Re: [R] R-help Digest, Vol 54, Issue 30
Ron Crump wrote: Hi, I have a dataframe that contains pedigree information; that is individual, sire and dam identities as separate columns. It also has date of birth. These identifiers are not numeric, or not sequential. Obviously, an identifier can appear in one or two columns, depending on whether it was a parent or not. These should be consistent. Not all identifiers appear in the individual column - it is possible for a parent not to have its own record if its parents were not known. Missing parental (sire and/or dam) identifiers can occur. I need to export the data for use in another program that requires the pedigree to be coded as integers, increasing with date of birth (therefore sire and dam always have lower identifiers than their offspring) and with missing values coded as 0. How would I go about doing this? You might look at http://www.qimr.edu.au/davidD/sib-pair.R, specifically the read.pedigree() and wrlink() functions. The former is not very impressive speedwise -- I usually perform these tasks in the my Sib-pair (Fortran) program, which is on the same webpage. It will order the pedigree by generational position, so a DOB is not required to do the sort. Terry Therneau's kinship package does that ordering, but doesn't include output routines for the Linkage format. David Duffy. | David Duffy (MBBS PhD) ,-_|\ | email: [EMAIL PROTECTED] ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
You don't have installed the akima pakage.
install.packages(akima, dep=T)
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/08/07, Ola Asteman [EMAIL PROTECTED] wrote:
I got the Warning message below when I tried to load Locfit. What is
wrong?
Regards
Ola Asteman
--
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(foreign)
library(mgcv)
This is mgcv 1.3-19
library(locfit)
Loading required package: akima
Error: package 'akima' could not be loaded
In addition: Warning message:
there is no package called 'akima' in: library(pkg, character.only = TRUE,
logical = TRUE, lib.loc = lib.loc)
--
This e-mail and any attachment may be confidential and may a...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
[EMAIL PROTECTED] napsal dne 28.08.2007 13:33:13:
You don't have installed the akima pakage.
install.packages(akima, dep=T)
And wait about two months and update your R version to 2.6.0. Or update
now to 2.5.1
Regards
Petr
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
On 28/08/07, Ola Asteman [EMAIL PROTECTED] wrote:
I got the Warning message below when I tried to load Locfit. What is
wrong?
Regards
Ola Asteman
--
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
library(foreign)
library(mgcv)
This is mgcv 1.3-19
library(locfit)
Loading required package: akima
Error: package 'akima' could not be loaded
In addition: Warning message:
there is no package called 'akima' in: library(pkg, character.only =
TRUE,
logical = TRUE, lib.loc = lib.loc)
--
This e-mail and any attachment may be confidential and m...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
scott flemming wrote: Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? Hi Scott, Maybe the feather.plot function in the plotrix package is what you want. Jim __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
On 6/5/07, scott flemming [EMAIL PROTECTED] wrote: Can R be used to draw 10 arrows in one line ? Um, sure. Assuming you actually also want to know how to do it, why don't you take a look at the help for arrows(). Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
Yes, but you need to be a bit more specific... When it comes to graphs and drawing lines, there isn't much R can't do... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of scott flemming Sent: 06 June 2007 04:49 To: r-help@stat.math.ethz.ch Subject: [R] R help Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? scott - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help
--- scott flemming [EMAIL PROTECTED] wrote: Hi, I wonder whether R can finish the following project: I want to make a chart to represent 10 genes. Each gene has orientation and length. Therefore, a gene can be represented by arrows. Can R be used to draw 10 arrows in one line ? scott Do you mean something like this? x - 1:10 y - 1:10 plot(x,y, type=n ) arrows(c(1,4,6),c(3,3,3), c(2,3, 7), c(4,4,2)) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help with apply and ccf
You could combine them with cbind, and then split the rows again inside
the function you're calling with apply.
Mat - cbind(mat1, mat2)
apply(Mat, 1, function(x){
row.mat1 - x[seq_len(length(x)/2)]
row.mat2 - x[length(x)/2 + seq_len(length(x)/2)]
cor(row.mat1, row.mat2)
})
Cheers,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Reseach Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[EMAIL PROTECTED]
www.inbo.be
Do not put your faith in what statistics say until you have carefully
considered what they do not say. ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens Michael Andric
Verzonden: dinsdag 22 mei 2007 17:35
Aan: r-help@stat.math.ethz.ch
Onderwerp: [R] R-help with apply and ccf
Dear R gurus,
I would like to use the ccf function on two matrices that are
each 196000 x 12. Ideally, I want to be able to go row by
row for the two matrices using apply for the ccf function and
get one 196000 X 1 array output. The apply function though
wants only one array, no? Basically, is there a way to use
apply when there are two arrays in order to do something like
correlation on a row by row basis?
Thanks for your help
Michael
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help with apply and ccf
I understand you to want correlations of corresponding rows (** not ccf, which returns a vector ccf for each pair of rows). If that is so, 1) ... in theory, diag(cor(t(A), t(B)) would work without apply, except 196,000 rows is probably too large, and it is probably too inefficient to compute and then throw away all the off-diagonals anyway. 2. ##Use a 3d array. ar - array(c(A,B),dim=c(dim(A),2)) ## this can also be done by abind() in the abind package apply(ar,1,function(x)cor(x[,1],x[,2])) ## Value is a vector 3. ## probably simplest and best sapply(seq_along(nrow(a)),function(i)cor(a[i,],b[i,])) ## Note: value is a vector, not an array Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Michael Andric Sent: Tuesday, May 22, 2007 8:35 AM To: r-help@stat.math.ethz.ch Subject: [R] R-help with apply and ccf Dear R gurus, I would like to use the ccf function on two matrices that are each 196000 x 12. Ideally, I want to be able to go row by row for the two matrices using apply for the ccf function and get one 196000 X 1 array output. The apply function though wants only one array, no? Basically, is there a way to use apply when there are two arrays in order to do something like correlation on a row by row basis? Thanks for your help Michael [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help Digest, Vol 46, Issue 27
On Wednesday 27 December 2006 06:00, [EMAIL PROTECTED] wrote:
jingjiangyan
I agree, you can use 'assign'. To be more explicit, you could use the
following function.
jingjiangyan -
function(formula, data)
{
m - match.call()
%,% - function(x,y)paste(x,y,sep=)
d.nm - as.character(m$data)
y.nm - as.character(formula[[2]])
x.nm - as.character(formula[[3]])
for(i in levels(data[[x.nm]])){
var.name - d.nm %,% . %,% i
var.val - data[[y.nm]][data[[x.nm]]==i]
cmd - var.name %,% - %,% var.val
eval(cmd)
assign(var.name, var.val, globalenv())
}
}
Next, assuming the data.frame listed in the previous posting, 'df'
exists in your workspace, the call
jingjiangyan(bb ~ aa, data=df)
would produce the desired results.
Cheers,
Grant Izmirlian
--
Հրանդ Իզմիրլյան
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-Help
You might want to contact the nortest maintainer, Juergen Gross (CCing), who is not listening to the traffic on this list. Uwe Ligges amna khan wrote: Respected Sir I am a very new user of R. I want to ask a question about the nortest package. In this package how we can write the code of ad.test, cvm.test, ks.test for other distributions like GEV, GPA etc. I request you to please guide to me. Kind Regards AMNA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
d - read.table(lahore.txt, header=TRUE) On 11/11/06, amna khan [EMAIL PROTECTED] wrote: Respected Sir I request you to please fill the following read.table function and read.csvfor my understanding by assuming my data attached with this maiL, because I am fail to run these functions using manual guidlines. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors()) read.csv(file, header = TRUE, sep = ,, quote=\, dec=., fill = TRUE, comment.char=, ...) read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill = TRUE, comment.char=, ...) I shall be really thankful to you. REGARDS -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
data = read.delim(lahore.txt) is enough for what you want to do. b On Nov 11, 2006, at 2:11 PM, amna khan wrote: Respected Sir I request you to please fill the following read.table function and read.csvfor my understanding by assuming my data attached with this maiL, because I am fail to run these functions using manual guidlines. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors()) read.csv(file, header = TRUE, sep = ,, quote=\, dec=., fill = TRUE, comment.char=, ...) read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill = TRUE, comment.char=, ...) I shall be really thankful to you. REGARDS -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] lahore.txt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
Not sure of what you ask... Does it help? $ read.table(Desktop/lahore.txt, header=T) Years lrmax n1 n2 n3 n4 arranged 1 1980 207.6 25 24 23 22 29.4 2 1981 92.7 24 23 22 21 49.4 3 1982 67.5 23 22 21 20 55.1 4 1983 93.8 22 21 20 19 58.0 5 1984 60.6 21 20 19 18 59.0 6 1985 117.4 20 19 18 17 59.1 7 1986 65.3 19 18 17 16 60.6 8 1987 59.1 18 17 16 15 65.3 9 1988 76.9 17 16 15 14 67.5 10 1989 123.1 16 15 14 13 69.6 11 1990 83.1 15 14 13 12 75.7 12 1991 75.7 14 13 12 11 76.8 13 1992 69.6 13 12 11 10 76.9 14 1993 55.1 12 11 10 9 83.1 15 1994 49.4 11 10 9 8 84.2 16 1995 76.8 10 9 8 7 87.0 17 1996 189.7 9 8 7 6 88.2 18 1997 151.1 8 7 6 5 92.7 19 1998 59.0 7 6 5 4 93.8 20 1999 88.2 6 5 4 3110.0 21 2000 110.0 5 4 3 2117.4 22 2001 87.0 4 3 2 1123.1 23 2002 29.4 3 2 1 0136.8 24 2003 84.2 2 1 0 0151.1 25 2004 58.0 1 0 0 0189.7 26 2005 136.8 0 0 0 0207.6 Le Samedi 11 Novembre 2006 20:11, amna khan a écrit : Respected Sir I request you to please fill the following read.table function and read.csvfor my understanding by assuming my data attached with this maiL, because I am fail to run these functions using manual guidlines. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors()) read.csv(file, header = TRUE, sep = ,, quote=\, dec=., fill = TRUE, comment.char=, ...) read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill = TRUE, comment.char=, ...) I shall be really thankful to you. REGARDS -- Nicolas Mazziotta __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
If you were trying to use the sep=\t argument, you might have encountered an error, as there are three tabs one of the two blank lines at the end of your data file. The default for read.table and read.delim (as has been suggested by David and Benilton) is whitespace, which consumes the unintended tabs w/o problem. Jeff. On Nov 11, 2006, at 2:31 PM, Benilton Carvalho wrote: data = read.delim(lahore.txt) is enough for what you want to do. b On Nov 11, 2006, at 2:11 PM, amna khan wrote: Respected Sir I request you to please fill the following read.table function and read.csvfor my understanding by assuming my data attached with this maiL, because I am fail to run these functions using manual guidlines. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors()) read.csv(file, header = TRUE, sep = ,, quote=\, dec=., fill = TRUE, comment.char=, ...) read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill = TRUE, comment.char=, ...) I shall be really thankful to you. REGARDS -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] lahore.txt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help in Newsreader?
Matthias Voigt [EMAIL PROTECTED] writes: Dear list, I am new to this all and therefore have following Newbie question: How can I receive and read R-help mailings in a newsreader like thunderbird? Use gmane.comp.lang.r.general on gmane.org HTH, Jens __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help in Newsreader?
On Fri, 2006-11-03 at 17:36 +0100, Matthias Voigt wrote: Dear list, I am new to this all and therefore have following Newbie question: How can I receive and read R-help mailings in a newsreader like thunderbird? Thanks Matthias If you go to the main R web site (http://www.r-project.org/) and click on the Mailing Lists link, then scroll down to Archives and Search Facilities, the second bullet indicates that the lists are available via Gmane, which mirrors the R lists (and many others) to an NNTP server. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help in a newsgroup
On Tue, 2006-07-18 at 11:30 -0700, Darren Weber wrote: Hi, I find a lot of the R-help email traffic overloads my inbox. My IT managers are not really happy for me to be subscribed to several high-traffic email lists. I don't want to lose my contact with the R-help emails, so I'm having to consider various ways of handling the traffic. Anyhow, I'm wondering how many people on the R-help email list would prefer that most of the traffic were in a newsgroup? In case your interested in that option, there is a group available at: [EMAIL PROTECTED] I think the subscription is through normal news group channels. The google search services on this group are nice too. This group is not divided into useful categories, like help, admin, develop etc., but it's not too difficult to create new groups for that. Best, Darren r-help is already available with an NNTP interface at gmane.org: http://dir.gmane.org/gmane.comp.lang.r.general There is also a web based interface, where you can see that your post is already available: http://news.gmane.org/gmane.comp.lang.r.general Similarly, r-devel is also present: http://dir.gmane.org/gmane.comp.lang.r.devel The Google group you reference is completely independent of the R e-mail lists, whereas the gmane interface is synchronized with the R e-mail lists. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-help in a newsgroup
On 7/18/2006 2:30 PM, Darren Weber wrote: Hi, I find a lot of the R-help email traffic overloads my inbox. My IT managers are not really happy for me to be subscribed to several high-traffic email lists. I don't want to lose my contact with the R-help emails, so I'm having to consider various ways of handling the traffic. Anyhow, I'm wondering how many people on the R-help email list would prefer that most of the traffic were in a newsgroup? In case your interested in that option, there is a group available at: [EMAIL PROTECTED] I think the subscription is through normal news group channels. The google search services on this group are nice too. This group is not divided into useful categories, like help, admin, develop etc., but it's not too difficult to create new groups for that. If you prefer the newsgroup interface, you should also look at gmane. Gabor G posted a list of the newsgroups here: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/75239.html recently. Duncan Murdoch Best, Darren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] r-help at stat.math.ethz.ch
Xin jasonshi510 at hotmail.com writes: Dear All: Then error messga there: initial value in 'vmmin' is not finite In addition: There were 38 warnings (use warnings() to see them). Could you give some advice please? Thanks a lot! Xin Shi [[alternative HTML version deleted]] __ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html A little more information (and an informative Subject: line) would help. A reproducible example (let us know how you're calling optim(), and ideally show your data or a subsample of it that produces the same problem --- see the posting guide). A few ideas: - the 'vmmin' error message says that your starting values are giving non-finite results -- this could be because some of your x and y values are negative (which in your could would lead to infinite values). Bottom line: try your objective function with your starting parameter values and see what happens - you could use dnbinom(...,log=TRUE) if you wanted - you may need to be careful with constraining alpha, beta, delta, as you could end up with negative means. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 39, Issue 13
r-help@stat.math.ethz.ch on Saturday, May 13, 2006 at 6:00 AM -0500 wrote:
lme(biomass~age, random=~woods/age)?
Jörn
Consult Pinheiro and Bates (2000, Mixed-effects models in S and S-Plus,
Springer, ISBN 0-387-98957-0 ref 7 at
http://www.r-project.org/doc/bib/R-books.html ) for how to fit more elaborate
models, but two straightforward ones that might be adequate
are
lme( biomass~age, random=~1|woods )
and
lme( biomass~age, random=~age|woods )
In the lme4 library corresponding syntax is
lmer( biomass~age+(1|woods) )
and
lmer( biomass~age+(age|woods) )
For vignettes on the lme4 library see the mlmRev library and
@ARTICLE{Rnews:Bates:2005,
AUTHOR = {Douglas Bates},
TITLE = {Fitting Linear Mixed Models in {R}},
JOURNAL = {R News},
YEAR = 2005,
VOLUME = 5,
NUMBER = 1,
PAGES = {27--30},
MONTH = {May},
URL = {[ http://CRAN.R-project.org/doc/Rnews/
]http://CRAN.R-project.org/doc/Rnews/}
}
alan
--
Alan B. Cobo-Lewis, Ph.D. (207) 581-3840 tel
Department of Psychology(207) 581-6128 fax
University of Maine
Orono, ME 04469-5742[EMAIL PROTECTED]
http://www.umaine.edu/visualperception
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 38, Issue 30
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help
Ezra I don't know what the elements of your matrix are, but if there are a large proportion of 0s you can work with sparse matrices in the Matrix package. Harold -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erez Sent: Tuesday, April 25, 2006 8:39 AM To: r-help@stat.math.ethz.ch Subject: [R] R help Hello, I'm working with large matrix data and i would like to know if there is any way to reduce the size of it because even that I'm increasing the memory limit and that i have 1 gb memory the program throwing me out. There is any way to use a smaller size data (such as using bits or so) to reduce the size of it. Erez __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help
A similar question was just asked. See: http://tolstoy.newcastle.edu.au/R/help/06/04/25898.html On 4/25/06, Erez [EMAIL PROTECTED] wrote: Hello, I'm working with large matrix data and i would like to know if there is any way to reduce the size of it because even that I'm increasing the memory limit and that i have 1 gb memory the program throwing me out. There is any way to use a smaller size data (such as using bits or so) to reduce the size of it. Erez __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help
Hi more memory new comp new OS think about possibility to reformulate the problem with help of database and loading/processing data in chunks. Couple of similar questions were answered not long ago so check archives. HTH Petr On 24 Apr 2006 at 13:06, Erez wrote: Date sent: Mon, 24 Apr 2006 13:06:12 +0200 From: Erez [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject:[R] R help Hello, I'm trying to create a large matrix and it's extends the limit boundaries. The matrix is 100,000x2874 and R is throwing me out, what shall i do? Thanks Erez __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-Help
Read them in as zoo objects (you can replace textConnection(Lines1) with the filename) and then merge them using all = FALSE to retain only common time points. Note that in my English locale I had to modify your Apl to Apr. Lines1 - Date x y Jan-1,2005120 230 Jan-2,2005123 -125 Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-7,200511299 Mar-5,2005200 311 Lines2 - Date x y Jan-2,2005123 -125 Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-5,200511299 Jan-6,2005-23 12 Mar-5,2005200 311 Lines3 - Date x y Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-5,200511299 Mar-5,2005200 311 Apr-23,2005 123 200 library(zoo) DF1 - read.zoo(textConnection(Lines1), header = TRUE, format = %b-%d,%Y) DF2 - read.zoo(textConnection(Lines2), header = TRUE, format = %b-%d,%Y) DF3 - read.zoo(textConnection(Lines3), header = TRUE, format = %b-%d,%Y) merge(DF1, DF2, DF3, all = FALSE) On 4/20/06, stat stat [EMAIL PROTECTED] wrote: Dear r-users, Suppose I have three datasets: Dataset-1: Date x y Jan-1,2005120 230 Jan-2,2005123 -125 Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-7,200511299 Mar-5,2005200 311 Dataset-2: Date x y Jan-2,2005123 -125 Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-5,200511299 Jan-6,2005-23 12 Mar-5,2005200 311 Dataset-3: Date x y Jan-3,2005-110 300 Jan-4,2005114 -21 Jan-5,200511299 Mar-5,2005200 311 Apl-23,2005 123 200 Now I want to get the common dates along with x and y from this above three datasets keeping the same order in date-variable as it is. For ex. I want to get: Datex y xy x y (from dataset-1) (from dataset-2) (from dataset-3) Jan-3,2005-110 300 -110 300 -110 300 Jan-4,2005 114 -21 114-21 114 -21 Mar-5,2005200 311 200 311 200 311 Can anyone give me any R code to implement this for any number of datasets ? Thanks and regards thanks in advance - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-Help
I think this does what you require.
#Read your data in whatever way you wish:
d1-data.frame(Date=c(2005/1/1,2005/2/1,2005/1/3,2005/1/4,2005/
1/7,2005/3/5),
x=c(119,123,-110,114,11,200),
y=c(230,-125,300,-21,299,311))
d2-data.frame(Date=c(2005/1/3,2005/1/4,2005/1/5,2005/1/6,2005/
3/5),
x=c(-220,116,888,-239,201),
y=c(301,-23,3000,122,312))
d3-data.frame(Date=c(2005/1/4,2005/1/5,2005/3/5,2005/4/23),
x=c(392,511,600,723),
y=c(-81,6699,9311,1200))
#Make a list
listof-list(d1,d2,d3)
#loop over any number of datasets merging as you go
for ( dataset in 1:length(listof)-1) {
if (dataset == 1) {
res-merge(listof[dataset],listof[dataset+1],all=T,by=Date)
} else {
res-merge(res,listof[dataset+1],all=T,by=Date)
}
}
# Hope that helps
JS
---
John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
tel +44 (0)1603 251490
fax +44 (0)1603 255167
e-mail [EMAIL PROTECTED]
e-disclaimer at http://www.ifr.ac.uk/edisclaimer/
Web sites:
www.ifr.ac.uk
www.foodandhealthnetwork.com
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of stat stat
Sent: 20 April 2006 09:17
To: r-help@stat.math.ethz.ch
Subject: [R] R-Help
Dear r-users,
Suppose I have three datasets:
Dataset-1:
Date x y
Jan-1,2005120 230
Jan-2,2005123 -125
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-7,200511299
Mar-5,2005200 311
Dataset-2:
Date x y
Jan-2,2005123 -125
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-5,200511299
Jan-6,2005-23 12
Mar-5,2005200 311
Dataset-3:
Date x y
Jan-3,2005-110 300
Jan-4,2005114 -21
Jan-5,200511299
Mar-5,2005200 311
Apl-23,2005 123 200
Now I want to get the common dates along with x and y from this above
three datasets keeping the same order
in date-variable as it is.
For ex. I want to get:
Datex y xy
x y
(from dataset-1) (from dataset-2) (from
dataset-3)
Jan-3,2005-110 300 -110 300
-110 300
Jan-4,2005 114 -21 114-21 114
-21
Mar-5,2005200 311 200 311 200
311
Can anyone give me any R code to implement this for any number of
datasets ?
Thanks and regards
thanks in advance
-
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 38, Issue 19
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 38, Issue 9
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 37, Issue 26
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 37, Issue 15
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 37, Issue 12
Hi r-users, I would like to know if R have any solution to the Address standardization. The problem is to classify a database of addresses with the real addresses of a streets of Spain. Ideally, I would like to assign Postal code, census data and other geographic information. If this is not possible I would like to know solutions in R about text mining, text classification, distance within text data,... Any help will be appreciate Thanks in advance Ferran Carrascosa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 37, Issue 12
From: Ferran Carrascosa Hi r-users, I would like to know if R have any solution to the Address standardization. The problem is to classify a database of addresses with the real addresses of a streets of Spain. Ideally, I would like to assign Postal code, census data and other geographic information. I have no idea about this one... If this is not possible I would like to know solutions in R about text mining, text classification, distance within text data,... RSiteSearch(text mining) produced hits that look relevant. Andy Any help will be appreciate Thanks in advance Ferran Carrascosa __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help list: temporary problem in local archives
Dimitri == Dimitri Szerman [EMAIL PROTECTED] on Mon, 6 Mar 2006 14:17:33 -0300 writes: Dimitri Hi, Dimitri It seems the list faced some problems during the Dimitri weekend, so I am re-sending this message. To be specific: The only problems it saw was that the local *archiving* had stopped working from ~ Friday 17:30 MET. The archiver now works again (and I have spent about an hour to ensure that everything shows up in the archives as it should). Dimitri's message actually *did* appear well on the list (yesterday). Martin Maechler, ETH Zurich your mailing list manager __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help list: temporary problem in local archives
Martin == Martin Maechler [EMAIL PROTECTED] on Mon, 6 Mar 2006 18:37:06 +0100 writes: Dimitri == Dimitri Szerman [EMAIL PROTECTED] on Mon, 6 Mar 2006 14:17:33 -0300 writes: Dimitri Hi, Dimitri It seems the list faced some problems during the Dimitri weekend, so I am re-sending this message. Martin To be specific: The only problems it saw was that the local *archiving* Martin had stopped working from ~ Friday 17:30 MET. Martin The archiver now works again (and I have spent about an hour to Martin ensure that everything shows up in the archives as it should). well, unfortunately, I have managed to wipeout the index.html file of the full archive there. AARgh! [the archives, its HTML pages, everything is still there, but all the older parts are currently not *linked* to] Recreating everything from scratch (1997) would need so many hours --- where mailman delivery to r-help was completely blocked --- that I'm considering other plans to get that file back (and only recreate the March 2006 part). All this mess just because of a spam that I wanted to have removed, something which needs careful manual intervention; I have failed in my care at one place. Martin Martin Dimitri's message actually *did* appear well on the list Martin (yesterday). Martin Martin Maechler, ETH Zurich Martin your mailing list manager __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 37, Issue 1
Mi nueva dirección de correo es: [EMAIL PROTECTED] New e-mail address: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 36, Issue 21
Hello, dear R users. I've already sent a question here, but I'm not sure that it had been read. I need to visualize classification of my numerical data based on 2-3 factors. As I suppose, the best way is a tree. With an orbitrary function at the ends (leaves), or at least with means of my data at the ends. What is the way to do it? As I found, ctree offers binary classification, but it that the only way? Of course, tree is not only way, may be you could offer other ways. Thank you. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 36, Issue 21
Evgeniy Kachalin wrote: Hello, dear R users. I've already sent a question here, but I'm not sure that it had been read. I need to visualize classification of my numerical data based on 2-3 factors. As I suppose, the best way is a tree. With an orbitrary function at the ends (leaves), or at least with means of my data at the ends. What is the way to do it? As I found, ctree offers binary classification, but it that the only way? Of course, tree is not only way, may be you could offer other ways. Or the best way of it is to do it with replacement, like a 'heatmap', but with means in the cells instead of colors, if it is possible. Sorry for the second letter. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help, specifying the places to decimal
have a look at ?round() Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://www.med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Subhabrata [EMAIL PROTECTED] To: r-help r-help@stat.math.ethz.ch Sent: Monday, February 13, 2006 9:33 AM Subject: [R] R-help, specifying the places to decimal Hello - R-experts, Is there any way with which we can specify the number after decimal point to take. Like I have a situation where the values are comming 0.160325923 but I only want 4 place to decimal say 0.1603. Is there any way for that. I am no expert in R- and this may sound simple to many.sorry Thanks for any help. With Regards Subhabrata __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help, specifying the places to decimal
In addition to round() mentioned earlier, if you are merely looking to *display* your results differently, you may want to check out the digits option, e.g. in summary(): (This is the method signature for data.frame 's): summary(object, maxsum = 7, digits = max(3, getOption(digits)-3), ...) (Begin quoted message) Date: Mon, 13 Feb 2006 14:03:55 +0530 From: Subhabrata [EMAIL PROTECTED] Subject: [R] R-help, specifying the places to decimal To: r-help r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello - R-experts, Is there any way with which we can specify the number after decimal point to take. Like I have a situation where the values are comming 0.160325923 but I only want 4 place to decimal say 0.1603. Is there any way for that. I am no expert in R- and this may sound simple to many.sorry Thanks for any help. With Regards Subhabrata -- -- Vivek Satsangi Student, Rochester, NY USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 24
I've been reluctant to step into this topic, but now feel that it may be helpful to make a certain point. On the internet, for the most part, the person behind the email is invisible and intangible. It is therefore possible, when someone puts their foot down, to stamp inadvertently on someone else's already broken toes. A friend of mine, very intelligent, very knowledgeable and creative, very articulate, nevertheless when writing uses spelling which can be a close approximation to random, and some interesting variants of grammar and vocabulary as well. The reason: dyslexia. While most of us hit the wrong keys at times (and when we read back over what we've written tend to see what we intended to write rather than what we did write), and when backed against the wall would admit that we could have got it right if we had paid better attention, there are some people who can't help getting it wrong. But, on the internet, one cannot readily recognise who they are (though in some cases, if one knows the signs, one may guess). Best wishes to all, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 25-Jan-06 Time: 10:06:35 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 24
[Gabor Grothendieck] [...] this list is inhabited by some rather rude participants but everyone puts up with them in the hope that they do have some useful remarks. I've been witnessing this list for about one year, and also read *lots* of archived messages. While it is true that a few members do not use white gloves, are rather fond on concise replies, and do express strong opinions at times, they never went overboard insulting people and always kept a reasonable measure, at least so far that I could see (yet who knows, outliers might happen! :-). (*) Our whole society is a bit shy and shivers easily when opinions are expressed nowadays, I often observed than people quickly get insecure, feel attacked, and overreact (by running away or starting a fight). there is even a group of thought that feels it is a justifiable way to keep the list volume under control. This may work because of the starred paragraph above, that is, for wrong reasons. Best is, and this often occurs on the R list, when everything (facts, opinions) is being shared efficiently, without useless arguing. Then, threads quickly fade out. -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 24
Dear Prof Ripley, First of all, unless you are an english professor, then I do not think you have any business policing language. I'm still very much a student, both in R, and regarding signal analysis. My competence on the subject as compared too your own level of expertise, or my spelling for that matter, may be a contension for you, but it would have been better had you kept that opinion too yourself. There are plenty of other reasons besides laziness or carelessness that people will consistently error in language use, such as learning disorders, head injuries, and/or vertigo. On the contrary, I am aware of the definition of a periodogram, and I know what the unnormalized periodogram in the data I presented looks like. Spec.pgram() is actually normalized too something, because it's discrete integral is not well above the SS amplitude of the signal it computed the periodogram for. In other words, the powers are not in units of around 4,000, which the peak would be if the units were merely the modulus squared of the Fourier coeficients of the data I presented. Alas, the modulus squared of the Fourier coeficients IS the TWO SIDED unnormalized periodogram, ranging from [-fc, fc] | fc=nyquist critical frequency. The definition of the ONE SIDED periodogram IS the modulus squared of the Fourier coeficients ranging over [0, fc], but since the function is even, data points in (0, fc) non-inclusive, need to be multiplied by 2. Thus is according too the definition given by Press, et al (1988, 1992, 2002, c.f. cp 12 13). I'm assuming that R returns an FFT in the same layout as Press, et al describe. Press, et al. are also very clear about the existence of far too many ways of normalizing the periodogram too document, which they stated before delving into particularly how they normalized to the mean squared amplitude of the signal that the periodogram was computed from. In the page before, and perhaps this is where some of the confusion arises from, they document the calculations for MS and SS amplitudes and time integral squared amplitude of the signal in the time domain, not the frequency domain. The page after that, their example only shows how to normalize a periodogram so its sum is equal too the MS amplitude. In short, but starting from SS amplitude: a). sum(a[index=(1:N) or t=(0:N-1)]^2) = SS amplitude calculated in time domain b). 1/N * sum(Mod(fft[-fc:fc])^2) = two sided periodogram that sums too the SS amplitude c). Same as b but over the range [0, fc], and (0, fc) multiplied by 2 is the one sided periodogram, also sums too the SS amplitude For MS amplitude, the procedures are identical, only the time domain is divided by N, and the frequency domain figures are divided by N^2 instead of N. When the periodogram is in power per unit time, as in the above, so that the power is interpretable at N/2+1 independent frequencies, it is a normalized periodogram. spec.pgram() IS normalized, I just do not know what it's normalized too because I can not seem to get spec.pgram to stop tapering (at which point the normalization should be dead on, not just close). By the way, normalized does not automatically mean anything unless to what is stated. I could normalize something arbitrarily to the number of tics on my dogs back side, and still call it normed, or erroneously refer too it as unnormed. If normalized is suposed to mean something specific, then I am confident that more than 90% of undergraduates are not familiar with what the term should mean. Stats and coding and using programs are a human endeavor. This human seems to have made meaning out of terms differently than what those who wrote the documentation seem to have intended. Only, I do not know where the documentation or my understanding may have been missled (R docs, Numerical Recipes, or any other source I looked at since I started). Cheers, KeithC. First, please look up `too' in your dictionary. Second, please study the references on the help page, which give the details. That is what references are for! The references will also answer your question about the reference distribution. The help page does not say it is `normalized' at all: it says it computes the peridogram, and you seem unaware of the definitions of the latter (and beware, there are more than one). On Tue, 24 Jan 2006, Keith Chamberlain wrote: __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 24
Dear Mr. Chamberlain: You asked for free consulting, and as near as I can tell, you got pretty good advice. Now you complain that you don't like the packaging. If you can't stand the heat, get out of the kitchen. Professor Brian Ripley has an international reputation based on solid contributions to human knowledge over many years. He is an expert in statistical science, not diplomacy. Professor Ripley has been incredibly generous in donating substantial portions of his time for many years both to help make R what it is today and to answering questions on this listserve. I think he deserves a great deal of respect for not only the time he has devoted to this but to how much he has achieved with that time. What would you like him to do as a result of your email? Retire? Stop contributing to this listserve and to the R project more generally? I sincerely hope he does not consider such. It would be a great loss to humanity if he did. Mr. Chamberlain, if English (or as Prof. Ripley might say, American) is your mother tongue, then your deplorable lack of skill in its use raises serious questions about the standard of academic excellence at the University of Colorado, which I had previously thought was a great university and the finest Colorado had to offer. Of course, if English is a second language for you, then I would not complain. Rather, I would be humbled and honored that you chose to meet the rest of the world in my native tongue. Another question: The web lists you as a senior in psychology. Have you learned anything in your study of psychology? I would think that psychology students should meet a much higher standard for social skills and communications than you have displayed today. Would you like me to forward your correspondence to, say, the editor of the Flatiron News there in Boulder or Prof. W. Edward Craighead, the chair of the Psychology Dept., asking if a degree from the once-great University of Colorado is supposed to imply that the degree holder meets any standard for academic excellence in comportment and the use of language? Sincerely, Spencer Graves [EMAIL PROTECTED] wrote: Dear Prof Ripley, First of all, unless you are an english professor, then I do not think you have any business policing language. I'm still very much a student, both in R, and regarding signal analysis. My competence on the subject as compared too your own level of expertise, or my spelling for that matter, may be a contension for you, but it would have been better had you kept that opinion too yourself. There are plenty of other reasons besides laziness or carelessness that people will consistently error in language use, such as learning disorders, head injuries, and/or vertigo. On the contrary, I am aware of the definition of a periodogram, and I know what the unnormalized periodogram in the data I presented looks like. Spec.pgram() is actually normalized too something, because it's discrete integral is not well above the SS amplitude of the signal it computed the periodogram for. In other words, the powers are not in units of around 4,000, which the peak would be if the units were merely the modulus squared of the Fourier coeficients of the data I presented. Alas, the modulus squared of the Fourier coeficients IS the TWO SIDED unnormalized periodogram, ranging from [-fc, fc] | fc=nyquist critical frequency. The definition of the ONE SIDED periodogram IS the modulus squared of the Fourier coeficients ranging over [0, fc], but since the function is even, data points in (0, fc) non-inclusive, need to be multiplied by 2. Thus is according too the definition given by Press, et al (1988, 1992, 2002, c.f. cp 12 13). I'm assuming that R returns an FFT in the same layout as Press, et al describe. Press, et al. are also very clear about the existence of far too many ways of normalizing the periodogram too document, which they stated before delving into particularly how they normalized to the mean squared amplitude of the signal that the periodogram was computed from. In the page before, and perhaps this is where some of the confusion arises from, they document the calculations for MS and SS amplitudes and time integral squared amplitude of the signal in the time domain, not the frequency domain. The page after that, their example only shows how to normalize a periodogram so its sum is equal too the MS amplitude. In short, but starting from SS amplitude: a). sum(a[index=(1:N) or t=(0:N-1)]^2) = SS amplitude calculated in time domain b). 1/N * sum(Mod(fft[-fc:fc])^2) = two sided periodogram that sums too the SS amplitude c). Same as b but over the range [0, fc], and (0, fc) multiplied by 2 is the one sided periodogram, also sums too the SS amplitude For MS amplitude, the procedures are identical, only the time domain is divided by N, and
Re: [R] R-help Digest, Vol 35, Issue 24
[EMAIL PROTECTED], addressing to Brian Ripley] First of all, unless you are an english professor, then I do not think you have any business policing language. We all do mistakes (English or otherwise). I'm very grateful that people forgive my own errors, and I try to be tolerant to others. (Yet, it happens that people lacking good will ask for stronger reactions.) This is the business of everybody, really, building a better community in every possible aspect, and the means for this go through interaction and collaboration. Let's all be humble enough to ponder the criticism of others, improve ourselves, and so increase the value of our share. -- François Pinard http://pinard.progiciels-bpi.ca __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 24
Its not really you. Its a fact of life that this list is inhabited by some rather rude participants but everyone puts up with them in the hope that they do have some useful remarks. This has been discussed repeatedly on the list and there is even a group of thought that feels it is a justifiable way to keep the list volume under control. On 1/24/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Prof Ripley, First of all, unless you are an english professor, then I do not think you have any business policing language. I'm still very much a student, both in R, and regarding signal analysis. My competence on the subject as compared too your own level of expertise, or my spelling for that matter, may be a contension for you, but it would have been better had you kept that opinion too yourself. There are plenty of other reasons besides laziness or carelessness that people will consistently error in language use, such as learning disorders, head injuries, and/or vertigo. On the contrary, I am aware of the definition of a periodogram, and I know what the unnormalized periodogram in the data I presented looks like. Spec.pgram() is actually normalized too something, because it's discrete integral is not well above the SS amplitude of the signal it computed the periodogram for. In other words, the powers are not in units of around 4,000, which the peak would be if the units were merely the modulus squared of the Fourier coeficients of the data I presented. Alas, the modulus squared of the Fourier coeficients IS the TWO SIDED unnormalized periodogram, ranging from [-fc, fc] | fc=nyquist critical frequency. The definition of the ONE SIDED periodogram IS the modulus squared of the Fourier coeficients ranging over [0, fc], but since the function is even, data points in (0, fc) non-inclusive, need to be multiplied by 2. Thus is according too the definition given by Press, et al (1988, 1992, 2002, c.f. cp 12 13). I'm assuming that R returns an FFT in the same layout as Press, et al describe. Press, et al. are also very clear about the existence of far too many ways of normalizing the periodogram too document, which they stated before delving into particularly how they normalized to the mean squared amplitude of the signal that the periodogram was computed from. In the page before, and perhaps this is where some of the confusion arises from, they document the calculations for MS and SS amplitudes and time integral squared amplitude of the signal in the time domain, not the frequency domain. The page after that, their example only shows how to normalize a periodogram so its sum is equal too the MS amplitude. In short, but starting from SS amplitude: a). sum(a[index=(1:N) or t=(0:N-1)]^2) = SS amplitude calculated in time domain b). 1/N * sum(Mod(fft[-fc:fc])^2) = two sided periodogram that sums too the SS amplitude c). Same as b but over the range [0, fc], and (0, fc) multiplied by 2 is the one sided periodogram, also sums too the SS amplitude For MS amplitude, the procedures are identical, only the time domain is divided by N, and the frequency domain figures are divided by N^2 instead of N. When the periodogram is in power per unit time, as in the above, so that the power is interpretable at N/2+1 independent frequencies, it is a normalized periodogram. spec.pgram() IS normalized, I just do not know what it's normalized too because I can not seem to get spec.pgram to stop tapering (at which point the normalization should be dead on, not just close). By the way, normalized does not automatically mean anything unless to what is stated. I could normalize something arbitrarily to the number of tics on my dogs back side, and still call it normed, or erroneously refer too it as unnormed. If normalized is suposed to mean something specific, then I am confident that more than 90% of undergraduates are not familiar with what the term should mean. Stats and coding and using programs are a human endeavor. This human seems to have made meaning out of terms differently than what those who wrote the documentation seem to have intended. Only, I do not know where the documentation or my understanding may have been missled (R docs, Numerical Recipes, or any other source I looked at since I started). Cheers, KeithC. First, please look up `too' in your dictionary. Second, please study the references on the help page, which give the details. That is what references are for! The references will also answer your question about the reference distribution. The help page does not say it is `normalized' at all: it says it computes the peridogram, and you seem unaware of the definitions of the latter (and beware, there are more than one). On Tue, 24 Jan 2006, Keith Chamberlain wrote: __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
Re: [R] R-help Digest, Vol 35, Issue 23
summary.aov(aovRes, split=list(interval = list(i1 vs i2 = 1, i2 vs i3 = 2, i3 vs i4 = 3, i4 vs i5 = 4, i5 vs i6 = 5))) try class(aovRes) #- aovlist ! summary.aovlist(aovRes, spit=...) or simply summary(aovRes, spit=...) Hoping this helps, Herwig -- Dr. Herwig Meschke Wissenschaftliche Beratung Hagsbucher Weg 27 D-89150 Laichingen phone +49 7333 210 417 / fax +49 7333 210 418 email [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] r-help, how can i use my own distance matrix without usin g dist()
Use something like hclust(as.dist(mydist), ...) ought to work. Andy -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, January 18, 2006 4:47 PM To: r-help@stat.math.ethz.ch Subject: [R] r-help, how can i use my own distance matrix without using dist() Dear R-helpers, i am a beginner of R and i am using cluster package to do hierarchical clustering i am wondering if i can use my own distance matrix to do the hierarchical clustering without using dist() function. if i have my own distance matrix, how can i ask hclust() function to recongnize it( as the output of dist() function). thank you very much and i looking forward to hearing from you. Marshall __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] r-help, how can i use my own distance matrix without using dist()
see ?dist there's an example x - matrix(rnorm(100), nrow=5) m - as.matrix(dist(x)) d - as.dist(m) 'as.dist' is what you're probably looking for regards, Marco [EMAIL PROTECTED] wrote: Dear R-helpers, i am a beginner of R and i am using cluster package to do hierarchical clustering i am wondering if i can use my own distance matrix to do the hierarchical clustering without using dist() function. if i have my own distance matrix, how can i ask hclust() function to recongnize it( as the output of dist() function). thank you very much and i looking forward to hearing from you. Marshall __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html - Photo Books. You design it and well bind it! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 14
On Sun, 15 Jan 2006, Werner Wernersen wrote: Dear all, Is anybody aware of a tutorial, introduction, overview or alike for cluster analysis with R? I have been searching for something like that but it seems there are only a few rather specialized articles around. As an overview (rather than an introduction or tutorial), the Cluster task view might be helpful to you: http://CRAN.R-project.org/src/contrib/Views/Cluster.html Z I would very much appreciate any hint. Thanks a million, Werner ___ Telefonate ohne weitere Kosten vom PC zum PC: http://messenger.yahoo.de __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 14
Dear all, Is anybody aware of a tutorial, introduction, overview or alike for cluster analysis with R? I have been searching for something like that but it seems there are only a few rather specialized articles around. I would very much appreciate any hint. Thanks a million, Werner ___ Telefonate ohne weitere Kosten vom PC zum PC: http://messenger.yahoo.de __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 14
On Sun, 15 Jan 2006, Werner Wernersen wrote: Is anybody aware of a tutorial, introduction, overview or alike for cluster analysis with R? I have been searching for something like that but it seems there are only a few rather specialized articles around. Chapter 11 of MASS (the book discussed in the FAQ). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 7
Uwe Ligges пишет:
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * - signs,
for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
--
Evgeniy
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 7
Hi!
Just use your factors for indexing c(15,16,17) and
c(red,green,blue). So, with the iris data:
with(iris, plot(Sepal.Length, Sepal.Width,
pch=c(15,16,17)[as.integer(Species)],
col=c(red,green,blue)[as.integer(Species)] ))
Best regards,
Kyosti Kurikka
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * - signs,
for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
--
Evgeniy
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 7
Evgeniy Kachalin wrote:
Uwe Ligges пишет:
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * -
signs, for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Yes, it can recycle, but in the example above it does not recycle but
takes the whole Species vector.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
What about adding 14 as in as.integer(Species)+14, or 1 for the colors,
respectively?
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
This is one qay of many.
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
You can set up your own pch variable of course, if you don't like it
this fast and easy way.
Uwe Ligges
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 7
Hello, dear participants! Could you tip me, is there any simple and nice way to build scatter-plot for three different types of data (, and o and * - signs, for example) with legend. Now i can guess only that way: plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue') points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green') points( etc What is the simple and nice way? Thank you very much for your kindness and help. -- Evgeniy Kachalin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 35, Issue 7
Evgeniy Kachalin wrote: Hello, dear participants! Could you tip me, is there any simple and nice way to build scatter-plot for three different types of data (, and o and * - signs, for example) with legend. Now i can guess only that way: plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue') points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green') points( etc What is the simple and nice way? Thank you very much for your kindness and help. Example: with(iris, plot(Sepal.Length, Sepal.Width, pch = as.integer(Species))) with(iris, legend(7, 4.4, legend = unique(as.character(Species)), pch = unique(as.integer(Species Uwe Ligges __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help: gls with correlation=corARMA
Thank you for your extra efforts in pinpointing the source of my problem. That is a smart workaround, to reduce the parameters until invertibility conditions are satisfied. The concern in my case is what effect the constant will have on the covariance matrix and the resulting estimates for the slope in the model. I might look at other cases where the invertibility condition was satisfied and compare the slope estimates and standard errors for the unscaled and scaled time series parameters. The example below was one of many series. I should have been quicker to realize that someone might use the same form as my example to mess with someones machine. I have used tryCatch over the weekend to skip the gls fit in cases where this error occurred (4282 out of 187283 series). There were no errors when I fit a (0,0,1)x(0,0,1) model (e.g. q=13), instead of q=25. Thank you again for your time and explanation. Sincerely, Steve Gaffigan On Sun, 11 Dec 2005, Spencer Graves wrote: The error message is misleading. It should say something like, Error in corARMA(q = 25, value = -ma.coefs, fixed = T) : The moving average process specified is not invertible, having roots outside the unit circle. Instead it says, Error in corARMA(q = 25, value = -ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value. I'm copying Doug Bates on this reply in case he wants to try to fix this. I got an answer just by shrinking your ma.coefs' by a factor of 0.8: mod.gls=gls(obs~model,correlation=corARMA(q=25,value=0.8*ma.coefs,fixed=T), method=ML) This seemed to produce an answer for me; it least it did not give me an error message. In case you are interested in how I determined this, I will outline the steps I took in analyzing this problem. First, I copied the web address you gave for the data into a web browser to make sure it was honest text and not something that might corrupt my computer. You are to be commended for providing an example that allowed me to replicate your problem. If the example had been smaller and simpler, it would have made my job easier and might have gotten you an earlier reply from someone else. Then I ran your code and got the error you reported: ... mod.gls=gls(obs~model, + correlation=corARMA(q=25,value=ma.coefs,fixed=T), + method=ML) Error in corARMA(q = 25, value = ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value Next, I considered ways to simplify this problem and still get the same error message. I decided to try the corARMA part by itself: corARMA(q=25,value=ma.coefs,fixed=T) Error in corARMA(q = 25, value = ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value Progress. Then I typed corARMA at a command prompt and copied the code into a scrit file. The I typed debug(corARMA) and repeated the corARMA(...) command. After tracing through the corARMA code line by line, I found that the error message is issued from '.C(ARMA_unconstCoef, ...)'. I gave that up: This approach did not help in this case, thoug it has in others. Then I tried some simpler examples: 'corARMA(q=1,value=.5,fixed=T)' and 'corARMA(q=1,value=-.5,fixed=T)' did NOT give me that error message, but 'corARMA(q=2,value=c(.8, -.5),fixed=T)' did. Then I checked a time series book for the conditions for invertibility. I found that all the roots of the characteristic equation must lie outside the unit circle. So I checked the following: round(Mod(polyroot(c(1, ma.coefs))), 3) [1] 1.069 0.995 0.995 0.995 0.995 0.995 0.995 0.995 0.995 1.069 1.069 1.069 [13] 0.995 0.995 0.995 0.995 1.069 1.069 1.069 1.069 1.069 1.069 1.069 1.069 [25] 1.930 Then I shrunk the ma.coefs' by 0.999 and got larger roots but still some inside the unit circle. So I tried 0.99 and 0.9 with the same result. With 0.8, all the roots were outside the unit circle. hope this helps. spencer graves [EMAIL PROTECTED] wrote: Dear Madams/Sirs, Hello. I am using the gls function to specify an arma correlation during estimation in my model. The parameter values which I am sending the corARMA function are from a previous fit using arima. I have had some success with the method, however in other cases I get the following error from gls: All parameters must be less than 1 in absolute value. None of the parameters (individually) are greater than or equal to 1. Please copy the code below into R to reproduce the error. Thanks. Is my logic incorrect? In the corARMA function, there's a call to pre-compiled C code with the name ARMA_unconstCoef. Is the source code for such compiled code freely available for download? Thanks for your suggestions. Sincerely Steve Gaffigan
Re: [R] R-help Digest, Vol 34, Issue 14
Guten Tag, Ich bin vom 12. bis 23. Dezember 2005 im Militär-WK. Ich werde die Mails somit nur verzögert beantworten können. Für dringende Fälle: Während diesen zwei Wochen bin ich via Natel (am besten per SMS) erreichbar unter der Nummer 079 438 27 68. Mit freundlichem Gruss Dominik Schaub __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help: gls with correlation=corARMA
The error message is misleading. It should say something like, Error in corARMA(q = 25, value = -ma.coefs, fixed = T) : The moving average process specified is not invertible, having roots outside the unit circle. Instead it says, Error in corARMA(q = 25, value = -ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value. I'm copying Doug Bates on this reply in case he wants to try to fix this. I got an answer just by shrinking your ma.coefs' by a factor of 0.8: mod.gls=gls(obs~model,correlation=corARMA(q=25,value=0.8*ma.coefs,fixed=T), method=ML) This seemed to produce an answer for me; it least it did not give me an error message. In case you are interested in how I determined this, I will outline the steps I took in analyzing this problem. First, I copied the web address you gave for the data into a web browser to make sure it was honest text and not something that might corrupt my computer. You are to be commended for providing an example that allowed me to replicate your problem. If the example had been smaller and simpler, it would have made my job easier and might have gotten you an earlier reply from someone else. Then I ran your code and got the error you reported: ... mod.gls=gls(obs~model, + correlation=corARMA(q=25,value=ma.coefs,fixed=T), + method=ML) Error in corARMA(q = 25, value = ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value Next, I considered ways to simplify this problem and still get the same error message. I decided to try the corARMA part by itself: corARMA(q=25,value=ma.coefs,fixed=T) Error in corARMA(q = 25, value = ma.coefs, fixed = T) : All parameters must be less than 1 in absolute value Progress. Then I typed corARMA at a command prompt and copied the code into a scrit file. The I typed debug(corARMA) and repeated the corARMA(...) command. After tracing through the corARMA code line by line, I found that the error message is issued from '.C(ARMA_unconstCoef, ...)'. I gave that up: This approach did not help in this case, thoug it has in others. Then I tried some simpler examples: 'corARMA(q=1,value=.5,fixed=T)' and 'corARMA(q=1,value=-.5,fixed=T)' did NOT give me that error message, but 'corARMA(q=2,value=c(.8, -.5),fixed=T)' did. Then I checked a time series book for the conditions for invertibility. I found that all the roots of the characteristic equation must lie outside the unit circle. So I checked the following: round(Mod(polyroot(c(1, ma.coefs))), 3) [1] 1.069 0.995 0.995 0.995 0.995 0.995 0.995 0.995 0.995 1.069 1.069 1.069 [13] 0.995 0.995 0.995 0.995 1.069 1.069 1.069 1.069 1.069 1.069 1.069 1.069 [25] 1.930 Then I shrunk the ma.coefs' by 0.999 and got larger roots but still some inside the unit circle. So I tried 0.99 and 0.9 with the same result. With 0.8, all the roots were outside the unit circle. hope this helps. spencer graves [EMAIL PROTECTED] wrote: Dear Madams/Sirs, Hello. I am using the gls function to specify an arma correlation during estimation in my model. The parameter values which I am sending the corARMA function are from a previous fit using arima. I have had some success with the method, however in other cases I get the following error from gls: All parameters must be less than 1 in absolute value. None of the parameters (individually) are greater than or equal to 1. Please copy the code below into R to reproduce the error. Thanks. Is my logic incorrect? In the corARMA function, there's a call to pre-compiled C code with the name ARMA_unconstCoef. Is the source code for such compiled code freely available for download? Thanks for your suggestions. Sincerely Steve Gaffigan data=read.table(http://ak.aoos.org/data/sample_070989.dat,header=T) attach(data) mod.ols=lm(obs~model) mod.sma=arima(residuals(mod.ols),order=c(0,0,1),seasonal=list(order=c(0,0,2),period=12)) theta.1=mod.sma$coef[1] THETA.1=mod.sma$coef[2] THETA.2=mod.sma$coef[3] ma.coefs=c(-theta.1,double(10),-THETA.1,theta.1*THETA.1,double(10),-THETA.2,theta.1*THETA.2) library(nlme) mod.gls=gls(obs~model,correlation=corARMA(q=25,value=ma.coefs,fixed=T),method=ML) detach(data) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!
Re: [R] R-help Digest, Vol 33, Issue 27
From: Duncan Murdoch [EMAIL PROTECTED] I'd recommend using the RWinEdt package instead for a different way to integrate winedit with R. winedit and winedt are two different editors, last I checked. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help: conversion of long decimal numbers into hexadeci
On 10-Nov-05 Antje Döring wrote: Hi there, could somebody help me to convert a decimal number into a hexadecimal number? I know that there is the function sprintf, but the numbers I want to convert consist of 20 or more numbers. Spintf is not able to convert these big numbers. If I understand aright, you have decimal integers with 20 or more digits (and you want to get these as hexadecimal). You are probably out of luck for a direct approach, since 10^20 2^64 (indeed 2^66), so you will have overflowed a 64-bit integer. However, I'm not sure what the limitations on integer types are in R on all platforms. If, however, all you need is to do these conversions, and you do not really need to use R (how off-topic can I get ... ?), then (at any rate on Linux/Unix systems where the program is installed by default) you can use the aribitrary-precision calculator 'bc'. Session: $ bc bc 1.06 Copyright 1991-1994, 1997, 1998, 2000 Free Software Foundation, Inc. This is free software with ABSOLUTELY NO WARRANTY. For details type `warranty'. obase=16 1234567898765432123456789 1056E0F555A18EBDA7D15 123456789876543212345678987654321 6163E6712EBBAA4E3D62B41F4B1 12345678987654321234567898765432123456789876543212345678987654321 1E02BC221DC9369C8981C6F859501BD313D339F09180862B41F4B1 quit Und so weiter ... and of course you can go in the opposite direction by ibase=16 (to set hex as the input base) and obase=10 (to set decimal as the output base). 'bc' is a classic Unix tool, and features as an illoustration of complex programming in C, with lex and yacc and all, in The Unix Programming Environment (as I recall) by Kernighan and Ritchie. I don't need it often, but when you need it it's very handy (e.g. now). Hoping this helps, Ted. PS: $ bc -l bc 1.06 Copyright 1991-1994, 1997, 1998, 2000 Free Software Foundation, Inc. This is free software with ABSOLUTELY NO WARRANTY. For details type `warranty'. scale=1000 pi=4*a(1) pi 3.141592653589793238462643383279502884197169399375105820974944592307\ 81640628620899862803482534211706798214808651328230664709384460955058\ 22317253594081284811174502841027019385211055596446229489549303819644\ 28810975665933446128475648233786783165271201909145648566923460348610\ .. 08302642522308253344685035261931188171010003137838752886587533208381\ 42061717766914730359825349042875546873115956286388235378759375195778\ 18577805321712268066130019278766111959092164201988 (last digit wrong because of truncation) E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 10-Nov-05 Time: 17:28:05 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 32, Issue 26
r-help@stat.math.ethz.ch on Wednesday, October 26, 2005 at 6:00 AM -0500 wrote: Ronaldo, Try Harold's suggestion. The df still won't agree, because lmer (at least in its current version) just puts an upper bound on the df. But that should be OK, because all those t tests are approximations anyways, and you can get better confidence intervals (credible intervals, whatever) by using the mcmcsamp() function that works with lmer() alan Doran, Harold [EMAIL PROTECTED] responded: There is an issue with implicit nesting in lmer. In your lme() model you nest block/irrigation/density/fertilizer. In lmer you need to do something like (I dind't include all of your variables, but I think the makes the point) lmer(yield~irrigation*density*fertilizer+(1|fertilizer:density)+(1|density), data) Which notes that fertilizer is nested in density. Try this and then compare the results. Ronaldo Reis-Jr. [EMAIL PROTECTED], wrote: I make the correct model with aov, lme do compare with lmer. But I cant make a correct model in lmer. Look that the aov and lme results are similars, but very different from lmer. In aov and lme is used the correct DF for each variable, in lmer it use a same DF for all? Denom=54. -- Alan B. Cobo-Lewis, Ph.D. (207) 581-3840 tel Department of Psychology(207) 581-6128 fax University of Maine Orono, ME 04469-5742[EMAIL PROTECTED] http://www.umaine.edu/visualperception __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 32, Issue 26
In addition to the response below, Doug Bates has talked about this on
this list previously. I did
RSiteSearch('bates degrees of freedom lmer')
The first one that came up has Doug's response to this question as well
Harold
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Alan Cobo-Lewis
Sent: Wednesday, October 26, 2005 8:53 AM
To: r-help@stat.math.ethz.ch
Subject: Re: [R] R-help Digest, Vol 32, Issue 26
r-help@stat.math.ethz.ch on Wednesday, October 26, 2005 at 6:00 AM -0500
wrote:
Ronaldo,
Try Harold's suggestion. The df still won't agree, because lmer (at
least in its current version) just puts an upper bound on the df. But
that should be OK, because all those t tests are approximations anyways,
and you can get better confidence intervals (credible intervals,
whatever) by using the mcmcsamp() function that works with lmer() alan
Doran, Harold [EMAIL PROTECTED] responded:
There is an issue with implicit nesting in lmer. In your lme() model
you nest block/irrigation/density/fertilizer. In lmer you need to do
something like (I dind't include all of your variables, but I think
the makes the point)
lmer(yield~irrigation*density*fertilizer+(1|fertilizer:density)+(1|den
sity), data)
Which notes that fertilizer is nested in density.
Try this and then compare the results.
Ronaldo Reis-Jr. [EMAIL PROTECTED], wrote:
I make the correct model with aov, lme do compare with lmer.
But I cant make a correct model in lmer. Look that the aov and lme
results are similars, but very different from lmer. In aov and lme is
used the correct DF for each variable, in lmer it use a same DF for
all? Denom=54.
--
Alan B. Cobo-Lewis, Ph.D. (207) 581-3840 tel
Department of Psychology(207) 581-6128 fax
University of Maine
Orono, ME 04469-5742[EMAIL PROTECTED]
http://www.umaine.edu/visualperception
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 31, Issue 30
With lme4, use of mcmcsamp can be insightful. (Douglas Bates drew my attention to this function in a private exchange of emails.) The distributions of random effects are simulated on a log scale, where the distributions are much closer to symmetry than on the scale of the random effects themselves. As far as I can see, this is a straightforward use of MCMC to estimate model parameters; it is not clear to me the results from the lmer() fit are used. John Maindonald. On 30 Sep 2005, at 8:00 PM, [EMAIL PROTECTED] wrote: From: Roel de Jong [EMAIL PROTECTED] Date: 29 September 2005 11:19:38 PM To: r-help@stat.math.ethz.ch Subject: [R] standard error of variances and covariances of the randomeffects with LME Hello, how do I obtain standard errors of variances and covariances of the random effects with LME comparable to those of for example MlWin? I know you shouldn't use them because the distribution of the estimator isn't symmetric blablabla, but I need a measure of the variance of those estimates for pooling my multiple imputation results. Regards, Roel. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Bioinformation Science, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 31, Issue 9
?summary.lm and check the Value section.
Wuming
On 9/10/05, Ping Yao [EMAIL PROTECTED] wrote:
Hi:
I use lm (linear model) to analyze 47 variables , 8 responses
So I use loop to finish it .
I want the program to show the results that P-value is less than 0.05.
How can I cite the P-valus from lm result ?
Ping
The code:
#using LM to model general fati
for (j in 48:52) {
for (i in 3:46){
gen.fat-y_x[,j]
gen.fat-as.numeric(gen.fat)
snp_marker-y_x[,i]
x-colnames(y_x)
#snp_marker-as.matrix(snp_marker)
#mode(snp_marker)
cat(phenotype is = ,x[j] , \n)
cat(snp marker is = ,x[i] , \n)
zz-summary(lm.D9 - lm(gen.fat~snp_marker))
print(zz)
return
}
}
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 31, Issue 9
Hi Ping,
You can use zz$coefficients[,4] to get the p values for each estimated
coefficients in your context.
Wuming
On 9/11/05, Ping Yao [EMAIL PROTECTED] wrote:
Wuming:
Thanks for your help.
I use the fuction:
call(fstatistic,zz)
call(p-value,zz)
I can get each variable P-values,but I can't get P-value of the model.
How can I do ?
one of the results is following :
Call:
lm(formula = gen.fat ~ snp_marker)
Residuals:
Min 1Q Median 3Q Max
-10.5455 -3.0481 0.4545 3.9519 6.9519
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept)13.0481 0.4518 28.881 2e-16 ***
snp_markerallele2 0.5107 0.9102 0.561 0.5753
snp_markerBoth 1.4974 0.6927 2.162 0.0318 *
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 4.607 on 212 degrees of freedom
Multiple R-Squared: 0.02166,Adjusted R-squared: 0.01244
F-statistic: 2.347 on 2 and 212 DF, p-value: 0.0981
I use the code :
zz-summary(lm.D9 - lm(gen.fat~snp_marker))
coe-coef(lm.D9)# the bare coefficients
if (coe[2]=.05||coe[3]=.05||coe[4]=.05||coe[5]=.05) {
cat(phenotype is = ,x[j] , \n)
cat(snp marker is = ,x[i] , \n)
sign-call(fstatistic,zz)
call(p-value,zz)
#print(coe)
print(zz)
}
On 9/10/05, Wuming Gong [EMAIL PROTECTED] wrote:
?summary.lm and check the Value section.
Wuming
On 9/10/05, Ping Yao [EMAIL PROTECTED] wrote:
Hi:
I use lm (linear model) to analyze 47 variables , 8 responses
So I use loop to finish it .
I want the program to show the results that P-value is less than 0.05.
How can I cite the P-valus from lm result ?
Ping
The code:
#using LM to model general fati
for (j in 48:52) {
for (i in 3:46){
gen.fat-y_x[,j]
gen.fat-as.numeric(gen.fat)
snp_marker-y_x[,i]
x-colnames(y_x)
#snp_marker-as.matrix(snp_marker)
#mode(snp_marker)
cat(phenotype is = ,x[j] , \n)
cat(snp marker is = ,x[i] , \n)
zz-summary( lm.D9 - lm(gen.fat~snp_marker))
print(zz)
return
}
}
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 31, Issue 9
Hi:
I use lm (linear model) to analyze 47 variables , 8 responses
So I use loop to finish it .
I want the program to show the results that P-value is less than 0.05.
How can I cite the P-valus from lm result ?
Ping
The code:
#using LM to model general fati
for (j in 48:52) {
for (i in 3:46){
gen.fat-y_x[,j]
gen.fat-as.numeric(gen.fat)
snp_marker-y_x[,i]
x-colnames(y_x)
#snp_marker-as.matrix(snp_marker)
#mode(snp_marker)
cat(phenotype is = ,x[j] , \n)
cat(snp marker is = ,x[i] , \n)
zz-summary(lm.D9 - lm(gen.fat~snp_marker))
print(zz)
return
}
}
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 30, Issue 26
Dear R helpers, For me ( i.e. R 2.1.1 on Mac OS X), using trellis.device (postscript, onefile = F, etc ... with the lattice library within a R function works fine to obtain the desired graph as an EPS file , provided that : 1) the command dev.off() is not included in this function 2) and it is issued at the command level after the function has been exited I would like to know if there is a way to close the EPS file within the function itself, freeing the user to issue the closing command (I already tried trellis.device (), and trellis.device (null) without any success). Regards, J.-M. Jean-Marc Ottorini LERFoB, UMR INRA-ENGREF 1092 email [EMAIL PROTECTED] INRA - Centre de Nancy voice +33-0383-394046F54280 - Champenoux fax+33-0383-394034 France __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
Diego, Have you checked out the home site for nls2? Specifically the system requirements page? http://www.inra.fr/miaj/public/AB/nls2/available.html That says that nls2 requires a Unix-like operating system. Basically, the script for building the library is for such systems only, it also depends upon a lex (flex) library being available. Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of HM Diego Hernán Sent: 22 August 2005 18:47 To: r-help@stat.math.ethz.ch Subject: [R] R-help Hello I need help with the way to install nls2 library for windows, or the script that can be used for install the nls2 library. Do you know if this library works in windows? Best regards. Diego Rojas Cali-Colombia __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 30, Issue 6
On Fri, 5 Aug 2005 Julia Reid wrote: Subject: [R] GAP pointer I am trying to do a simple segregation analysis using the GAP package. I have the documentation for pointer but I desperately need an example so that I can see how to format the datfile and the jobfile. For each individual, I have FamilyId, SubjectId, FatherId, MotherId, and AffectedStatus (0/1). I would like to obtain the likelihood ratio statistic for transmission. I would greatly appreciate any help on this subject. Best to all, Julia Reid I wouldn't use Pointer myself (there are lots of more recent packages*), but look at the examples in http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/pointer/pointer.tar.Z and the manual, which is in the book: Morton N.E., Rao D.C Lalouel J-M (1983). Methods in Genetic Epidemiology. Karger PO Box, CH-4009 Basel (Switzerland). ISBN 3-8055-3668-2 which you will find in many academic libraries. David Duffy. * Don't you use Pap or JPap at Myriad? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 28, Issue 28
On Tuesday 28 June 2005 15:30, [EMAIL PROTECTED] wrote: Re : 37. Re: A. Mani : colours in Silhouette (Mulholland, Tom) Message: 37 Date: Tue, 28 Jun 2005 09:08:24 +0800 From: Mulholland, Tom [EMAIL PROTECTED] Subject: Re: [R] A. Mani : colours in Silhouette To: [EMAIL PROTECTED], r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 It's not so much a problem, as not working the way you expected. cluster:::plot.partition is used to do the plotting. If you look at the code for this you can see the difficulty in putting every possible permutation into the code. If for example you want the silhouette plot to be red using col = red is not intuitive as the cluster plot (which comes up first) has more than one colour. If you have a look at methods(plot) (assuming that you have loaded the cluster package) you will see that there is a specific piece of code in the form of plot.silhouette. It has an asterisk next to it so you need to use cluster:::plot.silhouette to see the code. It has what you need. args(cluster:::plot.silhouette) function (x, nmax.lab = 40, max.strlen = 5, main = NULL, sub = NULL, xlab = expression(Silhouette width * s[i]), col = gray, do.col.sort = length(col) 1, border = 0, cex.names = par(cex.axis), do.n.k = TRUE, do.clus.stat = TRUE, ...) data(ruspini) pr4 - pam(ruspini, 4) si - silhouette(pr4) plot(si,col = red) I tried that before with many more options and got a blank image. It must have been due to the options. The issue is that whenever code is written there is always a choice as to what functionality is put in place. Just because something can be done, does not mean it will or in some cases should be done. In this case the help for plot.partition notes that For more flexibility, use 'plot(silhouette(x), ...)', see 'plot.silhouette'. Tom Thanks for that I found out something I will find useful in the future. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of A. Mani Sent: Tuesday, 28 June 2005 4:30 AM To: r-help@stat.math.ethz.ch Subject: [R] A. Mani : colours in Silhouette Hello, In cluster analysis with cluster, how does one colour the silhouette plots ? For example in using pam. There seems to be some problem there. Everything else can be coloured. Thanks, A. Mani Member, Cal. Math. Soc __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] r-help
Sotdikov Mansor wrote: There is a function 'simMD()' in 'popgen' library which package, not library. simulates a sample of genotype data as follows: library(popgen) x - simMD(20, 2, 2, p = NULL, c(0.09, 0.05), ac = 2, beta = 1) x , , 1 [,1] [,2] [1,]11 [2,]11 ... [37,]12 [38,]22 [39,]22 [40,]22 , , 2 [,1] [,2] [1,]22 [2,]12 [3,]12 ... [38,]21 [39,]12 [40,]12 How can I repeat this function, for example, 1000 times to generate 1000 samples and assign each output to distinct 'vector' Xi, where i=1,2,...,1000 The above does not look like a vector (even if internally represented as such). The goal is to generate a large number of samples using this function and then use them in further analysis. I'd write them into a list by replicate(1000, YourCall) If you really want objects X1, ..., Xn, you should read the FAQ and ?assign. Uwe Ligges Any suggestions would be appreciated Sitdikov Mansor __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] r-help
Sotdikov Mansor [EMAIL PROTECTED] writes: There is a function 'simMD()' in 'popgen' library which simulates a sample of genotype data as follows: library(popgen) x - simMD(20, 2, 2, p = NULL, c(0.09, 0.05), ac = 2, beta = 1) x ... How can I repeat this function, for example, 1000 times to generate 1000 samples and assign each output to distinct 'vector' Xi, where i=1,2,...,1000 The goal is to generate a large number of samples using this function and then use them in further analysis. Any suggestions would be appreciated Sitdikov Mansor replicate(5, list(simMD(20, 2, 2, p = NULL, c(0.09, 0.05), ac = 2, beta = 1))) for larger values of 5 ;-) The list() is there to prevent dimensions from getting lost. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
On 6/21/05, McClatchie, Sam (PIRSA-SARDI) [EMAIL PROTECTED] wrote: Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 - Colleagues Is there a function in R that is an equivalent of zoom in matlab? This is very useful for being able to magnify details in a plot. I have searched the help for zoom, interactive zooming, and magnify. The R search engine (reached from help.start() ) keywords by topic entry for dynamic graphics seems to have no content, unless I made a mistake. From within R try: RSiteSearch(zoom) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
Try RSiteSearch(zoom plot). There are some good suggestions there. Cheers Francisco From: McClatchie, Sam (PIRSA-SARDI) [EMAIL PROTECTED] To: R-Help-Request (E-mail) r-help@stat.math.ethz.ch Subject: [R] R-help Date: Wed, 22 Jun 2005 09:05:05 +0930 Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 - Colleagues Is there a function in R that is an equivalent of zoom in matlab? This is very useful for being able to magnify details in a plot. I have searched the help for zoom, interactive zooming, and magnify. The R search engine (reached from help.start() ) keywords by topic entry for dynamic graphics seems to have no content, unless I made a mistake. Here is the matlab function description: --- zoom Zoom in and out on a 2-D plot Syntax zoom on zoom off zoom out zoom reset zoom zoom xon zoom yon zoom(factor) zoom(fig, option) Description zoom on turns on interactive zooming. When interactive zooming is enabled in a figure, pressing a mouse button while your cursor is within an axes zooms into the point or out from the point beneath the mouse. Zooming changes the axes limits. * For a single-button mouse, zoom in by pressing the mouse button and zoom out by simultaneously pressing Shift and the mouse button. * * For a two- or three-button mouse, zoom in by pressing the left mouse button and zoom out by pressing the right mouse button. Clicking and dragging over an axes when interactive zooming is enabled draws a rubber-band box. When the mouse button is released, the axes zoom in to the region enclosed by the rubber-band box. Double-clicking over an axes returns the axes to its initial zoom setting. zoom off turns interactive zooming off. zoom out returns the plot to its initial zoom setting. zoom reset remembers the current zoom setting as the initial zoom setting. Later calls to zoom out, or double-clicks when interactive zoom mode is enabled, will return to this zoom level. zoom toggles the interactive zoom status. zoom xon and zoom yon set zoom on for the x- and y-axis, respectively. zoom(factor) zooms in or out by the specified zoom factor, without affecting the interactive zoom mode. Values greater than 1 zoom in by that amount, while numbers greater than 0 and less than 1 zoom out by 1/factor. zoom(fig, option) Any of the above options can be specified on a figure other than the current figure using this syntax. Remarks zoom changes the axes limits by a factor of two (in or out) each time you press the mouse button while the cursor is within an axes. You can also click and drag the mouse to define a zoom area, or double-click to return to the initial zoom level. Best fishes Sam Sam McClatchie, Biological oceanography South Australian Aquatic Sciences Centre PO Box 120, Henley Beach 5022 Adelaide, South Australia email [EMAIL PROTECTED] Telephone: (61-8) 8207 5448 FAX: (61-8) 8207 5481 Research home page http://www.members.iinet.net.au/~s.mcclatchie/ /\ ...xX(° °)Xx / \\ (((° (((° ...xX(°O°)Xx __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 28, Issue 11
Dear all, I'm new using R and in (geo)statistics. I have a problem with solving my homework questions. We are working with variograms and trying to write down basic equations for different models (spherical, exponential, Gaussian). I tried to use the 'gstat' and 'geoR' packages to solve the questions but as I said before I'm new in R and always encountered with some syntax errors (I can send some specific examples later). If one of you used this packages and could help me, I will be very glad. Best Wishes, Emre Duran __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest, Vol 28, Issue 11
dwfu wrote: Dear all, I'm new using R and in (geo)statistics. I have a problem with solving my homework questions. We are working with variograms and trying to write down basic equations for different models (spherical, exponential, Gaussian). I tried to use the 'gstat' and 'geoR' packages to solve the questions but as I said before I'm new in R and always encountered with some syntax errors (I can send some specific examples later). If one of you used this packages and could help me, I will be very glad. Please read the posting guide which tells you: - Use an informative subject line. - Basic statistics and classroom homework: R-help is not intended for these. - Provide small reproducible examples. Uwe Ligges Best Wishes, Emre Duran __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help,
On May 19, 2005, at 7:01 AM, Jean Eid wrote:
I do not fully understand your example but if you need to act on the
columns of a dataframe why don't you just call its columns the title
you
want. something like
X-matrix(rnorm(1000), ncol=4)
colnames(X)-c(foo, foo1, foo2, foo3)
X-as.data.frame(X)
par(mfrow=c(2,2))
lapply(colnames(X), function(x) plot(X[,x], ylab=y, xlab=x,
main=x))
Taking this back a bit to the original question:
par(mfrow=c(4,3),mar=c(2, 4, 2, 1) + 0.1)
sapply(names(my.list) , function(x)
{
plot(colnames(my.list[[x]]) , apply(my.list[[x]],2,mean), type=o,
pch = 16, ylab = Index
, xlab = ,main=x)
}
)
HTH
Jean
On Thu, 19 May 2005, Luis Ridao Cruz wrote:
R-help,
I usually call lapply to plot some dat frames structures.Something
like
this:
par(mfrow=c(4,3),mar=c(2, 4, 2, 1) + 0.1)
lapply(my.list , function(x)
{
plot(colnames(x) , apply(x,2,mean), type=o, pch = 16, ylab =
Index
, xlab = )
}
)
But it is difficult for me to put a title on every plot according to
the list names.
I guess the re other ways to do it but the structure above is so handy
to me that I want to stick to it.
Any suggestions?
I run on Windows XP machine
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major2
minor1.0
year 2005
month04
day 18
language R
Thanks in advance
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Digest
On Fri, 6 May 2005, Sebastian Schoenherr wrote: Hi folks, I have to create my own time series, Is it possible to generate ARIMA time series, where i can define the range of the values in the y axis. (e.g: Values only between 0 and 1) No. Take a look at the definition of an ARIMA process. Suppose e.g. you have an AR(1) process. Then if innovations are positive and the coefficient is positive the value can be arbitrarily large. You can construct all sorts of similar counter-examples. This isn't a real problem is it? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [R-help] install problem
On Mon, 21 Mar 2005, Tae-Young Goo wrote: Hello. I've tried to install R to IBM AIX(v.5.1) machine. I've used compile options indicated by R-admin. There are several sets there, so which exactly? Then, I met following error messages. /home/local/R_2.0.1/lib/R/bin/exec/R is unchanged /home/local/R_2.0.1/lib/R/modules/R_X11.so is unchanged /home/local/R_2.0.1/lib/R/modules/internet.so is unchanged Those are not error messages. cp: lapack.so: file was not found. So there were some earlier error messages about that. This error has broken out at the last stage of make install Please let me know what is wrong. Please let us know what you did. In particular AIX is tricky, and you need to follow the instructions in the R-admin.html manual very carefully. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Time Series
I think 1) You have the units wrong: these appear to be the figures quoted for KB of compressed files, and the compression is nothing like 1024:1. 2) This is not `a series' unless you add a time base, e.g. via a call to ts(). Surely subscribers are aware that they do not get many MB/day and that extrapolation to that level is just speculation. On Sat, 26 Feb 2005 [EMAIL PROTECTED] wrote: Hi Folks, While I was browsing in the R-help archives yesterday, I got curious about the time series of the sizes of the monthly archives in MB. This turned out to have an unexpected feature or two, which I leave to readers to explore for themselves. I'm now wondering at what point in time we might expect to be receiving 1000MB/month (30+MB/day). It's not that far away, it seems, but there are a couple of interesting modelling questions behind it. In particular, I wonder by what mechanism the numbers grow, according to the law which the data seem to indicate. Over to you. (just my 0.001 MB worth ... excluding headers) Ted To save you the trouble, the following sets up the series: MB-c(55,19,19,18,19,17,35,27,47, 55,32,50,55,41,49,50,28,53,42,81,54, 99,60,84,80,76,75,78,61,83,97,141,122, 96,144,173,153,226,202,131,165,183,175,168,187, 240,272,262,195,236,244,285,249,326,345,392,268, 455,320,418,453,468,422,447,400,323,516,478,327, 450,487,535,658,573,606,659,543,655,722,677,567, 519,703,886,793,719,816,812,730,698,831,969,736, 855) April 1997 -- January 2005 E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Feb-05 Time: 10:31:05 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Time Series
On 26-Feb-05 Prof Brian Ripley wrote: I think 1) You have the units wrong: these appear to be the figures quoted for KB of compressed files, and the compression is nothing like 1024:1. Sorry, yes, you are correct: it is KB and not MB (a slip of the eye on my part). 2) This is not `a series' unless you add a time base, e.g. via a call to ts(). Well, in R terms that is strictly correct; but a sequence of data corresponding to successive regular time points is usually described as a time series! Surely subscribers are aware that they do not get many MB/day and that extrapolation to that level is just speculation. Granted (see above). But anyway, this sort of thing is not the real point, which is that (regardless of units) this 'sequence' of data has interesting features (which prompted me to submit my somewhat tongue-in-cheek posting). The original (quoted below) now suitably amended. On Sat, 26 Feb 2005 [EMAIL PROTECTED] wrote: Hi Folks, While I was browsing in the R-help archives yesterday, I got curious about the time series of the sizes of the monthly archives in KB [was MB]. This turned out to have an unexpected feature or two, which I leave to readers to explore for themselves. I'm now wondering at what point in time we might expect to be receiving 1000KB/month (30+KB/day) [was MB]. It's not that far away, it seems, but there are a couple of interesting modelling questions behind it. In particular, I wonder by what mechanism the numbers grow, according to the law which the data seem to indicate. Over to you. (just my 0.001 MB worth ... excluding headers) Ted To save you the trouble, the following sets up the sequence [was series; and MB]: KB-c(55,19,19,18,19,17,35,27,47, 55,32,50,55,41,49,50,28,53,42,81,54, 99,60,84,80,76,75,78,61,83,97,141,122, 96,144,173,153,226,202,131,165,183,175,168,187, 240,272,262,195,236,244,285,249,326,345,392,268, 455,320,418,453,468,422,447,400,323,516,478,327, 450,487,535,658,573,606,659,543,655,722,677,567, 519,703,886,793,719,816,812,730,698,831,969,736, 855) April 1997 -- January 2005 E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Feb-05 Time: 10:31:05 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Feb-05 Time: 12:06:29 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Time Series
Ted.Harding at nessie.mcc.ac.uk writes: : : Hi Folks, : : While I was browsing in the R-help archives yesterday, : I got curious about the time series of the sizes of : the monthly archives in MB. : : This turned out to have an unexpected feature or two, : which I leave to readers to explore for themselves. : : I'm now wondering at what point in time we might expect : to be receiving 1000MB/month (30+MB/day). It's not that : far away, it seems, but there are a couple of interesting : modelling questions behind it. : : In particular, I wonder by what mechanism the numbers : grow, according to the law which the data seem to indicate. : : Over to you. : : (just my 0.001 MB worth ... excluding headers) : : Ted : : To save you the trouble, the following sets up the series: : : MB-c(55,19,19,18,19,17,35,27,47, : 55,32,50,55,41,49,50,28,53,42,81,54, : 99,60,84,80,76,75,78,61,83,97,141,122, : 96,144,173,153,226,202,131,165,183,175,168,187, : 240,272,262,195,236,244,285,249,326,345,392,268, : 455,320,418,453,468,422,447,400,323,516,478,327, : 450,487,535,658,573,606,659,543,655,722,677,567, : 519,703,886,793,719,816,812,730,698,831,969,736, : 855) : : April 1997 -- January 2005 There were some discussions on this about a year ago: http://tolstoy.newcastle.edu.au/R/help/04/04/1071.html http://tolstoy.newcastle.edu.au/R/help/04/04/1095.html http://tolstoy.newcastle.edu.au/R/help/04/04/1109.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Time Series
Prof Brian Ripley wrote: I think 1) You have the units wrong: these appear to be the figures quoted for KB of compressed files, and the compression is nothing like 1024:1. 2) This is not `a series' unless you add a time base, e.g. via a call to ts(). Surely subscribers are aware that they do not get many MB/day and that extrapolation to that level is just speculation. So let's be immensely unfair and do some speculation ... Assuming 1000MB/month means a compressed archive file of (very) *roughly* 250MB. Looking at the data with linear models, lm(sqrt(MB) ~ monthindex) seems not to be the worst model (removing the first observation, perhaps). So a very *rough* extrapolation shows us that we will get 1000MB/month around 2142. I hope I'll get a better machine in 137 years to handle all the expected traffic. ;-) Best, Uwe On Sat, 26 Feb 2005 [EMAIL PROTECTED] wrote: Hi Folks, While I was browsing in the R-help archives yesterday, I got curious about the time series of the sizes of the monthly archives in MB. This turned out to have an unexpected feature or two, which I leave to readers to explore for themselves. I'm now wondering at what point in time we might expect to be receiving 1000MB/month (30+MB/day). It's not that far away, it seems, but there are a couple of interesting modelling questions behind it. In particular, I wonder by what mechanism the numbers grow, according to the law which the data seem to indicate. Over to you. (just my 0.001 MB worth ... excluding headers) Ted To save you the trouble, the following sets up the series: MB-c(55,19,19,18,19,17,35,27,47, 55,32,50,55,41,49,50,28,53,42,81,54, 99,60,84,80,76,75,78,61,83,97,141,122, 96,144,173,153,226,202,131,165,183,175,168,187, 240,272,262,195,236,244,285,249,326,345,392,268, 455,320,418,453,468,422,447,400,323,516,478,327, 450,487,535,658,573,606,659,543,655,722,677,567, 519,703,886,793,719,816,812,730,698,831,969,736, 855) April 1997 -- January 2005 E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Feb-05 Time: 10:31:05 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help Time Series
On 26-Feb-05 Uwe Ligges wrote: So let's be immensely unfair and do some speculation ... Assuming 1000MB/month means a compressed archive file of (very) *roughly* 250MB. Looking at the data with linear models, lm(sqrt(MB) ~ monthindex) seems not to be the worst model (removing the first observation, perhaps). Well, Uwe, disregarding the confusion over units, your model (and caveat) coincides with mine, leading to KB = (2.448731+0.282701*T + noise)^2 where T is in months and the first observation is at T=1. (Actually, I think the initial burn-in might be a bit longer, say over 3-4 months, and there is a slight suggestion that the growth has been slightly flattening out recently). And what intrigued me is the question: what mechanism might lead to a quadratic growth law? One possible interpretation is the following: Suppose that the number of postings is proportional to the number of R users. A quadratic has first difference linear in T. So the average number of additional postings per month can be seen as a sum of two components: a) a constant kernel b) a component proportional to the increment in postings in the previous month. Interpreting this as number of users, it could suggest that recruitment to R could be due to two causes: recruitment by a core of fixed size, and recruitment by recent recruits! Of course this is far from the only possibility. Another might be that postings to R-help reflect the number of issues that users are concerned to get help or information on. This might reflect: a) a core of die-hard FAQs asked by more and more people; b) a growing corpus of packages which more and more people need guidance with. And so on. An essential missing piece of data (where I'm concerned) is the sequence of numbers of subscribers to R-help. Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 26-Feb-05 Time: 14:00:46 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R-help
This is what you are trying to get at I think: dev.off() ## start with a new graphics device # X11() or postscript() #par(mar = c(3,3,1,3), oma = c(0,0,0,0), mgp = c(2, 1, 0), bg = white) par(mar = rep(5,4)) plot(x-rnorm(100),y-rnorm(100), ylab = This is y, xlab = This is x) z-rnorm(100)*250 par(new=T) ## Tell R not to reinitialize graphic device ## for subsequent plots plot(x,z,col='blue',axes=F, xlab=, ylab=) axis(side=4,col.axis='blue', labels = T) mtext(This is z, 4, 2, col = blue) par(new=F) HTH, Andy -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Luis Ridao Cruz Sent: Tuesday, February 22, 2005 9:29 AM To: r-help@stat.math.ethz.ch Subject: [R] R-help R-help, I am tring to create a plot with two y-axis. I found an example which is fine but the problem is that the range of the second y-axes appears in the first y-axes causing confusion. The example I refer to is : ## dev.off() ## start with a new graphics device # X11() or postscript() plot(x-rnorm(100),y-rnorm(100)) z-rnorm(100)*250 par(new=T) ## Tell R not to reinitialize graphic device ## for subsequent plots plot(x,z,col='blue',axes=F) axis(side=4,col.axis='blue') par(new=F) ## which can be found at : http://www.demog.berkeley.edu/faq/node21.html I also have a home made-example with exactly the same problem (pretty much the same as above) Any solution? Thanks in advance. version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.1 year 2004 month11 day 15 language R __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R-Help : running MIX package
On 28-Jan-05 Jeanhee Hong wrote: Hello all. I am inexperienced with R and am clumsily trying to work through it for specific multiple imputations Id like to run for my thesis.In running the MIX package, I keep getting an error message regarding the use of the prelim.mix command. Error in as.integer.default(list(alcohol = c(1, 1, 1, 1, 1, 1, 1, 1, 1, : (list) object cannot be coerced to integer I cannot find the source of this error. I am assuming its somewhere in the format of my data but cant quite seem to figure it out. I have followed the procedures in the manual in terms of listing categorical variables first and making sure they take positive integer values...Has anyone encountered this same error? Any help would be appreciated.Thank you. I have not seen such an error message myself, but the occurrence of list in it is ominous! According to the R code of prelim.mix, this should not be introduced by prelim.mix itself and so is likely to be somehow present in the data you submit to the function (which cannot be checked without looking at how you define your data). Please try the following. The function call prelim.mix(x,p) assumes that x is a *matrix* whose first p columns are the values of the p categorical variables (coded, as you note, as positive integers). So make sure that x is indeed a *matrix* and not some other R structure (which may, e.g. a data-frame, look like a matrix but isn't one). 'matrix' is a very specific data structure in R, and is not to be confused with other structures which may look like matrices. One way to ensure this could be to use x-as.matrix(your.data.frame) (assuming that your.data.frame already has its columns satisfying the requisite conditions). Another (which is what I've mainly used) is to construct x by using 'cbind': I've tended to find that for the sort of data one often gets, some preliminary manipulation of the categorical variables (at least) is required so as to get them into the required form, and this is best done separately. So, once you have established your p categorical variables cat1,...,catp and your k continuous variables cont1,...,contk, something like x - cbind(cat1,cat2,...,catp,cont1,cont2,...,contk) would create a matrix called x. Hoping this helps, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 [NB: New number!] Date: 28-Jan-05 Time: 09:52:02 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R-Help : running MIX package
On 28-Jan-05 Ted Harding wrote: On 28-Jan-05 Jeanhee Hong wrote: Hello all. I am inexperienced with R and am clumsily trying to work through it for specific multiple imputations Id like to run for my thesis.In running the MIX package, I keep getting an error message regarding the use of the prelim.mix command. Error in as.integer.default(list(alcohol = c(1, 1, 1, 1, 1, 1, 1, 1, 1, : (list) object cannot be coerced to integer [...] [...] So make sure that x is indeed a *matrix* and not some other R structure (which may, e.g. a data-frame, look like a matrix but isn't one). 'matrix' is a very specific data structure in R, and is not to be confused with other structures which may look like matrices. [...] By experiment I have confirmed my guess: with X a dataframe (30 rows, 4 cols of which the first two categorical) I get exactly the same error message as you with prelim.mix(X,2) whereas, after x - as.matrix(X) prelim.mix(x,2) everything is fine . Note that both X and x give outputs which look exactly the same, though they are not the same kind of object. Only 'x' will do for prelim.mix! Cheers, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 [NB: New number!] Date: 28-Jan-05 Time: 12:13:03 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help search and Java(tm)?
Dan Bolser [EMAIL PROTECTED] writes: I found this great search source(http://www.statslab.cam.ac.uk/~djw1005/Stats/Interests/search.R;) helpHTML() Has (or will) this become the standard search method? I think it got superseded by Jon Baron's RSiteSearch() function which is finding its way into r-devel. Is R 'Free Software'? The dependence on Java seems a bit of a pain for 'freeness'. A pain yes, but free software can rely on non-free compilers and OS's if need be. It's just more convenient to build on tools that everyone can get hold of. Did the above make it into CRAN? Well, you could check... It doesn't look like there is enough of the ancillary matter (help pages etc.) for a CRAN package. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help
I don't understand your question. PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html;. In particular, have you read the R Data Import / Export documentation that some with R [available, from www.r-project.org - Manuals or R - help.start()]? Have you tried read.spss in library(foreign)? [help(package=foreign) provides additional documentation.] If you've tried all these without satisfaction, please explain what you've tried, the error message, the version of R, operating system, etc., as requested in the posting guide. hope this helps. spencer graves gauri wrote: Hi, I was wondering as to how I could convert SPSS data imported to R into tabular form. In the sense, direct usage of read.table( ) doesnt help. Thanks - Meet the all-new My Yahoo! Try it today! [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
Did you do a search at www.r-project.org - R site search? Searching for .dbf there just now exposed a read.shape function in the maptools package. hope this helps. p.s. Did you read the posting guide! http://www.R-project.org/posting-guide.html;? Tips provided there may help you answer questions like this for yourself. Failing that, they may also help you formulate your questions so you are more likely to get useful replies. Buena suerte. Fuensanta Saura Igual wrote: Dear all, Does anyone know how to read files with .dbf extension? Thanks for your time. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
I believe .dbf files are more commonly DBase files, in which case see package RODBC. On Mon, 13 Sep 2004, Spencer Graves wrote: Did you do a search at www.r-project.org - R site search? Searching for .dbf there just now exposed a read.shape function in the maptools package. hope this helps. p.s. Did you read the posting guide! http://www.R-project.org/posting-guide.html;? Tips provided there may help you answer questions like this for yourself. Failing that, they may also help you formulate your questions so you are more likely to get useful replies. Buena suerte. Fuensanta Saura Igual wrote: Dear all, Does anyone know how to read files with .dbf extension? Thanks for your time. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-help
Hi Jim, you could try this: mat - matrix(sample(1:25), 5, 5) mat row(mat)[mat==max(mat)] col(mat)[mat==max(mat)] I hope it 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: Jim Gustafsson [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, August 25, 2004 11:07 AM Subject: [R] R-help Dear R users, I have just start working with R and would need some help. If you have a matrix as: [,1][,2] [,3] [1,] 11 24 11 [2,] 16 29 16 [3,]215 2 and you want the position where you can find the maximum value, in this case row 2 and column 2. How could you get the position? The values in the matrix is likelihood function values, and each row and column represent values from two parameters. So the idea is to seek which parameter values maximise the likelihood and therefore I need boot row and column position. Regards Jim -- This e-mail and any attachment may be confidential and may also be privileged. If you are not the intended recipient, please notify us immediately and then delete this e-mail and any attachment without retaining copies or disclosing the contents thereof to any other person. Thank you. -- [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.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://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help in Firefox on Windows XP
Thank you Brian, Installing 0.8 first and then upgrading solved the problem. I noticed that installing 0.9 from scratch creates a registry key [HKEY_LOCAL_MACHINE\SOFTWARE\mozilla.org\Mozilla] CurrentVersion=1.7 Installing 0.8 creates [HKEY_LOCAL_MACHINE\SOFTWARE\mozilla.org\Mozilla] CurrentVersion=1.6 and upgrading to 0.9 afterwards does not change this entry. This might be the reason. Prof Brian Ripley wrote: Works for me. Did it work with Firefox 0.8? (I upgraded from 0.8.) I would try 0.8 and then upgrade. On Thu, 17 Jun 2004, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? Prof Brian Ripley wrote: Works for me. Did it work with Firefox 0.8? (I upgraded from 0.8.) I would try 0.8 and then upgrade. On Thu, 17 Jun 2004, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? __ [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 help in Firefox on Windows XP
On Thu, 2004-06-17 at 12:06, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? Erich Erich, Do you also have JavaScript enabled in the Firefox Tools - Options settings? Both Java and JavaScript need to be enabled for the help.start() search engine to function properly. I reviewed the release notes at http://www.mozilla.org/products/firefox/releases/ and did not see anything relating to Java there, as had been the case with prior releases. The message that you are getting on the status line suggests that the R search applet is being found and properly enabled, which is typically the primary source of problems. Check the above and let us know. Marc Schwartz __ [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 help in Firefox on Windows XP
Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. A workaround (which is slow, provisional, and as yet untested on your configuration) is to use a different help engine, namely source(http://www.statslab.cam.ac.uk/~djw1005/Stats/Interests/search.R;) helpHTML() Damon. __ [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 help in Firefox on Windows XP
Works for me with Firefox 0.8. James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 Prof Brian Ripley [EMAIL PROTECTED] 06/17/04 02:10PM Works for me. Did it work with Firefox 0.8? (I upgraded from 0.8.) I would try 0.8 and then upgrade. On Thu, 17 Jun 2004, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [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-help
If you want pairwise correlations for the cols of matrix x and N is some parameter to your routine that does not vary throughout the calculation then: apply(x,2,function(a)apply(x,2,function(b)Transmer.cor(a,b,N))) Replace both occurrences of 2 with 1 if you want rows. Ruedi Epple ruedi.epple at bluewin.ch writes: : : Hi, : I have begun to use R some months ago. I have solved many problems, but now : I do not reach my aim. : I have written a function ?Tranmer.cor? with the parameters x, y and N, which : calculates weighted correlation coefficients. It works, when I define the : parameters each time I want to run it. But I cannot tell ?Tranmer.cor? that : it works trough a whole matrix, so that I get a correlation matrix with all : the combinations of variables I have in my data.frame. : There must be a little thing that I have not checked yet. : Thanks for your advice. : Ruedi Epple : : : Dr. Ruedi Epple : Stebligerweg 4 : CH-4450 Sissach : 061/971 67 15 : ruedi.epple at bluewin.ch : ruedi.epple at bfs.admin.ch : __ [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-help
Jim Gustafsson [EMAIL PROTECTED] wrote: I have a problem. Boy, do you ever. I would like to put my SAS-code into R. Could I do that, if yes, how? Right. I have a couple of questions for you too. (1) How long is a piece of string? (2) How do I bring peace, prosperity, and universal brotherhood to the world? Finally, let me draw your attention to the addendum which is appended to all r-help postings these days: PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html cheers, Rolf Turner [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
