) more equal the own mother and more different to the mothers of the other daugthers. I hope you get that in english. ;-) Thanks, Martin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET One solution is to transform the data in a way, that the euclidean distance of the transformed values represents some other distance of the original values. This works at least for the Mahalanobis-Distance, when one applies a multivariate technique to a PCA transformed and re-scaled matrix, but I don't know if there are transformations for some other distance measures. Thomas P. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
I don't exactly understand what you do, could you show me the program that you execute to do that? n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET One solution is to transform the data in a way, that the euclidean distance of the transformed values represents some other distance of the original values. This works at least for the Mahalanobis-Distance, when one applies a multivariate technique to a PCA transformed and re-scaled matrix, but I don't know if there are transformations for some other distance measures. Thomas P. Accédez au courrier électronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tél : 08 92 68 13 50 (0,34/mn) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] useR! 2004 keynote lecture slides
Dear useRs, there has been some interest on this list into material about the presentations at useR! 2004. The slides from the keynote lectures are now available from the conference web page at http://www.ci.tuwien.ac.at/Conferences/useR-2004/ thanks to the R-core team members who were willing to give the talks and provide their pdf-slides. For the user-contributed presentations, there are (mostly) only abstracts available on the conference web page - for further information you could look at the web pages of the presenters which are in many cases linked from the participants page. For the useR! organization team, Achim __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
Thomas Petzoldt wrote: n.bouget wrote: Hi, I want to know which distance is using in the function kmeans and if we can change this distance. Indeed, in the function pam, we can put a distance matrix in parameter (by the line pam-pam(dist(matrixdata),k=7) ) but we can't do it in the function kmeans, we have to put the matrix of data directly ... Thanks in advance, Nicolas BOUGET One solution is to transform the data in a way, that the euclidean distance of the transformed values represents some other distance of the original values. This works at least for the Mahalanobis-Distance, when one applies a multivariate technique to a PCA transformed and re-scaled matrix, but I don't know if there are transformations for some other distance measures. Thomas P. Other solutions from an ecological paper are: Chord distance Chi square metric Chi square distance Hellinger Distance Distance between species profiles All these can be seen as Euclidean distances of some transformation of the data. The paper Ecologically meaningful transformations for ordination of species data Pierre Legendre, and Eugene D. Gallagher (2001) Oecologia Vol. 129, Issue 2, 271-280, explains the concept and how to do the transformations. An R example is given in the help file of decostand() in Jari Oksanen's vegan library for two of the transformations mentioned above. Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
Gavin Simpson wrote: ... An R example is given in the help file of decostand() in Jari Oksanen's vegan library for two of the transformations mentioned above. ^^^ Pre-empting the usual response about proper terminology, I of course meant package not library. Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] - making a Windows library from Unix source code
Hi! Normally you are building R packages using cd c:\Program Files\R\rw1081\src R CMD build fatigue Sincerely. *** REPLY SEPARATOR *** On 5/11/2004 at 6:32 PM Livingstone, Paul wrote: Hi All, I'm using R1.8.1 on Windows XP. I'm having trouble producing an R library from source code. A colleague has written the source code, in Unix. I've copied the source code across to Windows (with the help files, data files, description and index) and am trying to compile it into a library. I've sourced each of the *.r files and they appear to work. I've very carefully followed the instructions in the R for Windows FAQ and readme.packages. I've downloaded and installed Perl, R tools, copied across the text to C:\Program Files\R\rw1081\src\library\fatigue (note: the package is called fatigue) then I type at the DOS prompt cd c:\Program Files\R\rw1081\src\gnuwin32 make pkg-fatigue and get the error message(s) make[1]: *** [zzzfirst] Error 255 make: *** [pkg-fatigue] Error 2 How do I look up what Error 255 means? Or can you tell me what Error 255 means and how I might fix it? Any other hints or ideas on how to use make or compile code that appears to work? thanks, Paul. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] privileged slots,
On Thu, 27 May 2004 22:55:20 +0200, Torsten Steuernagel
[EMAIL PROTECTED] wrote :
2. Is it true
that one can gain execution speed by accessing slots using the
function slots(object,name,check=FALSE)-value would speed up
execution?
Try this:
get(@-)
function (object, name, value)
{
arg - substitute(name)
if (is.name(arg))
name - as.character(arg)
slot-(object, name, TRUE, value)
}
So @- actually calls slot-. Using slot- instead, you save the
additional overhead the call to @- introduces. If there will be a real
performance gain in replacing @- certainly depends on what you're
doing.
I'd advise against doing this kind of optimization. It will make your
code harder to maintain, and while it might be faster today, if @-
is really a major time sink, it's an obvious candidate for
optimization in R, e.g. by making it .Internal or .Primitive. When
that happens, your optimized code will likely be slower (if it even
works at all).
Duncan Murdoch
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[R] Adding key to simple plot() function
I am generating a simple x,y plot to show geographical positions where point data has been taken. Rather than plot a graph and lay points on top I've opted to generate the map from the point data, ie plot(-x,-y). This works fine, though I am wanting to label each point 1:20 and have a key alongside - is this possible without getting into trellis plots? I have very limited time available so don't want to embark on trellis functions which I've never used before.. Also, my x,y labels currently have a negative sign in front of them which I'd like to remove, but if I negate the labels they no longer fit on the graph as my data points are -x and -y... Any suggestions? Thanks, Laura __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Regression model type II
I am trying to fit regression models type II with R, but it seems to me that most (all) of the linear model functions are for type I regressions. Does anyone knows whether type II regressions functions exist in R. Benjamin -- Benjamin Planque IFREMER Laboratoire d'Ecologie Halieutique BP 21105 44311 Nantes Cedex 03 France Tel: +33 (0)2 40 37 41 17 Fax: +33 (0)2 40 37 40 75 e-mail: [EMAIL PROTECTED] http://www.ifremer.fr/drvecohal/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Adding key to simple plot() function
Laura, For your axis issues, look at plotting without axes [plot(,axes=F) and then see ?axis for making them on your own. As for labeling your data, look at ?points and ?text. Sean On 5/28/04 8:27 AM, Laura Quinn [EMAIL PROTECTED] wrote: I am generating a simple x,y plot to show geographical positions where point data has been taken. Rather than plot a graph and lay points on top I've opted to generate the map from the point data, ie plot(-x,-y). This works fine, though I am wanting to label each point 1:20 and have a key alongside - is this possible without getting into trellis plots? I have very limited time available so don't want to embark on trellis functions which I've never used before.. Also, my x,y labels currently have a negative sign in front of them which I'd like to remove, but if I negate the labels they no longer fit on the graph as my data points are -x and -y... Any suggestions? Thanks, Laura __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] optim(method=SANN)
Hello List I'm working on a combinatoric problem in which the object is to minimize the badness() of a vector. I think this class of problem is only soluble by optim() using method=SANN. The badness() of anything is = 0, and when I've found a solution with zero badness, I want optim() to stop (carrying on beyond zero badness cannot improve the solution). Efficiency is crucial here. The ?optim manpage states For 'SANN' 'maxit' gives the total number of function evaluations. There is no other stopping criterion. How best to make optim() stop as soon as it finds a zero badness solution? -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre SO14 3ZH tel +44(0)23-8059-7743 [EMAIL PROTECTED] (edit in obvious way; spam precaution) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] distance in the function kmeans
[EMAIL PROTECTED] wrote: I don't exactly understand what you do, could you show me the program that you execute to do that? I did such things sometimes ago, so the following is (as usual) without warranty. There are several methods, e.g. using Choleski factorization, singular value decomposition or principal components. Given mdata as original data matrix it works with hclust and should be applicable to kmeans too: # with svd z - svd(scale(mdata, scale=F))$u cl - hclust(dist(z), method=ward) # with princomp (rescaled) pc - princomp(mdata, cor=FALSE) pcdata - as.data.frame(scale(pc$scores)) cl - hclust(dist(pcdata), method=ward) ... but as I mentioned, this is only an example, that methods working with the Euclidean distance can be applied to other distance measures, when an appropriate transformation of the data exist and, according to Gavin, there are indeed some other possibilities. Thomas P. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Simple list manipulation question
I have a list of vectors $A AB BC CD $B GF HG FH FJ and I want to convert it into a dataframe of form A AB A BC A CD B GF B HG B FH B FJ Just can't quite come up with a nice R solution for it. Thanks, Sean __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Simple list manipulation question
Hallo! x-unlist(yourlist) names(x) # maybee you have to postprocess the names a little dataframe(names(x),x) Sincerely Eryk *** REPLY SEPARATOR *** On 5/28/2004 at 8:49 AM Sean Davis wrote: I have a list of vectors $A AB BC CD $B GF HG FH FJ and I want to convert it into a dataframe of form A AB A BC A CD B GF B HG B FH B FJ Just can't quite come up with a nice R solution for it. Thanks, Sean __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Simple list manipulation question
R L - list(A=c(AB,BC,CD),B=c(GF,HG,FH,FJ)) R stack(L) values ind 1 AB A 2 BC A 3 CD A 4 GF B 5 HG B 6 FH B 7 FJ B Sean Davis sdavis2 at mail.nih.gov writes: : : I have a list of vectors : : $A : AB BC CD : : $B : GF HG FH FJ : : and I want to convert it into a dataframe of form : : A AB : A BC : A CD : B GF : B HG : B FH : B FJ : : Just can't quite come up with a nice R solution for it. : : Thanks, : Sean : __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] any simple examples for SJAVA please
Hi! Are there any simple examples for SJAVA please? Thanks, Laura R Version 1.9.0 Windows _ Is your PC infected? Get a FREE online computer virus scan from McAfee® Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any simple examples for SJAVA please
Hallo Laura! What I have heard at UseR there are no stable running SJava at the Windows platform. ( I wish that I am wrong!) I knew that Simon Urbanek is using and developing a java interface to R. google: simon urbanek Sincerely Eryk *** REPLY SEPARATOR *** On 5/28/2004 at 7:58 AM Laura Holt wrote: Hi! Are there any simple examples for SJAVA please? Thanks, Laura R Version 1.9.0 Windows _ Is your PC infected? Get a FREE online computer virus scan from McAfee® Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] privileged slots
Hi!
The simplest way to find the document is
?checkSlotAssignmen
A function which is described there and which Matthias Kohl mentioned in his e-mail
You will find it also using the html search form of the html documentation searching
for RClassUtils.
Its true that the document is a little hidden what I havent noticed (Sorry Martin).
The functions described in it are not listed in the 00index.html file of the methods
package. (Why!?) I found the document by the first trial by typing
?checkSlotAssignment.
There was a lot of discussion going on at about S4 at the useR confernce. Much more
than at this list. Maybee because the only understandable text about S4 about wich i
knew is Programming with Data J. Chambers. (The descriptions to the method package
is for me quite hard to read.)
Maybee also because no one knews how big exactly is the performance sacrifice caused
by the additional features. Therefore, this less official document is of some value
because it allows to make some benchmarks.
I was running some test cases to figure out how many(much?) time one can gain by
setting check=FALSE check=TRUE. And how using slot instead of @ infuences the
execution speed.
I run a for loop with x in 1:1 with the following assignments in the loop:
[s]
[EMAIL PROTECTED] - paste(test,x,sep=) 2.550
2.71 NA NA
slot(tmp,info,check=T) - paste(test,x,sep=) 2.360 2.50 NA NA
slot(tmp,info,check=F) - paste(test,x,sep=) 0.670 0.80 NA NA
paste(test,x,sep=) 0.500
0.63 NA NA
object.size(tmp)
[1] 1208
It means that a type check takes about 0.0002 seconds on a P4 3000 Windows XP with
hyperthreding. Its not much.
It means thats no reason to be scared of S4 because of performance. The overhad is
even less 0.2
Last but not least: There where also some discussions about having the OPTION to pass
arguments to function by reference.
Sincerely
Eryk
Ps.:
The UseR conference was great!
Thanks to the organizers from me too.
*** REPLY SEPARATOR ***
On 5/27/2004 at 10:55 PM Torsten Steuernagel wrote:
On 27 May 2004 at 19:12, Wolski wrote:
But this document is quite intersting.
Which document are you refering to ?
I have just two R questions which arised reading the document which a
core members of the R-project cant find.
I can't find it either.
1. Is it intended to introduce privileged slots in the future version of
R?
You are talking about access control like C++ (private, protected,
public) has, aren't you ? I can't answer for the R Core Team but I'm
also interested in a similar functionality. Please check the setClass()
docs for the access argument. I suppose this is intended to provide
such functionality in the future.
2. Is it true
that one can gain execution speed by accessing slots using the
function slots(object,name,check=FALSE)-value would speed up
execution?
Try this:
get(@-)
function (object, name, value)
{
arg - substitute(name)
if (is.name(arg))
name - as.character(arg)
slot-(object, name, TRUE, value)
}
So @- actually calls slot-. Using slot- instead, you save the
additional overhead the call to @- introduces. If there will be a real
performance gain in replacing @- certainly depends on what you're
doing.
- Torsten
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Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin 'v'
tel: 0049-30-83875219 / \
mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski
[[alternative HTML version deleted]]
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Re: [R] any simple examples for SJAVA please
Hi, like you I'm trying to use SJava and I meet with many difficulties. I try to run examples from Calling R from Java written by Duncan Temple Lang available from http://www.omegahat.org/SJava (there are many examples on this web site). Now I have an error that my R version is R 1.6.1 while I have version 1.9.0 on windows NT. This causes a crash when I run my Java code: fatal error: enable to open the base package I still waiting for a solution Best A 07:58 28/05/2004 -0500, Laura Holt a écrit : Hi! Are there any simple examples for SJAVA please? Thanks, Laura R Version 1.9.0 Windows _ Is your PC infected? Get a FREE online computer virus scan from McAfee® Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sorting Data?
On 05/28/04 12:21, Martin Klaffenboeck wrote:
Am 27.05.2004 22:43:02 schrieb(en) Jonathan Baron:
On 05/27/04 21:58, Martin Klaffenboeck wrote:
Hello,
Im reading through some manuals, but I cannot find my answer.
I have a file containing many data:
Vpn CodeFamily Age F1 F2 ... F17
1 1 M 46 1 2 ... 1
2 1 D 18 3 2 ... 4
3 2 M 50 3 3 ... 3
...
and so on.
Now I can read it by:
F = read.table(file, header=T)
but now I want to seperate the mothers (M) and daugthers (D) of the
family with all the data in all other fields. How can I do that?
The 'Code' Tells me which mother belongs to which dougther. I want
to
make a matrix where I have the mothers on one and the daugthers on
the
other axis and compair the distance of every question (F1...F17) and
the distance of the sum of this questions. The questions are
semantic
differencials, 5 values. F4, and F7 must have reverse polarity in
this
case.
The following is not tested and probably contains at least one error.
Thanks, that helps me much as I am a R newbie.
Lets assume that there is one mother per daughter and one
daughter per mother, and your file is Myfile, and the Codes are
in order. One way is this:
Ok, we really have only one daughter per mother in our sample.
Im sorting by:
Myfile - read.table(Fragebogen.data, header=TRUE)
Myfile - Myfile[order(e[, 'Code'], Myfile[, 'Family']), ]
Code has one equal code for mother and daugther the same - so I know
which mother has which daughter, Family tells me if the person it she
mother or the daugther.
Myfile$F4 - -Myfile$F4 # reverse polarity
Myfile$F7 - -Myfile$F7
Is this also true, if we have a semantic differential with 5 steps?
(from 1 to five. I have one missing value (NA), should I set it to 0?)
(please tell me also if I use incorrect words).
You didn't know that I assume. So now I'm doing:
Myfile$F3 - 5-Myfile$F3
that seems to be good for me, please tell me what you think.
Mothers - Myfile[Family=M,]
Daughters - Myfile[Family=D,]
Hm. This seems not to work for me i was testing arround, for me seems
to work:
Mothers - Myfile[Myfile[[Family]]==M,]
Daugthers - ...
My mistake here was to use = instead of ==. If you use my method
with ==, it might work too.
I hope we have the same results now. ;-) Im really a newbie in R.
Itemdiffs - Mothers[,-(1:4)]-Daughters[,-(1:4)] # the -(1:4)
# removes cols 1:4
Ok, this seems to work, also but I don't really know what I am doing
with it.
Type the names of the variables to find out what you are doing.
If they are too big, then subset them, for example,
Mothers[1:5,]
Daughters[1:5,]
Itemdiffs[1:5,]
Also the other things.
I have to test the hypothesis: Does a daugther answer the questions
(semantic differential) more equal the own mother and more different to
the mothers of the other daugthers.
I don't think this is a trivial problem at all, so I am hesitant
to offer advice. I see now that you reall do want a matrix,
where you have mothers in the columns and daughters in the rows,
and distance (difference, similarity) measures in the cells.
Perhaps you have several such measures, so you want a
three-dimensional array.
You might do something like this. First define a function to
measure your distance, like
Itemdist - function(x,y) {sum(abs(x[-(1:4)]-y[-(1:4)]))}
Dists - matrix(NA,nrow(Daughters),nrow(Mothers))
for (i in 1:nrow(Daughters)
{for (j in 1:nrow(Mothers))
{Dists[i,j] - Itemdist(Daughters[i,],Mothers[j,])}}
Then you would want to show that the diagonal of the resulting
matrix is higher (or lower) than the other cells. Here is where
I yield to experts. If I were doing it, I might consider
comparing these cells to some measure of the expectation of what
they ought to be, but I would not just do a t test comparing them
to all the other cells because the other cells are not
independent of each other. (One daughter might by odd and be
dissimilar from everyone, and this would show up in an entire
row.) I'm sure there is some simple idea that I'm missing here.
I hope you get that in
english. ;-)
It seems that many people on the list read German (including me,
but I'm scared to write it), but the official language is
English.
Thanks,
Martin
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[R] Merging nlme output
Dear list: I am trying to merge two files together from output I get based on the coef() command. Here is what I am running into. I have two simple linear mixed models mod1.lme-lme(math~year, data=sample, random=~year|childid/schoolid) mod2.lme-lme(math~year, data=sample, random=~year|childid) I then call the coefficients and store them in the following objects using mod1.coef-coef(mod1.lme, level=2) mod2.coef-coef(mod2.lme) The problem is that the IDs are different for the two dataframes and I cannot seem to figure out how to make the merge happen nicely. For example, this is output from mod1.lme for the first 5 students mod1.coef[1:5,] (Intercept) year 2020/273026452 0.03923346 0.9575926 2020/273030991 0.91772318 1.0773731 2020/273059461 0.43865139 1.0111789 2020/278058841 1.11292376 1.0526057 2020/292017571 1.09661340 1.0774692 As opposed to out for the first 5 cases in mod2.coef mod2.coef (Intercept) year 101480302-1.13483082 0.7023644 173559292 0.52818576 0.8639216 174743401-1.18038537 0.6824612 174755092 0.04760782 0.7402835 179986251-2.42848405 0.5677182 You can see that the ID variable for the first output includes the grouping variable schoolid followed by a / and then the childid. I am interested in exploring the differences in the growth trajectories between the two models and would like to merge the two datasets to be able to do so. What do I need to do to somehow eliminate the schoolid and / from mod1.lme so that I can use the merge() command? Thanks, Harold C. Doran Director of Assessment One Massachusetts Avenue, NW · Suite 700 Washington, DC 20001-1431 202.336.7075 [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Crossed random effects in lme
Søren Højsgaard [EMAIL PROTECTED] writes: Dear all, In the SASmixed package there is an example of an analysis of a split-plot experiment. The model is fm1Semi - lme( resistance ~ ET * position, data = Semiconductor, random = ~ 1 | Grp) where Grp in the Semiconductor dataset is defined as ET*Wafer. Is it possible to specify the grouping directly some way, e.g. like fm1Semi - lme( resistance ~ ET * position, data = Semiconductor, random = ~ 1 | ET*Wafer) Actually that does work with lme from the as-yet-unreleased version 0.6-1 of the lme4 package. See the slides from my presentation at useR!2004 http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Bates.pdf I'm back at my home now and will endeavor to get lme4_0.6-1 released as soon as possible. -- Douglas Bates[EMAIL PROTECTED] Statistics Department608/262-2598 University of Wisconsin - Madisonhttp://www.stat.wisc.edu/~bates/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] orca binary?
Uwe Ligges [EMAIL PROTECTED] writes:
Laura Holt wrote:
Dear R People:
Is there a binary version for rorca, please?
Given I recall correctly, I tried to build rorca for Windows one or
two years ago without success. But maybe Tony (In this context I
recall that I'm still owing him a pizza) knows of a binary?
Hah. I should swing by and collect next week.
Seriously, you should be able to do a source install or a quick build
(I probably could do one later today using the Linux cross-compiler),
since it's just raw R code.
If someone does it before I do, let me know.
best,
-tony
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RE: RE: [R] ANOVA and contrasts
Dear FZ In one way I have not problem... The problem arise to establish the contrasts for 2 way with interactions and I desire the SS of each one of the contrasts. Thanks, Jos Cludio Faria UESC/DCET Brasil 73-634.2779 [EMAIL PROTECTED] [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] axis.POSIXct: Datetime data and plotting
At 2:10 PM -0400 5/27/04, Barrowman, Nick wrote: But is there any easy way to avoid this problem? It is confusing and inconvenient that axis.POSIXct(1,d,format=f) and axis.POSIXct(3,at=d,format=f) give seemingly contradictory scales. In one case you provide the locations of the tick marks, in the other case you let the function decide the locations. Why, in general, would anyone expect the two to be the same? (And that applies regardless of whether we're dealing with datetime values; the regular axis() function doesn't always give me tick marks at locations that I prefer.) Gabor Grothendieck's suggestion to use the Date class instead of POSIXt is a good one. -Don At 2:10 PM -0400 5/27/04, Barrowman, Nick wrote: I've run into a problem with the datetime axis generated by axis.POSIXct. It appears a similar issue was discussed in October 2003 under the subject line datetime data and plotting (see https://stat.ethz.ch/pipermail/r-help/2003-October/039071.html), but I wasn't able to determine whether there is a straightforward solution. The code below produces a graph with apparently contradictory date labels on the top and bottom axes: f - %Y/%m/%d d - as.POSIXct(strptime(c(2003/1/15,2003/1/16, 2003/1/17,2003/1/18,2003/1/19),format=f)) plot(d,1:length(d),axes=F);box() axis(2) abline(v=d[3]) axis.POSIXct(1,d,format=f) axis.POSIXct(3,at=d,format=f) On my copy of R (I have appended the version information below my signature), this produces a graph with a vertical line that lines up with 2003/01/17 on the top axis, but not on the bottom axis. The issue seems to relate to time zones: here's what d looks like on my computer: d [1] 2003-01-15 Eastern Standard Time [2] 2003-01-16 Eastern Standard Time [3] 2003-01-17 Eastern Standard Time [4] 2003-01-18 Eastern Standard Time [5] 2003-01-19 Eastern Standard Time (Actually I'm on Eastern Daylight Time, but let's ignore that for now.) Changing the axes to display not only the date but also the time shows what's going on: f - %Y/%m/%d f2 - %Y-%m-%d %H:%M d - as.POSIXct(strptime(c(2003/1/15,2003/1/16, 2003/1/17,2003/1/18,2003/1/19),format=f)) plot(d,1:length(d),axes=F);box() axis(2) abline(v=d[3]) axis.POSIXct(1,d,format=f2) axis.POSIXct(3,at=d,format=f2) The bottom axis put the ticks at 19:00 on each date. This seems an odd time until you note that Eastern Standard Time is 5 hours behind UTC, so 19:00 EST is 00:00 UTC. But is there any easy way to avoid this problem? It is confusing and inconvenient that axis.POSIXct(1,d,format=f) and axis.POSIXct(3,at=d,format=f) give seemingly contradictory scales. Many thanks for any help! Nick Barrowman, Ph.D. Chief Biostatistician, Chalmers Research Group Children's Hospital of Eastern Ontario Research Institute 401 Smyth Road, Ottawa, Ontario, K1H 8L1, Canada Tel (613) 737-7600 ext. 3971 Fax (613) 738-4800 Email [EMAIL PROTECTED] URL www.chalmersresearch.com version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.0 year 2004 month04 day 12 language R __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] simulate dependent probabilities
I need to simulate from a random process and am not sure how to go about it. The process is the probability of an event occuring between a pair of points on a line. (This probability is between 0 and 0.5). I have estimates of these probabilities for a series of points, their standard errors and the correlation matrix (which is AR(1)). Eg (for 4 points) estimated prob (q): 0.1163 0.1280 0.0698 standard error: 0.0320 0.0288 0.0259 asymptotic correlation matrix: 1. -0.0880 1. 0. -0.0739 1. The vector q is used in a further analysis, treated as known. I would like to simulate alternative vectors q, which could be used in the further analysis in order to generate some empirical confidence interval. But I don't know where to start with such simulation. (In practice, q has about 50 elements). Although I know how to use cholesky decomposition to simulate dependent variables from a MVN distribution, I am stuck on two counts here: - the distribution for q - how to incorporate the dependence into the simulation. I would appreciate any suggestions. Chris. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RE: SCO R
SCO is grasping for straws. and is now gasping. vexatious lawsuits will only drive so far before puttering out. eventually the curtain gets pulled back on glorified attempts at racketeering. cheers. Message: 76 Date: Thu, 27 May 2004 21:08:12 -0500 From: Deepayan Sarkar [EMAIL PROTECTED] Subject: Re: [R] SCO R To: [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 On Thursday 27 May 2004 20:18, Greg Tarpinian wrote: Actually, it was very recent. I pulled the electronic version of the article from the Forbes website: I would think twice before taking forbes articles too seriously. For instance, they seem to think that protecting intellectual property rights are all right when it's some big commercial company doing the protecting, but not when they are on the other side of the table. See this article from last year: http://www.forbes.com/2003/10/14/cz_dl_1014linksys.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Build R-1.9.0 with static libraries ?
I am still unable to build a binary for R (linux Red Hat 9 distribution) which would be self-consistent (without shared objects and use of dynamics librairies). I would be very grateful if someone could explain and/or help me... so please set MAIN_LD as it suggests (and that's why I quoted the whole thing for you to read!) OK, I've set MAIN_LD to 'gcc -Bstatic' but now 'make' fails for the following reason: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library $BuildDir/library/methods/libs/methods.so: $BuildDir/library/methods/libs/methods.so: undefined symbol: R_GlobalEnv Execution halted Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library $BuildDir/library/stats/libs/stats.so: $BuildDir/library/stats/libs/stats.so: undefined symbol: R_GlobalEnv Execution halted Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library $BuildDir/library/tools/libs/tools.so: $BuilDir/library/tools/libs/tools.so: undefined symbol: R_NaString Error: couldn't find function .installPackageNamespaceInfo In addition: Warning message: package tools in options(defaultPackages) was not found Execution halted So I'm afraid I'm still missing a flag somewhere... I'm sorry but I'm not used compiling such packages so I cannot figure out where I made a mistake. Thanks again for your patience :-( Melanie -- Me'lanie PELEGRINI-ISSAC tel : (33 0)1 53 82 84 20 Unite' 483 INSERM fax : (33 0)1 53 82 84 48 9, quai Saint-Bernard email :[EMAIL PROTECTED] Bat C 6e etage 75005 PARIS __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to insert a bitmap in a grph device
If I have a plot and I want to insert a bitmap in the same devicehow to do it? Thank you Luis Ridao Cruz Fiskirannsóknarstovan Nóatún 1 P.O. Box 3051 FR-110 Tórshavn Faroe Islands Phone: +298 353900 Phone(direct): +298 353912 Mobile: +298 580800 Fax: +298 353901 E-mail: [EMAIL PROTECTED] Web:www.frs.fo __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RE: SCO R
My $.02 (sorry, couldn't resist). This is but one skirmish in the whole vexatious battle on intellectual property rights, which extends from software to many other venues, one of the most interesting of which is patents on human genes. An example I heard on the radio this morning was eHarmony.com patenting their algorithm for matchmaking, which, the commentator said, is based on a 431 item questionnaire (yet another reason to celebrate my long marriage; 431 questions -- yikes!) ! Needless to say, the potential fodder for editorializing both for and against this intrusion of scientific method into romance seems limitless. Do you think support vector machines or neural nets lurk in the background of their algorithm? Anyway, the only predictions that I think it safe to make are: (1) We have only begun to fight -- and, yes, seeming samaritans (or is it samurai?) like R and GPL may yet have to engage; (2) advances in technology will only turn the heat up and pose yet more problems, as we move relentlessly from thingy inventions running our world to 'idea-y inventions running it. Matchmaking, anyone? (Thanks for your indulgence). Cheers, Bert Siddique, Amer wrote: SCO is grasping for straws. and is now gasping. vexatious lawsuits will only drive so far before puttering out. eventually the curtain gets pulled back on glorified attempts at racketeering. cheers. Message: 76 Date: Thu, 27 May 2004 21:08:12 -0500 From: Deepayan Sarkar [EMAIL PROTECTED] Subject: Re: [R] SCO R To: [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 On Thursday 27 May 2004 20:18, Greg Tarpinian wrote: Actually, it was very recent. I pulled the electronic version of the article from the Forbes website: I would think twice before taking forbes articles too seriously. For instance, they seem to think that protecting intellectual property rights are all right when it's some big commercial company doing the protecting, but not when they are on the other side of the table. See this article from last year: http://www.forbes.com/2003/10/14/cz_dl_1014linksys.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Bert Gunter Non-Clinical Biostatistics Genentech MS: 240B Phone: 650-467-7374 The business of the statistician is to catalyze the scientific learning process. -- George E.P. Box __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to pass defined function with more than one arguments to apply?
Dear all:
I meet a problem of apply function. I have a matrix called tb
tb
V1 V2 V3
1 0 3 1
2 1 4 0
3 0 3 0
4 0 4 0
5 0 3 1
6 1 4 1
7 1 1 0
8 1 3 0
9 0 1 1
10 0 3 1
I hope to get the number of row that match c(0,3,1)
I do this way:
length(apply(t(tb) = = c (0,3,1), 2, all))
I defined a funtion, compare-function(vector1, vector2){...}. For example,
compare(1:3, 1:3) will return TRUE. compare(1:3,2:4) return FALSE.
Then I hope to call apply(tb,1,compare). But this can not work, because
apply only pass one argument to compare function. Does anyone know how to
solve this problem?
Thanks so much.
Anoly
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Re: [R] how to pass defined function with more than one arguments to apply?
Hi!
?apply
...: optional arguments to 'FUN'.
you can pass more arguments to your function.
length(apply(tb,comare,c(0,3,1)))
Sincerely
Eryk.
*** REPLY SEPARATOR ***
On 5/28/2004 at 12:05 PM anoly wrote:
Dear all:
I meet a problem of apply function. I have a matrix called tb
tb
V1 V2 V3
1 0 3 1
2 1 4 0
3 0 3 0
4 0 4 0
5 0 3 1
6 1 4 1
7 1 1 0
8 1 3 0
9 0 1 1
10 0 3 1
I hope to get the number of row that match c(0,3,1)
I do this way:
length(apply(t(tb) = = c (0,3,1), 2, all))
I defined a funtion, compare-function(vector1, vector2){...}. For
example,
compare(1:3, 1:3) will return TRUE. compare(1:3,2:4) return FALSE.
Then I hope to call apply(tb,1,compare). But this can not work, because
apply only pass one argument to compare function. Does anyone know how to
solve this problem?
Thanks so much.
Anoly
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Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin 'v'
tel: 0049-30-83875219 / \
mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski
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Re: [R] How to insert a bitmap in a grph device
On Fri, May 28, 2004 at 04:58:58PM +0100, Luis Rideau Cruz wrote: If I have a plot and I want to insert a bitmap in the same devicehow to do it? IIRC the pixmap package on CRAN helps with that. Dirk -- FEATURE: VW Beetle license plate in California __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to insert a bitmap in a grph device
Luis Rideau Cruz wrote: If I have a plot and I want to insert a bitmap in the same devicehow to do it? Yesterday we have learned, how to load and plot jpeg images (see: Is it possible to read jpeg files into R?) Now you need a way to insert this into another figure. For this purpose the grid and gridBase packages can be applied, which is explained in an article from Paul Murrel in R-News 02/2003 and in his lecture at the useR! conference, see: http://cran.r-project.org/doc/Rnews/ and http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/ useR! Thomas P. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to insert a bitmap in a grph device
Dirk Eddelbuettel wrote: IIRC the pixmap package on CRAN helps with that. Ah, I see, ?addlogo is much easier than grid in this case, as one sees in a (slightly modified) version of the help example: x - read.pnm(system.file(pictures/logo.ppm, package=pixmap)[1]) plot(sample(1:100)) for (i in 1:7) addlogo(x, px=c(0, (101/77)*11), py=c((i-1)*11, i*11), asp=1) Thank you Thomas P. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Generate a sequence of random integer values
On 28-May-04 Brian Davenhall wrote: I'm trying to generate a sequence of random integer values. I've tried to combine the random (r) and the sequence (seq) functions but this approach does not work. For example, if I use the following command: a - seq(1:100) a [1] 1 2 3 4 5 6 7 8 9 etc. This is a good start, but what I really want is something that would look like this instead [1] 3 96 45 67 8 24 99 63 8, etc. where the integer numbers between 1 and 100 are randomly chosen. Any help would be great, I've found workarounds in other stat packages, but would prefer to do this in R. (1:100)[sort(runif(100),index.return=TRUE)$ix] 37 99 22 66 12 36 90 48 55 45 98 59 92 20 46 23 2 74 80 5 63 27 56 60 51 76 39 87 19 96 29 15 18 100 52 3 70 8 67 42 43 57 91 21 25 78 41 1 34 68 77 9 72 73 11 89 83 94 65 13 14 81 24 58 35 44 10 79 50 49 6 28 17 33 4 71 82 31 75 30 85 93 26 69 38 84 32 54 64 53 88 61 86 97 7 62 95 47 16 40 but there may be a slicker way ... Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 167 1972 Date: 28-May-04 Time: 17:33:52 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] dotchart questions
I am trying to put 3 dotcharts side-by-side with minimal space between each. Each chart is for a different variable, but the vertical axes are the same. I want to have vertical axis labels on the lefthand chart but no vertical axis labels on the other two. Plus, I would like very little space between charts 1 2 and between charts 2 3. I have one approach but am not too happy with the results. A stripped down version of the code is below. Matrix A has the row labels (which are about 20 characters long in the real data). Matrix A1 has no row labels. A - matrix(1:12, ncol=3, byrow=F) A1 - A dimnames(A) - list(letters[1:4], letters[5:7]) dimnames(A1) - list(rep(,4), rep(,3)) par(mfrow = c(1,3), mgp = c(1.75, 1, 0.5), mar = c(3, 0, 1.5, 0), oma = c(2,2,2,2)) dotchart(A) dotchart(A1) dotchart(A1) Two questions: (1) Is there a way with par or something else to make the charts closer together. (2) With a lot of rows (45 in the real data) is there a way to control row spacing (other than getting rid of some rows). I checked the email archives but found no answers there or in the help file. I have R.1.8.1 Windows XP, 512 MB RAM Thanks, Richard Valliant, Ph.D. University of Maryland Joint Program for Survey Methodology 1218 Lefrak Hall College Park MD 20742 (301)-405-0932 FAX: (301) 314-7912 [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Negative binomial glm and dispersion
Using R 1.8.1, and the negative binomial glm implemented in MASS, the default when using anova and a chi-square test is to divide the deviance by the estimated dispersion. Using my UNIX version of S-plus (v 3.4), and the same MASS functions, the deviances are *not* divided by the estimated dispersion. Firstly, I'm wondering if anyone can enlighten about the correct procedure (I thought the F-test was more appropriate when dispersion is estimated)? Secondly, after a bit of muddling with the negative binomial pdf, I concluded that, like for the Poisson, phi is actually 1. This result is borne out by simulations. Is this correct? # an example in R 1.81 with library(MASS) y-rnegbin(n=100,mu=1,theta=1) x-1:length(y) model-glm(y~x,family=neg.bin(1)) summary(model)$dispersion [1] 1.288926 anova(model,test='Chisq) #... Df Deviance Resid. Df Resid. Dev P(|Chi|) NULL99102.038 x 10.18598101.853 0.705 # But the real chi-square probability is 1-pchisq(0.185,1) [1] 0.667 Thanks in advance, Dan Daniel Kehler Dept. of Biology Dalhousie University, B3H 4J1 Halifax, Nova Scotia, Canada Office: LSC 800 email: [EMAIL PROTECTED] phone: 902 494 3910 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Is there a way to represent the ... argument in signature?
Hi!
I guess that it cant work. but maybee I am wrong.
I would like to define a function rbind.
rbind
function (..., deparse.level = 1)
{
which works only for objects of class Myclass
Is it possible to use something like
setMethod(rbind,signature(...=Myclass,deparse.level=numeric)
This gives an error.
Or should I use
rbind.Myclass
Eryk.
Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin 'v'
tel: 0049-30-83875219 / \
mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski
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Re: [R] Is there a way to represent the ... argument in signature?
Have a look at rbind.zoo in the zoo package for an example.
Wolski wolski at molgen.mpg.de writes:
:
: Hi!
:
: I guess that it cant work. but maybee I am wrong.
: I would like to define a function rbind.
: rbind
: function (..., deparse.level = 1)
: {
: which works only for objects of class Myclass
:
: Is it possible to use something like
: setMethod(rbind,signature(...=Myclass,deparse.level=numeric)
: This gives an error.
: Or should I use
: rbind.Myclass
:
: Eryk.
:
: Dipl. bio-chem. Eryk Witold Wolski at MPI-Moleculare Genetic
: Ihnestrasse 63-73 14195 Berlin 'v'
: tel: 0049-30-83875219 / \
: mail: wolski at molgen.mpg.de---W-W
http://www.molgen.mpg.de/~wolski
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Re: [R] orca binary?
I cross compiled it. If someone wants to donate a pre-configured
Windows computer to my research group, I could test it. Else, someone
else will have to. I can't.
It is http://www.analytics.washington.edu/~rossini/rorca/rorca.zip
best,
-tony
[EMAIL PROTECTED] (A.J. Rossini) writes:
Uwe Ligges [EMAIL PROTECTED] writes:
Laura Holt wrote:
Dear R People:
Is there a binary version for rorca, please?
Given I recall correctly, I tried to build rorca for Windows one or
two years ago without success. But maybe Tony (In this context I
recall that I'm still owing him a pizza) knows of a binary?
Hah. I should swing by and collect next week.
Seriously, you should be able to do a source install or a quick build
(I probably could do one later today using the Linux cross-compiler),
since it's just raw R code.
If someone does it before I do, let me know.
best,
-tony
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Re: [R] Sorting Data?
Am 28.05.2004 15:18:58 schrieb(en) Jonathan Baron:
Also the other things.
I have to test the hypothesis: Does a daugther answer the questions
(semantic differential) more equal the own mother and more different
to
the mothers of the other daugthers.
I don't think this is a trivial problem at all, so I am hesitant
to offer advice. I see now that you reall do want a matrix,
where you have mothers in the columns and daughters in the rows,
and distance (difference, similarity) measures in the cells.
Perhaps you have several such measures, so you want a
three-dimensional array.
Hm. I don't know. I tried the following:
Creating a new Variable by:
Fbg[['F.gesamt']] - rowSums(Fbg[11:27], na.rm=TRUE)
Which contains everything from F01 to F17 as sum().
Than I do the thing to split mothers from daugthers as you told me.
The next step i get:
dist(Muetter['F.gesamt'] - Toechter['F.gesamt'])
Which gives me some output, where I am not sure what it is. ;-(
But it looks like the thing I want, but I think I don't really have the
right data inside.
You might do something like this. First define a function to
measure your distance, like
Itemdist - function(x,y) {sum(abs(x[-(1:4)]-y[-(1:4)]))}
Dists - matrix(NA,nrow(Daughters),nrow(Mothers))
for (i in 1:nrow(Daughters)
{for (j in 1:nrow(Mothers))
{Dists[i,j] - Itemdist(Daughters[i,],Mothers[j,])}}
Hm. I get some syntax errors inside this. If you want you can have my
small sample I'm now createing a source file about. There I have 12
mother daugther pairs. I will get about 20 pairs within the next two
months, but then I will have my source file (loading by source(file.
R)) ready. The small sample is just to work now.
Thanks for your help,
Martin
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Re: [R] RE: SCO R
The intellectual property questions raised by the GNU General Public License (GPL) are under active discussion in PDF Solutions, where Sundar Dorai-Raj and I work. Sundar and I have recommended linking PDF commercial software to R. However, we have to be careful how we do this, because the GPL requires that the source for all derivative works be made public. Unfortunately, it seems unclear exactly what constitutes a derivative work, although the GPL states that it does not apply to independent and separate works ... when you distribute them as separate works. Does anyone have information on this, beyond the groklaw and Forbes items already mentioned? For example, are there good examples to follow, or are all the published case studies negative like those already been mentioned? It seems to me that a commercial company could comply with the GPL without jeopardizing its ability to pay employees and stockholders by distributing its software in two, separately installed pieces: The first would provide the base, commercial, proprietary software under a commercial license. The second would include all components distributed under the GPL license, and would add capabilities to the first. I think something like this would benefit both the R Foundation and commercial software distributors. However, our legal department has yet to rule on this, and our management is not eager to move without the blessing of our corporate legal. Therefore, more solid information, published case studies, etc., would help. Thanks, spencer graves Berton Gunter wrote: My $.02 (sorry, couldn't resist). This is but one skirmish in the whole vexatious battle on intellectual property rights, which extends from software to many other venues, one of the most interesting of which is patents on human genes. An example I heard on the radio this morning was eHarmony.com patenting their algorithm for matchmaking, which, the commentator said, is based on a 431 item questionnaire (yet another reason to celebrate my long marriage; 431 questions -- yikes!) ! Needless to say, the potential fodder for editorializing both for and against this intrusion of scientific method into romance seems limitless. Do you think support vector machines or neural nets lurk in the background of their algorithm? Anyway, the only predictions that I think it safe to make are: (1) We have only begun to fight -- and, yes, seeming samaritans (or is it samurai?) like R and GPL may yet have to engage; (2) advances in technology will only turn the heat up and pose yet more problems, as we move relentlessly from thingy inventions running our world to 'idea-y inventions running it. Matchmaking, anyone? (Thanks for your indulgence). Cheers, Bert Siddique, Amer wrote: SCO is grasping for straws. and is now gasping. vexatious lawsuits will only drive so far before puttering out. eventually the curtain gets pulled back on glorified attempts at racketeering. cheers. Message: 76 Date: Thu, 27 May 2004 21:08:12 -0500 From: Deepayan Sarkar [EMAIL PROTECTED] Subject: Re: [R] SCO R To: [EMAIL PROTECTED] Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 On Thursday 27 May 2004 20:18, Greg Tarpinian wrote: Actually, it was very recent. I pulled the electronic version of the article from the Forbes website: I would think twice before taking forbes articles too seriously. For instance, they seem to think that protecting intellectual property rights are all right when it's some big commercial company doing the protecting, but not when they are on the other side of the table. See this article from last year: http://www.forbes.com/2003/10/14/cz_dl_1014linksys.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Bert Gunter Non-Clinical Biostatistics Genentech MS: 240B Phone: 650-467-7374 The business of the statistician is to catalyze the scientific learning process. -- George E.P. Box __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How could I find R.exp?
Hi all, I try to create an import library for using dll. Following the instruction in the readme.package, I used the command lib /def:R.exp /out:Rdll.lib, however, the error message showed Cannot open file R.exp. I downloaded the source code R-1.9.0.tgz, but I can not find R.exp. Thanks! Rui Phone: (403)220-4501 Email: [EMAIL PROTECTED] Department of Mathematics and Statistics University of Calgary [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How could I find R.exp?
On Fri, 28 May 2004 11:52:58 -0600, Rui [EMAIL PROTECTED] wrote : Hi all, I try to create an import library for using dll. Following the instruction in the readme.package, I used the command lib /def:R.exp /out:Rdll.lib, however, the error message showed Cannot open file R.exp. I downloaded the source code R-1.9.0.tgz, but I can not find R.exp. Thanks! It's not part of the source code, it's produced when R is built, and should be in the src/gnuwin32 directory, as long as you chose to install Source Package Installation Files. Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] gauss.hermite?
Thanks to Andy Liaw, Marc Schwartz, Dimitris Rizopoulos and Tamas
Papp for quick replies. Before I sent the email, I found that it was
written by Jim Lindsey, but I could not find further information on him,
so I appreciate the links. Also, the Advanced Statistical Computing
course notes look quite interesting. In particular, the function
gaulag providing Gauss-Laguerre may help with a related problem,
taking expected values with respect to gamma distributions. (Laguerre
polynomials are orthogonal with respect to the a gamma distribution, and
perform the same role as Hermite polynomials relative to a normal
distribution.)
Thanks again. spencer graves
Tamas Papp wrote:
On Fri, May 28, 2004 at 09:04:53AM +0200, Dimitris Rizopoulos wrote:
Dear Spencer,
In Dr. Gray's course notes for Advanced Statistical Computing
(Appendix of Chapter 6) there are some functions for computing
abscissas and corresponding weights for several Gaussian integration
rules:
http://icommons.harvard.edu/~hsph-bio248-01/Lecture_Notes/
Also have a look at
@Book{judd98,
author = {Judd, Kenneth L},
title ={Numerical methods in economics},
publisher ={MIT Press},
year = 1998
}
especially one of the early chapters (integration is in its title,
but I don't have the book at the moment), which covers theory and
practice of numerical integration and quadrature rules.
Implementing these in R has been on my TODO list for a while, so I
would be happy to cooperate on this (but only in July or later).
Best,
Tamas
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[R] Problem: creating shared objects using lapack and blas
I am having trouble with creating shared objects with Fortran files, which use numerical libraries Lapack and Blas. I have read the section in Writing R Extensions but could not find what I needed and I am not at the stage to create a library. What I did was $R CMD SHLIB --output=car file1.f file2.f ... file50.f -llapack -lblas No error message so far, But $dyn.load(./car) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /home/zwang/R/pkg/car/src/./car: /home/zwang/R/pkg/car/src/./car: undefined symbol: slamch_ I think the way I used to link Lapack and Blas was not correct, even though it worked fine when I used for running Fortran code before. Thanks for any advice. Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] intro statistics course in San Francisco bay area
I'm in San Francisco looking for a basic statistics course... using R. I'll be using R for real work later on, so I'd prefer not to have to do the coursework with some other software. All leads are appreciated... Thanks, - JD __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Converting data frame to array?
Dear List, Please bear with a poor newbee, who might be doing everything backwards (I was brought up in pure math). I want to make a simple multi-linear regression on a set of data. I did some expreiments, and if X is a 4 by 2 array and Y is a 4 by 1 array, I can do a linear regression by lm(y~x). Now I have a tab-delimited text file with 10 rows of 300 measurements and an other file with 10 rows of one value each. When I read in those files using read.delim(), I get data frames, and apparently I can no longer do the multi-linear regression. Is there a way to convert the data frames into arrays, or am I going the wrong way about this? Sincerely Thomas Poulsen __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vector normal to a plane
Hi! In which library is this function? I cant find it using help.search() on my R installation. Eryk *** REPLY SEPARATOR *** On 5/28/2004 at 12:22 PM [EMAIL PROTECTED] wrote: Hi All, (I have a degree in math, but I am too embarassed to ask my colleagues, so here goes:) I would like to get a vector normal (orthogonal) to a plane formed by two other vectors. In matlab I do this: v1 = [.4, .6, .8]; v2 = [.9, .7, .2]; nn = cross(v1,v2) (gives ~[-.48, .65, -.24] if I do R cross(v1, v2), I get .94. Huh? Thanks for all your help, again. W __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (Correction) vector normal to a plane
if I do R cross(v1, v2), I get .94. Huh? Meant to say R crossprod(v1, v2) Sorry __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] vector normal to a plane
Hi All, (I have a degree in math, but I am too embarassed to ask my colleagues, so here goes:) I would like to get a vector normal (orthogonal) to a plane formed by two other vectors. In matlab I do this: v1 = [.4, .6, .8]; v2 = [.9, .7, .2]; nn = cross(v1,v2) (gives ~[-.48, .65, -.24] if I do R cross(v1, v2), I get .94. Huh? Thanks for all your help, again. W __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vector normal to a plane
[EMAIL PROTECTED] wrote: Hi All, (I have a degree in math, but I am too embarassed to ask my colleagues, so here goes:) I would like to get a vector normal (orthogonal) to a plane formed by two other vectors. In matlab I do this: v1 = [.4, .6, .8]; v2 = [.9, .7, .2]; nn = cross(v1,v2) (gives ~[-.48, .65, -.24] Huh? I don't have access to Matlab. Can you tell me how cross() is defined in Matlab (it's not obvious to me - at least not at 10:40 pm - how can anything get negative)? if I do R cross(v1, v2), I get .94. Huh? Ha! ;-) crossprod(v1, v2): 0.4*0.9 + 0.6*0.7 + 0.8*0.2 = 0.94 Uwe Ligges Thanks for all your help, again. W __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vector normal to a plane
Uwe Ligges wrote: [EMAIL PROTECTED] wrote: Hi All, (I have a degree in math, but I am too embarassed to ask my colleagues, so here goes:) I would like to get a vector normal (orthogonal) to a plane formed by two other vectors. In matlab I do this: v1 = [.4, .6, .8]; v2 = [.9, .7, .2]; nn = cross(v1,v2) (gives ~[-.48, .65, -.24] Huh? I don't have access to Matlab. Can you tell me how cross() is defined in Matlab (it's not obvious to me - at least not at 10:40 pm - how can anything get negative)? My apologies - and thanks to Rolf Turner who told me the truth (well, I anticipated that it's getting too late this friday evening). OK, I don't think what you are looking for is defined as a function in R. Anyway, for the 3D case it's pretty easy to write the result in one line of code ... Uwe if I do R cross(v1, v2), I get .94. Huh? Ha! ;-) crossprod(v1, v2): 0.4*0.9 + 0.6*0.7 + 0.8*0.2 = 0.94 Uwe Ligges Thanks for all your help, again. W __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vector normal to a plane
W is looking for the vector cross product (a specifically
three-dimensional object important in physics and engineering). The
crossproduct() function provides a matrix product so that crossprod(x,y)
is t(x)%*%y, something completely different.
For the three-dimensional case you could define the cross and dot products
%x%-function(a,b) {c(a[2]*b[3]-a[3]*b[2], -a[1]*b[3]+a[3]*b[1],
a[1]*b[2]-a[2]*b[1])}
%.%%-function(a,b) sum(a*b)
It would make sense, of course, to check that the arguments actually were
vectors of length 3.
-thomas
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RE: [R] Converting data frame to array?
Dear Thomas, In fact, the more common way to fit a linear regression in R is to use variables in a data frame (or list) along with a model formula specifying the model. All of this is explained in the Introduction to R manual that is distributed with R: see, in particular, Sec. 6.3 on data frames, Sec. 7 on reading data from files, and Sec. 11 on statistical models. Given two data frames, say d1 and d2, the first containing, e.g., observations on variables x1 and x2 and the second on y, one could do lm(y ~ x1 + x2, data=c(x1, x2)) or lm(y ~ x1 + x2, data=data.frame(x1, x2)). That said, it's not altogether clear to me what it is that you're trying to do. Are there 10 observations on 300 variables in the first data frame, constituting the predictors, and 10 observations on 1 variable in the second data frame, constituting the response? If so, you have many more predictors than observations, and it's not reasonable to perform a regression. Of course, I may not have this straight. I hope this helps, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of TAPO (Thomas Agersten Poulsen) Sent: Friday, May 28, 2004 2:11 PM To: [EMAIL PROTECTED] Subject: [R] Converting data frame to array? Dear List, Please bear with a poor newbee, who might be doing everything backwards (I was brought up in pure math). I want to make a simple multi-linear regression on a set of data. I did some expreiments, and if X is a 4 by 2 array and Y is a 4 by 1 array, I can do a linear regression by lm(y~x). Now I have a tab-delimited text file with 10 rows of 300 measurements and an other file with 10 rows of one value each. When I read in those files using read.delim(), I get data frames, and apparently I can no longer do the multi-linear regression. Is there a way to convert the data frames into arrays, or am I going the wrong way about this? Sincerely Thomas Poulsen __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] vector normal to a plane
Thomas Lumley tlumley at u.washington.edu writes:
:
: W is looking for the vector cross product (a specifically
: three-dimensional object important in physics and engineering). The
: crossproduct() function provides a matrix product so that crossprod(x,y)
: is t(x)%*%y, something completely different.
:
: For the three-dimensional case you could define the cross and dot products
:
: %x%-function(a,b) {c(a[2]*b[3]-a[3]*b[2], -a[1]*b[3]+a[3]*b[1],
: a[1]*b[2]-a[2]*b[1])}
Alternately, you could get the cofactors from solve:
cross3 - function(a,b) {
m - cbind(a,b,1)
solve(m)[3,]*det(m)
}
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[R] GLMM error in ..1?
I'm trying to use GLMM in library(lme4), R 1.9.0pat, updated just now. I get an error message I can't decipher: library(lme4) set.seed(1) n - 10 N - 1000 DF - data.frame(yield=rbinom(n, N, .99)/N, nest=1:n) fit - GLMM(yield~1, random=~1|nest, family=binomial, data=DF, weights=rep(N, n)) Error in eval(expr, envir, enclos) : ..1 used in an incorrect context, no ... to look in Is there something I can do to get past this short of working through the code for GLMM line by line? Also, I gather GLMM does not currently accept binomial(link=cloglog): fit - GLMM(1-yield~1, random=~1|nest, family=binomial(link=cloglog), + data=DF,weights=rep(N, n)) Error in getClass(thisClass) : family is not a defined class Error in GLMM(1 - yield ~ 1, random = ~1 | nest, family = binomial(link = cloglog), : S language method selection got an error when called from internal dispatch for function GLMM Thanks, spencer graves __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to pass defined function with more than one arguments to apply?
Not sure what you intend with regard to length but to get a logical
vector indicating which rows equal a particular vector:
f1 - function(tb, row) apply(tb,1,function(x)all(x==row))
# or without using apply:
f2 - function(tb, row) colSums( abs( (t(tb) - row) ) ) == 0
# or in terms of a general compare function:
f3 - function(tb, row, compare = function(x)all(x==row)) apply(tb,1,compare)
row - c(0,3,1)
f1(tb,row)
f2(tb,row)
f3(tb,row)
# If you want the number of matching rows:
length(which(f1(tb,row)))
etc.
anoly anoly16b at hotmail.com writes:
:
: Dear all:
: I meet a problem of apply function. I have a matrix called tb
: tb
:V1 V2 V3
: 1 0 3 1
: 2 1 4 0
: 3 0 3 0
: 4 0 4 0
: 5 0 3 1
: 6 1 4 1
: 7 1 1 0
: 8 1 3 0
: 9 0 1 1
: 10 0 3 1
:
: I hope to get the number of row that match c(0,3,1)
: I do this way:
: length(apply(t(tb) = = c (0,3,1), 2, all))
: I defined a funtion, compare-function(vector1, vector2){...}. For example,
: compare(1:3, 1:3) will return TRUE. compare(1:3,2:4) return FALSE.
: Then I hope to call apply(tb,1,compare). But this can not work, because
: apply only pass one argument to compare function. Does anyone know how to
: solve this problem?
:
: Thanks so much.
: Anoly
:
: __
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:
:
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[R] glmmPQL:
I'm getting a strange error from glmmPQL. Consider the following sample code: set.seed(8) N. - 1000 z - rnorm(N.) pr.good - exp(-1e-4*exp(2+2*z)) quantile(pr.good) DF. - data.frame(yield=rbinom(N., N., pr.good)/N., Offset=rep(-10, N.), nest=1:N.) fit - glmmPQL(fixed=1-yield~offset(Offset), random=~1|nest, family=binomial(link=cloglog), data=DF., weights=rep(N., N.)) Using R 1.9.0pat, Windows 2000, with MASS updated just a few hours ago, I get the following error: iteration 1 iteration 2 Error in logLik.reStruct(object, conLin) : NA/NaN/Inf in foreign function call (arg 3) Any suggestions? Best Wishes, Spencer Graves __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] GLMM error in ..1?
Is this the new experimental lme4 (version 0.6-x) ? If so, this is due to an error in our use of method dispatch. It has been fixed in the development version, and there should be a new release in a few days. On Friday 28 May 2004 19:32, Spencer Graves wrote: I'm trying to use GLMM in library(lme4), R 1.9.0pat, updated just now. I get an error message I can't decipher: library(lme4) set.seed(1) n - 10 N - 1000 DF - data.frame(yield=rbinom(n, N, .99)/N, nest=1:n) fit - GLMM(yield~1, random=~1|nest, family=binomial, data=DF, weights=rep(N, n)) Error in eval(expr, envir, enclos) : ..1 used in an incorrect context, no ... to look in Is there something I can do to get past this short of working through the code for GLMM line by line? Also, I gather GLMM does not currently accept binomial(link=cloglog): fit - GLMM(1-yield~1, random=~1|nest, family=binomial(link=cloglog), + data=DF,weights=rep(N, n)) Error in getClass(thisClass) : family is not a defined class Error in GLMM(1 - yield ~ 1, random = ~1 | nest, family = binomial(link = cloglog), : S language method selection got an error when called from internal dispatch for function GLMM __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: Problem: creating shared objects using lapack and blas
To solve my own problem, it seems better to follow instructions in Writing R Extensions to build a library. I am making progress. Thanks, Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 On Fri, 2004-05-28 at 13:11, Zhu Wang wrote: I am having trouble with creating shared objects with Fortran files, which use numerical libraries Lapack and Blas. I have read the section in Writing R Extensions but could not find what I needed and I am not at the stage to create a library. What I did was $R CMD SHLIB --output=car file1.f file2.f ... file50.f -llapack -lblas No error message so far, But $dyn.load(./car) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /home/zwang/R/pkg/car/src/./car: /home/zwang/R/pkg/car/src/./car: undefined symbol: slamch_ I think the way I used to link Lapack and Blas was not correct, even though it worked fine when I used for running Fortran code before. Thanks for any advice. Zhu Wang Statistical Science Department Southern Methodist University Dallas, TX 75275-0332 -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] distance in the function kmeans
My thread broke as I write this at home and there were no new messages on this subject after I got home. I hope this still reaches interested parties. There are several methods that find centroids (means) from distance data. Centroid clustering methods do so, and so does classic scaling a.k.a. metric multidimensional scaling a.k.a. principal co-ordinates analysis (in R function cmdscale the means are found in C function dblcen.c in R sources). Strictly this centroid finding only works with Euclidean distances, but these methods willingly handle any other dissimilarities (or distances). Sometimes this results in anomalies like upper levels being below lower levels in cluster diagrams or in negative eigenvalues in cmdscale. In principle, kmeans could do the same if she only wanted. Is it correct to use non-Euclidean dissimilarities when Euclidean distances were assumed? In my field (ecology) we know that Euclidean distances are often poor, and some other dissimilarities have better properties, and I think it is OK to break the rules (or `violate the assumptions'). Now we don't know what kind of dissimilarities were used in the original post (I think I never saw this specified), so we don't know if they can be euclidized directly using ideas of Petzold or Simpson. They might be semimetric or other sinful dissimilarities, too. These would be bad in the sense Uwe Ligges wrote: you wouldn't get centres of Voronoi polygons in original space, not even non-overlapping polygons. Still they might work better than the original space (who wants to be in the original space when there are better spaces floating around?) The following trick handles the problem euclidizing space implied by any dissimilarity meaasure (metric or semimetric). Here mdata is your original (rectangular) data matrix, and dis is any dissimilarity data: tmp - cmdscale(dis, k=min(dim(mdata))-1, eig=TRUE) eucspace - tmp$points[, tmp$eig 0.01] The condition removes axes with negative or almost-zero eigenvalues that you will get with semimetric dissimilarities. Then just call kmeans with eucspace as argument. If your dis is Euclidean, this is only a rotation and kmeans of eucspace and mdata should be equal. For other types of dis (even for semimetric dissimilarity) this maps your dissimilarities onto Euclidean space which in effect is the same as performing kmeans with your original dissimilarity. Cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
