Re: [R] ANOVA: Does a Between-Subjects Factor belong in the Error Term?
On 7/9/07, Alex Baugh <[EMAIL PROTECTED]> wrote: > > I am executing a Repeated Measures Analysis of Variance with 1 DV > (LOCOMOTOR > RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1 > Between-Subjects Factor (SEX). > > Does anyone know whether the between-subjects factor (SEX) belongs in the > Error Term of the aov or not? It does not. If you have between-subjects factors A, B and within-subjects factors X, Y, Z, use: aov( dv ~ a*b*x*y*z + Error(subj/(x*y*z)) The subj/(x*y*z) formula includes subj:x subj:y subj:z and all their interactions as error terms. The effect of a within subject factor 'x' is assessed against the error term subj:x -- Christophe Pallier (http://www.pallier.org) [[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] Help in installing rggobi in ubuntu linux
On 9 July 2007 at 22:38, Michael Lawrence wrote: | Looks like rggobi can't find GGobi. Make sure that PKG_CONFIG_PATH contains | the path to your ggobi.pc file. For example: | | export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig | | I would have assumed, however, that the ggobi package would have installed | to the /usr prefix, in which case pkg-config should have no problem finding | GGobi. | | On 7/8/07, Kenneth Cabrera <[EMAIL PROTECTED]> wrote: | > | > Hi R users. | > | > I am experimenting with ubuntu 7.04 Feisty. | > | > I install the ggobi package with apt-get. | > | > I got almost all the packages, but | > when I try to obtain rggobi, I got | > this message: Why don;t you install the Rggobi that is provided via Ubuntu? It is version 2.1.4-4-1 and it corresponds to the 2.1.4-2 version of Ggobi you just installed. Just do 'sudo apt-get install r-omegahat-ggobi' On Debian, we are now at 2.1.5-* for both (and we renamed it r-cran-rggobi as it now resides on CRAN). Hth, Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ 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] Help in installing rggobi in ubuntu linux
Looks like rggobi can't find GGobi. Make sure that PKG_CONFIG_PATH contains
the path to your ggobi.pc file. For example:
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
I would have assumed, however, that the ggobi package would have installed
to the /usr prefix, in which case pkg-config should have no problem finding
GGobi.
On 7/8/07, Kenneth Cabrera <[EMAIL PROTECTED]> wrote:
>
> Hi R users.
>
> I am experimenting with ubuntu 7.04 Feisty.
>
> I install the ggobi package with apt-get.
>
> I got almost all the packages, but
> when I try to obtain rggobi, I got
> this message:
>
>
> -
> install.packages("rggobi")
> Aviso en install.packages("rggobi") : argument 'lib' is missing: using
> '/usr/local/lib/R/site-library'
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> probando la URL
> 'http://cran.at.r-project.org/src/contrib/rggobi_2.1.4-4.tar.gz'
> Content type 'application/x-gzip' length 401451 bytes
> URL abierta
> ==
> downloaded 392Kb
>
> * Installing *source* package 'rggobi' ...
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for GGOBI... configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -g
> -DUSE_EXT_PTR=1 -D_R_=1 -fpic -g -O2 -c brush.c -o brush.o
> En el fichero incluÃdo de brush.c:1:
> RSGGobi.h:5:22: error: GGobiAPI.h: No existe el fichero ó directorio
> In file included from RSGGobi.h:6,
> from brush.c:1:
> conversion.h:174: error: expected â=â, â,â, â;â, âasmâ or
> â__attribute__â before âasCLogicalâ
> conversion.h:176: error: expected â=â, â,â, â;â, âasmâ or
> â__attribute__â before âasCRawâ
>
> --- snip ---
>
> brush.c:124: error: âtâ no se declaró aquà (primer uso en esta
> función)
> brush.c:124: error: âsâ no se declaró aquà (primer uso en esta
> función)
> brush.c:124: error: el objeto âGGOBI()â llamado
> no es una función
> brush.c: En el nivel principal:
> brush.c:135: error: expected â)â before âcidâ
> make: *** [brush.o] Error 1
> chmod: no se puede acceder a
> `/usr/local/lib/R/site-library/rggobi/libs/*': No existe el fichero ó
> directorio
> ERROR: compilation failed for package 'rggobi'
> ** Removing '/usr/local/lib/R/site-library/rggobi'
>
> The downloaded packages are in
> /tmp/RtmpVCacJd/downloaded_packages
> Warning message:
> installation of package 'rggobi' had non-zero exit status in:
> install.packages("rggobi")
>
> ---
>
> What am I doing wrong?
>
> Thank you for your help.
> --
> Kenneth Roy Cabrera Torres
> Cel 315 504 9339
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] CRANberries -- An RSS feed about New and Updated CRAN packages
LOL! -roger On 7/9/07, Barry Rowlingson <[EMAIL PROTECTED]> wrote: > Dirk Eddelbuettel wrote: > > > but the easiest way may just be to subscribe to Elijah's wonderful 'Planet > > R' > > feed aggregator > > My favourite RSS reader at the moment is the RSS cat caption generator: > > http://lol.ianloic.com/feed/dirk.eddelbuettel.com/cranberries/index.rss > > Barry > > __ > 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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] Within matrix
Unless you want to do this millions of times, efficiecy is probably not a big issue here, but simplicity always pays off. I'm presuming you are dealing with a single classification setup. Let f (n x 1) be a *factor* defining the classes Let X (n x p) be the data matrix. Then the steps I would use to find the between and within SSP matrices, 'by hand' are as follows: Tot <- scale(X, scale = FALSE) # sweep out the grand means Res <- resid(aov(X ~ f))# sweep out the class means WSS <- crossprod(Res) # within SSP matrix BSS <- crossprod(Tot - Res) # between SSP matrix Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, 10 July 2007 9:25 AM To: r-help@stat.math.ethz.ch Subject: [R] Within matrix Hi all, I am working on cluster, I am trying to evaluate a within and between matrix. Is there any facility for that ? I did my own function, but I am not a programmer, so I am affraid I am not really able to programme efficiant and fast function... Thanks Christophe Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre __ 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] Extracting sums for individual factors in data frames
Try this I used today aggregate(data, by=list(factor.name=data$FACTOR.NAME), sum) Norm Good CMIS/e-Health Research Centre A joint venture between CSIRO and the Queensland Government Lvl 20, 300 Adelaide Street BRISBANE QLD 4000 PO Box 10842 Adelaide Street BRISBANE QLD 4000 Ph: 07 3024 1640 Fx: 07 3024 1690 Em: [EMAIL PROTECTED] Web: http://e-hrc.net/ [[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] Question for svm function in e1071
thank you. This is definitely doable. - adschai- Original Message -From: David Meyer Date: Friday, July 6, 2007 6:34 amSubject: Re: [R] Question for svm function in e1071To: [EMAIL PROTECTED]: r-help@stat.math.ethz.ch> Adschai:> > The function is written in C++, so debugging the source code of > the R > svm() function will not really help. What you can do to make the > C-code > more verbose is the following:> > - get the sources of e1071> - in the src/ directory, look up the svm.cpp file> - In line 37, there is:> > > #if 0> void info(char *fmt,...)> > [...]> > replace the first line by:> > #if 1> > - build and install the package again.> > Best> David> > > > Sorry that I have many questions today. I am using svm function > on about> 180,000 points of training set. It takes very long time to run. > However,I would like it to spit out something to make sure that > the run is not> dead in between. Would you please suggest anyway to do ! so?> > [[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] making groups
It would be nice if you could supply an example of what your input looks like and then what you would like your output to look like. You would probably use 'tapply', but I would have to see what you data looks like. On 7/9/07, Mag. Ferri Leberl <[EMAIL PROTECTED]> wrote: > Dear everybody! > If I have an array of numbers e.g. the points my students got at an > examination, and a key to group the numbers, e.g. the key which > interval corresponds with which mark (two arrays of the same length or > one 2x(number of marks)), how can I get the array of absolute > frequencies of marks? > I hope I have expressed my problem clearly. > Thank you in advance. > Mag. Ferri Leberl > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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] Within matrix
Hi all, I am working on cluster, I am trying to evaluate a within and between matrix. Is there any facility for that ? I did my own function, but I am not a programmer, so I am affraid I am not really able to programme efficiant and fast function... Thanks Christophe Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre __ 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] parsing strings
Is this what you want:
> x <- "A10B10A10 B5AB 10 CD 12A10CD2EF3"
> x <- gsub(" ", "", x) # remove blanks
> y <- gregexpr("[A-Z]+\\s*[0-9]+", x )[[1]]
>
> substring(x, y, y + attr(y, 'match.length') - 1)
[1] "A10" "B10" "A10" "B5" "AB10" "CD12" "A10" "CD2" "EF3"
>
On 7/9/07, Drescher, Michael (MNR) <[EMAIL PROTECTED]> wrote:
> Hi All,
>
>
>
> I have strings made up of an unknown number of letters, digits, and
> spaces. Strings always start with one or two letters, and always end
> with one or two digits. A set of letters (one or two letters) is always
> followed by a set of digits (one or two digits), possibly with one or
> more spaces between the sets of letters and digits. A set of letters
> always belongs to the following set of digits and I want to parse the
> strings into these groups. As an example, the strings and the desired
> parsing results could look like this:
>
>
>
> A10B10, desired parsing result: A10 and B10
>
> A10 B5, desired parsing result: A10 and B5
>
> AB 10 CD 12, desired parsing result: AB10 and CD12
>
> A10CD2EF3, desired parsing result: A10, CD2, and EF3
>
>
>
> I assume that it is possible to search a string for letters and digits
> and then break the string where letters are followed by digits, however
> I am a bit clueless about how I could use, e.g., the 'charmatch' or
> 'parse' commands to achieve this.
>
>
>
> Thanks a lot in advance for your help.
>
>
>
> Best, Michael
>
>
>
>
>
>
>
> Michael Drescher
>
> Ontario Forest Research Institute
>
> Ontario Ministry of Natural Resources
>
> 1235 Queen St East
>
> Sault Ste Marie, ON, P6A 2E3
>
> Tel: (705) 946-7406
>
> Fax: (705) 946-2030
>
>
>
>
>[[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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parsing strings
strapply in package gsubfn can do that. The following matches the
indicated regular expression against x and applies the function
given in formula notation (which removes spaces) to each match,
outputting the result as a list:
library(gsubfn)
x <- c("AB10B10", "A10 B5", "AB 10 CD 12", "A10CD2EF3")
strapply(x, "[[:alpha:]] *[[:digit:]]+", ~ gsub(" ", "", x))
For more info, see the gsubfn home page at:
http://code.google.com/p/gsubfn/
and the various Links there.
On 7/9/07, Drescher, Michael (MNR) <[EMAIL PROTECTED]> wrote:
> Hi All,
>
>
>
> I have strings made up of an unknown number of letters, digits, and
> spaces. Strings always start with one or two letters, and always end
> with one or two digits. A set of letters (one or two letters) is always
> followed by a set of digits (one or two digits), possibly with one or
> more spaces between the sets of letters and digits. A set of letters
> always belongs to the following set of digits and I want to parse the
> strings into these groups. As an example, the strings and the desired
> parsing results could look like this:
>
>
>
> A10B10, desired parsing result: A10 and B10
>
> A10 B5, desired parsing result: A10 and B5
>
> AB 10 CD 12, desired parsing result: AB10 and CD12
>
> A10CD2EF3, desired parsing result: A10, CD2, and EF3
>
>
>
> I assume that it is possible to search a string for letters and digits
> and then break the string where letters are followed by digits, however
> I am a bit clueless about how I could use, e.g., the 'charmatch' or
> 'parse' commands to achieve this.
>
>
>
> Thanks a lot in advance for your help.
>
>
>
> Best, Michael
>
>
>
>
>
>
>
> Michael Drescher
>
> Ontario Forest Research Institute
>
> Ontario Ministry of Natural Resources
>
> 1235 Queen St East
>
> Sault Ste Marie, ON, P6A 2E3
>
> Tel: (705) 946-7406
>
> Fax: (705) 946-2030
>
>
>
>
>[[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] Split graphs
How many columns do you have? Is it 2 or 1000; can not tell from your email. A histogram of 2 values does not seem meaningful. Do you want 1000 separate histograms, one per page, or multiple per page? Yes you can do it, the question is what/how do you want to do it. On 7/9/07, tian shen <[EMAIL PROTECTED]> wrote: > Hello All, > I have a question, which somehow I think it is easy, however, I just > couldn't get it. > I want to histogram each row of a 1000*2 matrix( means it has 1000 rows), > and I want to see those 1000 pictures together. How can I do this? Am I able > to split a graph into 1000 parts and in each parts it contains a histogram > for one row? > > Thank you very much > > Jessie > > > - > > >[[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. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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] histogram with absolute figures
Well, how about an example of what you are doing, and a description of what the results you get and the results you want are? When I do a histogram, I get frequencies. Sarah On 7/9/07, Mag. Ferri Leberl <[EMAIL PROTECTED]> wrote: > Meanwhile I have recognized, that the breaks-option enforces density as > the default. But if I try to force frequencies (freq=TRUE) I get the > following feedback: > > Warning message: > the AREAS in the plot are wrong -- rather use freq=FALSE in: > plot.histogram(r, freq = freq, col = col, border = border, angle = > angle, > > And the machine hasn't promised too much: the result IS wrong. > Yours, > Mag. Ferri Leberl > > > > Am Freitag, den 06.07.2007, 16:17 -0400 schrieb Sarah Goslee: > > The default of hist() is counts rather than percentages. > > > > Sarah > > > > On 7/6/07, Mag. Ferri Leberl <[EMAIL PROTECTED]> wrote: > > > Dear everybody! > > > Is ist easily possible to make up a histogram with absolute numbers > > > instead of percentages? > > > Thank you in advance! > > > Yours, Mag. Ferri Leberl > > > > > > ___ > > -- 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] how to use mle with a defined function
Hi all,
sorry for the misleading in the previous email. here is my function to
calculate the maximum likelihood function for a multinormial distribution:
mymle <- function (sigmaX, sigmaY, constraints, env){
# build omega
omegaX = abs(sigmaX) * kin + abs(env) * diag(1.0, n, n)
omegaY = abs(sigmaY) * kin + abs(env) * diag(1.0, n, n)
omegaXY = (sqrt(sigmaX * sigmaY) - abs(constraints)) * kin
omega = array(0, c(2*n, 2*n))
for(i in 1:n){
for(j in 1:n){
omega[i, j] = omegaX[i, j]
omega[i+n, j+n] = omegaY[i, j]
omega[i+n, j] = omegaXY[i, j]
omega[i, j+n] = omegaXY[i, j]
}
}
# obtain det of omega
odet = unlist(determinant(omega))[1]
# Cholesky decomposition
C = chol(omega)
# beta parameter estimates
newY = t(C)%*%Y
newX = t(C)%*%X
# maximum likelihood estimates
Z = Y - X%*%(lm(newY~newX-1)$coef)
V = solve(t(C), Z)
# compute the -2log-likelihood
square = t(V)%*%V
0.5*odet + 0.5*square
}
here kin, n, X and Y are known, for example
> kin
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.02276611 0.04899597 0.05076599 0.06727600 0.05561066 0.05561066
[2,] 0.04899597 1.02087402 0.11497498 0.07623291 0.06423950 0.06423950
[3,] 0.05076599 0.11497498 1.02291870 0.07189941 0.11162567 0.11162567
[4,] 0.06727600 0.07623291 0.07189941 1.03277588 0.05522156 0.05522156
[5,] 0.05561066 0.06423950 0.11162567 0.05522156 1.03971863 0.54769897
[6,] 0.05561066 0.06423950 0.11162567 0.05522156 0.54769897 1.03971863
> Y
[1] 0.4054651 0.6931472 0.7884574 0.6931472 0.5306283 0.5306283 3.1696856
3.5467397 3.5862929 2.5494452 3.1354942 3.2188758
> X
[,1] [,2] [,3] [,4]
[1,]1 6900
[2,]1 6500
[3,]1 5000
[4,]1 5400
[5,]1 4800
[6,]1 4200
[7,]0011
[8,]0012
[9,]0012
[10,]0012
[11,]0011
[12,]0011
> n
[1] 6
when I call the function
fit <- mle(corr_add, start=list(sigmaX=0.855, sigmaY=0.5, constraints=0.15,
env=0.199),
method = "L-BFGS-B", lower=c(0.001, 0.001, 0.001, 0.001),
upper=c(1000,1000,1000,1000))
it always gave me error message something like
"Error in chol(omega) : the leading minor of order 8 is not positive
definite"
I checked the eigenvalues at each iteration and found that when it stopped
there existed negative eigenvalues. I don't know why this is not working
since omega supposed to be positive definite at each iteration. Any hints
would be very appreciated.
Lin
Lin Pan wrote:
>
> Hi all,
>
> I am trying to use mle() to find a self-defined function. Here is my
> function:
>
> test <- function(a=0.1, b=0.1, c=0.001, e=0.2){
>
> # omega is the known covariance matrix, Y is the response vector, X is the
> explanatory matrix
>
> odet = unlist(determinant(omega))[1]
>
> # do cholesky decomposition
>
> C = chol(omega)
>
> # transform data
>
> U = t(C)%*%Y
> WW=t(C)%*%X
>
> beta = lm(U~W)$coef
>
> Z=Y-X%*%beta
> V=solve(t(C), Z)
>
> 0.5*odet + 0.5*(t(V)%*%V)
>
> }
>
> and I am trying to call mle() to calculate the maximum likelihood
> estimates for function (0.5*odet+0.5*(t(V)%*%V)) by
>
> result = mle(test, method="Nelder-Mead")
>
> But I get the following error message:
>
> Error in optim(start, f, method = method, hessian = TRUE, ...) :
> (list) object cannot be coerced to 'double'
>
> I am pretty sure that the matrices, parameters etc are numerical before
> importing to the function. But why I still get such error message? Could
> anybody give some help on this? thanks a lot.
>
>
> Lin
>
--
View this message in context:
http://www.nabble.com/how-to-use-mle-with-a-defined-function-tf4015002.html#a11511446
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Split graphs
Jessie: How many pixels would you need to allocate for each of these 1000 parts? Is that feasible? Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of tian shen Sent: Monday, July 09, 2007 3:43 AM To: r-help@stat.math.ethz.ch Subject: [R] Split graphs Hello All, I have a question, which somehow I think it is easy, however, I just couldn't get it. I want to histogram each row of a 1000*2 matrix( means it has 1000 rows), and I want to see those 1000 pictures together. How can I do this? Am I able to split a graph into 1000 parts and in each parts it contains a histogram for one row? Thank you very much Jessie - [[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.
[R] parsing strings
Hi All, I have strings made up of an unknown number of letters, digits, and spaces. Strings always start with one or two letters, and always end with one or two digits. A set of letters (one or two letters) is always followed by a set of digits (one or two digits), possibly with one or more spaces between the sets of letters and digits. A set of letters always belongs to the following set of digits and I want to parse the strings into these groups. As an example, the strings and the desired parsing results could look like this: A10B10, desired parsing result: A10 and B10 A10 B5, desired parsing result: A10 and B5 AB 10 CD 12, desired parsing result: AB10 and CD12 A10CD2EF3, desired parsing result: A10, CD2, and EF3 I assume that it is possible to search a string for letters and digits and then break the string where letters are followed by digits, however I am a bit clueless about how I could use, e.g., the 'charmatch' or 'parse' commands to achieve this. Thanks a lot in advance for your help. Best, Michael Michael Drescher Ontario Forest Research Institute Ontario Ministry of Natural Resources 1235 Queen St East Sault Ste Marie, ON, P6A 2E3 Tel: (705) 946-7406 Fax: (705) 946-2030 [[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] Split graphs
Hello All, I have a question, which somehow I think it is easy, however, I just couldn't get it. I want to histogram each row of a 1000*2 matrix( means it has 1000 rows), and I want to see those 1000 pictures together. How can I do this? Am I able to split a graph into 1000 parts and in each parts it contains a histogram for one row? Thank you very much Jessie - [[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] making groups
Dear everybody! If I have an array of numbers e.g. the points my students got at an examination, and a key to group the numbers, e.g. the key which interval corresponds with which mark (two arrays of the same length or one 2x(number of marks)), how can I get the array of absolute frequencies of marks? I hope I have expressed my problem clearly. Thank you in advance. Mag. Ferri Leberl __ 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] Subject: transform excel data into graph
Is this you want?
library(gplots)
n
<-(0.465,0.422,0.45,0.59,0.543,0.498,0.44,0.35,0.64,0.5,0.473,0.134,0.543,0.
11,0.32)
graph <- matrix(n, nrow=5, ncol=3)
colnames(graph) <- c("Nick", "John", "Peter")
rownames(graph) <- c("Lesson1","Lesson2","Lesson3", "Lesson4","Lesson5")
g <- barplot2(graph, beside = TRUE,
col = "black",
angle=c(45,45,90,-45,180),
density=c(0,20,20,20,20),
legend = rownames(graph),
ylim = c(0, 1),
ylab="lable here",
plot.grid = TRUE)
N.Nguyen
What I want to do is a 2d-graph plot where I will have the name of the
student in the X-axis and the name of the lesson in the Y-axis and the
number from each pair will be used to construct the plot. I am newbie with R
and I don't know which package shall I use nor the commands with which I
will import my data in R so that the plot will be created...
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Writing Excel (.xls) files on non-Windows OSs using Perl
Since I wrote the xls2csv.pl and read.xls() code for gdata, a perl module for writing MS-Excel files has come on the scene. I don't have the time at the moment to create an csv2xls.pl file, but it should be straightforward, and I would gladly add it to the gdata package. -G On Jul 9, 2007, at 12:15PM , Uwe Ligges wrote: > > > Gabor Grothendieck wrote: >> Note that there already is a function, read.xls, in gdata that >> uses Perl. > > Note that Marc talked about *writing* in his original message. > > Uwe Ligges > > >> On 7/9/07, Marc Schwartz <[EMAIL PROTECTED]> wrote: >>> On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote: Hi, 2007/7/8, Marc Schwartz <[EMAIL PROTECTED]>: > [snip] > There exists the xlsReadWrite package on CRAN by Hans-Peter > Suter, which > is restricted to Windows, since it utilizes the non-FOSS MS > Office API > to write the Excel formats. The non-FOSS API is not the problem(#) but its implementation is: The 3rd party library I use is written in Pascal and supports Delphi and Kylix. Kylix would allow to port the package to Linux but as Kylix has unfortunately been abandoned by CodeGear (Borland) I am not ready/interested to spend my time on this dead road. Though it probably could be done quickly. A much more interesting way is to port the package using FreePascal. --> I plan to do this since long but... --> Maybe someone fluent on Linux and FreePascal could have a look at the pascal header files (treetron.googlepages.com) and make the demos run on Linux..., that would be great and speed up an eventual xlsReadWrite port! >>> Thanks for the clarification. >>> >>> However, I think that if you are going to pursue a cross-platform >>> solution, providing source code requiring compilation (as opposed >>> to a >>> pre-compiled Windows binary), you should consider what the >>> installation >>> requirements for your package would then be. >>> >>> If you are going to take the step of requiring a prospective end- >>> user to >>> have a particular Pascal compiler in place, you may as well have the >>> requirement for a Perl interpreter and associated packages. Since >>> Perl >>> is widely available and you are more likely to find Perl-fluent >>> coders >>> as opposed to Pascal-fluent coders (eg. I have not used Pascal >>> since the >>> late 80's), I would urge you to consider Perl as a future >>> substrate for >>> your functions. >>> >>> While compiled code will run faster than interpreted code, for these >>> types of file I/O functions, I am not sure that you lose much >>> with Perl >>> from a performance standpoint and you certainly gain the eyes of >>> a wider >>> audience with respect to use, debugging and enhancements. >>> >>> To that end, you (or any other interested parties) are free to >>> utilize >>> my code in any way you deem appropriate. I did not state this in my >>> original post, but I make the code available under GPL(v2), >>> freeing you >>> from any restrictions in its use, including your "Pro" version, >>> as long >>> as you make the source available in a fashion consistent with the >>> GPL >>> requirements. >>> >>> Regards, >>> >>> 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. >>> >> >> __ >> 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.
[R] Problems with e1071 and SparseM
Chris: yes, this is indeed a bug (in predict.svm) - will be fixed in the next release of e1071. Thanks for pointing this out, David -- Hello all, I am trying to use the "svm" method provided by e1071 (Version: 1.5-16) together with a matrix provided by the SparseM package (Version: 0.73) but it fails with this message: > > model <- svm(lm, lv, scale = TRUE, type = 'C-classification', kernel = 'linear') Error in t.default(x) : argument is not a matrix although lm was created before with read.matrix.csr (from the e1071) package. I also tried to simply convert a normal matrix to a SparseM matrix and then pass it, but I get the same error again. According to the manual of svm(), this is supposed to work though: " x: a data matrix, a vector, or a sparse matrix (object of class 'matrix.csr' as provided by the package 'SparseM')." Used R version: R version 2.4.0 Patched (2006-11-25 r39997) Does anyone know how I can use Sparse Matrices with e1071? This would be really important because the matrix is simply too large to write it out. Best regards, Chris __ 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] histogram with absolute figures
Meanwhile I have recognized, that the breaks-option enforces density as the default. But if I try to force frequencies (freq=TRUE) I get the following feedback: Warning message: the AREAS in the plot are wrong -- rather use freq=FALSE in: plot.histogram(r, freq = freq, col = col, border = border, angle = angle, And the machine hasn't promised too much: the result IS wrong. Yours, Mag. Ferri Leberl Am Freitag, den 06.07.2007, 16:17 -0400 schrieb Sarah Goslee: > The default of hist() is counts rather than percentages. > > Sarah > > On 7/6/07, Mag. Ferri Leberl <[EMAIL PROTECTED]> wrote: > > Dear everybody! > > Is ist easily possible to make up a histogram with absolute numbers > > instead of percentages? > > Thank you in advance! > > Yours, Mag. Ferri Leberl > > > > ___ __ 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] factanal frustration!
factanal() does not have an argument method="mle". Trying to do factor analysis on 1000 columns is quite unrealistic, but you may find rescaling the matrix helps. On Mon, 9 Jul 2007, Talbot Katz wrote: > Hi. > > It seems that nearly every time I try to use factanal I get the following > response: > >> faa2db1<-factanal(mretdb1,factors=2,method="mle",control=list(nstart=25)) > Error in factanal(mretdb1, factors = 2, method = "mle", control = > list(nstart = 25)) : >unable to optimize from these starting value(s) >> > > In the case cited above, mretdb1 is synthetic data created from two factors, > that is, mretdb1 has dimensions 3050*1000, and each of the thousand columns > has the form > c[i]=a1[i]*f1 + a2[i]*f2 + a3[i]*fn[,i] > where a1, a2, a3 are each vectors of length 1000, f1 and f2 are vectors of > length 3050, and fn is a matrix of dimension 3050*1000, such that f1, f2, > and all the columns of fn are mutually uncorrelated. I wanted to see how > closely the factors returned by factanal are to the ones that generated the > data. But, as you can see, factanal hasn't cooperated! > > I would greatly appreciate advice from factanal users, especially those who > have experienced the same error. Thanks! > > -- TMK -- > 917-656-5351 cell > 212-460-5430 home > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ANOVA: Does a Between-Subjects Factor belong in the Error Term?
Alex Baugh wrote: > I am executing a Repeated Measures Analysis of Variance with 1 DV (LOCOMOTOR > RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1 > Between-Subjects Factor (SEX). > > Does anyone know whether the between-subjects factor (SEX) belongs in the > Error Term of the aov or not? And if it does belong, where in the Error Term > does it go? The 3 possible scenarios are listed below: > > > > e.g., > > 1. Omit Sex from the Error Term: > > >> My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error >> > (Subject/(Timepoint*Acx.Cond)), data=locomotor.tab) > > note: Placing SEX outside the double paretheses of the Error Term has the > same statistical outcome effect as omitting it all together from the Error > Term (as shown above in #1). > > > > 2. Include SEX inside the Error Term (inside Double parentheses): > > >> My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error >> > (Subject/(Timepoint*Acx.Cond+Sex)), data=locomotor.tab) > > > > 3. Include SEX inside the Error Term (inside Single parentheses): > > > >> My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error >> > (Subject/(Timepoint*Acx.Cond)+Sex), data=locomotor.tab) > > note: Placing SEX inside the single parentheses (as shown above in #3) > generates no main effect of Sex. Thus, I'm fairly confident that option #3 > is incorrect. > > > > Scenarios 1,2, and 3 yield different results in the aov summary. > > You don't generally want terms with systematic effects to appear as error terms also, so 3 is wrong. In 2 you basically have a random effect of sex within subject, which is nonsensical since the subjects presumably have only one sex each. This presumably generates an error stratum with 0 DF, which may well be harmless. That leaves 1 as the likely solution. You'll probably do yourself a favour if you learn to expand error terms, a/b == a + a:b, etc.; that's considerably more constructive than trying to think in terms of whether things are inside or outside parentheses. > > Thanks for your help! > > Alex > > > > > > __ 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] Antwort: Re: pgup/pgdown in R Graphics Window under Linux ['Watchdog': checked]
On 7/8/07, Paul Matthias Diderichsen <[EMAIL PROTECTED]> wrote: > Hi Deepayan, > > "Deepayan Sarkar" <[EMAIL PROTECTED]> schrieb am 06.07.2007 > 02:05:02: > > On 7/5/07, Paul Matthias Diderichsen > > <[EMAIL PROTECTED]> wrote: > >> library(lattice) > >>> xyplot(speed~dist|speed, data=cars, layout=c(3,3)) > > If this is your use case, you might be interested in > > http://cran.r-project.org/src/contrib/Descriptions/plotAndPlayGTK.html > > Thanks a lot for the pointer; this package seems to be very useful when > coding your own plots. However, it's not exactly my use case - rather an > example to illustrate the the X11 graphics device is apparently not too > useful for multi-page plots. > > The motivation for my question was that I want to use xpose4 ( > http://xpose.sourceforge.net/) under linux. Xpose is a program that > provides functions for producing diagnostic plots for population PKPD > model evaluation. I am not able to rewrite the entire package, wrapping > every call to multi-page plot functions with plotAndPlayGTK. > > That's why I was hoping that there exist some obscure configuration option > for X11 (seems not to be the case, cf. Prof Ripley's reply) or an > alternative graphic device that runs under linux. The tools seem to be there already (recordPlot and replayPlot), and it seems mostly a matter of capturing the relevant keypresses etc. I have no idea how hard that would be with the X11 device, but I have added some basic functionality to the Qt based device I've been playing with. You are welcome to try it --- details can be found at http://dsarkar.fhcrc.org/R/R-Qt.html I'm sure doing something similar with the Gtk/Cairo devices wouldn't be too hard (for those who know what they are doing). -Deepayan __ 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] Loading problem with XML_1.9
Weijun and I corresponded off-list so that I could
get a copy of the data.
On a relatively modest machine with 2G of RAM, 10G swap,
dual core 1Ghz 64bit AMDs, the code below takes approximately
100 seconds. It is not optimized in any particular way, so
there is room for improvement.
doc <- xmlTreeParse("mi1.txt.gz", useInternal = TRUE)
mols <- getNodeSet(doc, "//molecule")
ans =
lapply(mols,
function(node, targets) {
names = as.character(xpathApply(node, "//name/text()",
xmlValue))
if(any(names %in% targets))
xpathApply(node, "//moleculeName", xmlValue)
else
character()
}, c("Vps4b", "SKD1", "frm-1"))
ans = ans[sapply(ans, length) > 0]
We can read the file without uncompressing which probably
slows things down slightly.
The parsing of the tree takes about 20 seconds and occupies
approximately 1G (very roughly).
Then we find all the nodes of which there
are 25452. Then we loop over each of these and
do a sub-query using XPath and see if
the text child in the nodes are in the set
of interest (entirely made up for my test), and if so
fetch the content of any within this
node.
It would be nice if we could build the hash for targets
just once.
And we could get clever with the XPath query to try do
the matching and selection in one query. This might actually slow things
down.
(There are garbage collection issues with XPath sub-queries
for which I am still deciding on the optimal strategy.)
So perhaps the lesson her is that for those working with XML,
XPath is worth using before more specialized approaches
and large XML data files can fit into memory. The tree
is not using contiguous memory so nodes can be squeezed into
available spaces.
D.
Luo Weijun wrote:
> Thanks, Dr. Lang,
> I used xmlEventParse() + branches concept as you
> suggested, it really works, and the memory issue is
> gone. Now I can query large XML files from within R.
> but here is another problem: it is too slows (a simple
> query has not finished for 1.5h), even though the
> number of relevant records is very limited, but the
> whole XML file has more than 500 thousand
> similarly-structured records. And the parser has to go
> through all of them as to find the matches. Attached
> is part of the XML files with two records. I am trying
> to retrieve the content of nodes from
> records where nodes bear specific
> gene names.
> Is it possible to locate based on node content (or
> xmlValue) rather than node names (since they are the
> same in all records) first and then parse the xml
> record locally? Would query based on XPath be faster
> in this case? I understand that we do have the
> facility in the XML package for XPath based queries,
> called getNodeSet(). But that requires reading the
> whole XML tree into the memory first, which is not
> feasible for my large XML file. Or can I call
> XML::XPath statements using your R-Perl interface
> package? Any suggestions/thoughts? Thank you!
> Weijun
>
>
> Part of my XML file:
>
>
> 20119043
> protein20
> 1009020
> 20GI6677981
> SKD120
> Vps4b20
> 8030489C12Rik20
> Mouse homologue of
> yeast Vacuolar protein sorting 4 (Vps4); Suppressor of
> potassium transport defect 1. Mem
> ber of mammalian class E Vps proteins involved in
> endosomal transport; AAA-type
> ATPase.20Mo
> use homologue of yeast Vacuolar protein sorting 4
> (Vps4); Suppressor of potassium transport defect 1.
> Member of mammalian class E Vps prot
> eins involved in endosomal transport; AAA-type
> ATPase.20
>
> 337974miClust80
>
>
> 200
>
> 20158189434SBP1
> 00
> 20158217953mVps2
> 00
>
>
>
> 30116226
> protein30
> 960630
> 30HGNC9859
> RAP1GDS130
> GDS130
> MGC11885930
> MGC11886130
>
> 300
>
> 93569116280RAC1
> 00
> 104132103040RHOA
> 00
> 12181874726MBIP
> 00
>
>
> --- Duncan Temple Lang <[EMAIL PROTECTED]>
> wrote:
>
>> Well, as you mention at the end of the mail,
>> several people have given you suggestions about
>> how to solve the problem using different approaches.
>> You might search on the Web for how to install a 64
>> bit version of libxml2?
>> Using xmlTreeParse(, useInternalNodes = TRUE) is an
>> approach
>> to reducing the memory consumption as is using the
>> handlers
>> argument. And if size is really the issue, you
>> should consider
>> the SAX model which is very memory efficient and
>> made available
>> via the xmlEventParse() function in the XML package.
>> And it even provides the concepts of branches to
>> provide a
>> hybrid of SAX and DOM-style parsing together.
>>
>> However, to solve the problem of the xmlMemDisplay
>> symbol not being found, you can look for where
>> that is used and remove it.It is in
>> src/DocParse.c
>> in the routine RS_XML_MemoryShow(). You can remove
>> the line
>> xmlMemDisplay(stderr)
>> or indeed the entire routine. Then re-install and
>> reload the package.
>>
>> D.
>>
>>
>> Luo Weijun wrote:
>>> Hello Dr. Lang an
Re: [R] a little problem on selecting a subset from dataset A accordingto dataset B?
You might want to be careful since what you are comparing is floating point numbers. You might want to scale them and then convert to integers to make sure that you are getting the numbers you think you should be getting. (FAQ 7.31) On 7/9/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > AB <- with(B, subset(A, coords.x1 %in% X1)) > > AB > coords.x1 coords.x2 > 0 542250.9 3392404 > 7 541512.5 3394722 > 8 541479.3 3394878 > 9 538903.4 3395943 > 18 543274.0 3389919 > 19 543840.8 3392012 > > > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of zhijie zhang > Sent: Monday, 9 July 2007 2:43 AM > To: R-help@stat.math.ethz.ch > Subject: [R] a little problem on selecting a subset from dataset A > accordingto dataset B? > > Dear Friends, > I want to extract the records from A according to B, but the results > are > not correct because R says : > The length of long object is not integer times on the length of short > object. > Anybody have met the same problem? How to do it correctly? > > length(A)=47 > length(B)=6 > > A[A$coords.x1==B$X1,] #the program for the above task. I should get 6 > records, but i only get former 4 records for the above reason. > > Thanks. > The folloing shows dataset A and B. > > > > A > coords.x1 coords.x2 > 0 542250.89 3392404.1 > 1 538813.87 3388339.0 > 2 536049.19 3385821.6 > 3 533659.62 3383194.2 > 4 530642.30 3376834.9 > 5 529573.15 3378177.8 > 6 530853.82 3394838.8 > 7 541512.51 3394721.6 > 8 541479.33 3394877.8 > 9 538903.39 3395942.5 > 10 536019.95 3396286.1 > 11 538675.23 3384213.2 > 12 535127.95 3381255.4 > 13 533852.24 3378660.4 > 14 531360.91 3379273.8 > 15 539289.14 3375759.8 > 16 543410.51 3384353.1 > 17 543089.27 3388170.1 > 18 543274.03 3389919.2 > 19 543840.77 3392012.4 > 20 553383.55 3402401.8 > 21 554621.51 3397938.9 > 22 564096.42 3397524.4 > 23 567529.64 3398702.9 > 24 561798.76 3404864.0 > 25 562868.34 3405502.2 > 26 563145.22 3403192.1 > 27 562419.87 3404090.4 > 28 558321.85 3403879.9 > 29 567050.74 3404973.1 > 30 570609.70 3408742.4 > 31 556777.57 3397858.0 > 32 531353.38 3368596.6 > 33 533513.50 3372749.3 > 34 537543.19 3364284.8 > 35 538779.41 3368224.8 > 36 525930.09 3374067.7 > 37 522990.85 3369213.1 > 38 528826.37 3359019.0 > 39 533865.85 3362595.4 > 40 531200.25 3365053.0 > 41 551054.10 3377181.3 > 42 546974.19 3369284.8 > 43 572315.59 3359541.1 > 44 562703.63 3355173.4 > 45 558959.31 3357804.4 > 46 558531.39 3361741.1 > > > > B > X1X2 > 1 542250.89 3392404.1 > 2 541512.51 3394721.6 > 3 541479.33 3394877.8 > 4 538903.39 3395942.5 > 5 543274.03 3389919.2 > 6 543840.77 3392012.4 > > -- > With Kind Regards, > > oooO: > (..): > :\.(:::Oooo:: > ::\_)::(..):: > :::)./::: > ::(_/ > : > [*** > ] > Zhi Jie,Zhang ,PHD > Tel:86-21-54237149 > Dept. of Epidemiology,School of Public Health,Fudan University > Address:No. 138 Yi Xue Yuan Road,Shanghai,China > Postcode:200032 > Email:[EMAIL PROTECTED] > Website: www.statABC.com > [*** > ] > oooO: > (..): > :\.(:::Oooo:: > ::\_)::(..):: > :::)./::: > ::(_/ > : > >[[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. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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] ANOVA: Does a Between-Subjects Factor belong in the Error Term?
I am executing a Repeated Measures Analysis of Variance with 1 DV (LOCOMOTOR RESPONSE), 2 Within-Subjects Factors (AGE, ACOUSTIC CONDITION), and 1 Between-Subjects Factor (SEX). Does anyone know whether the between-subjects factor (SEX) belongs in the Error Term of the aov or not? And if it does belong, where in the Error Term does it go? The 3 possible scenarios are listed below: e.g., 1. Omit Sex from the Error Term: >My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error (Subject/(Timepoint*Acx.Cond)), data=locomotor.tab) note: Placing SEX outside the double paretheses of the Error Term has the same statistical outcome effect as omitting it all together from the Error Term (as shown above in #1). 2. Include SEX inside the Error Term (inside Double parentheses): >My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error (Subject/(Timepoint*Acx.Cond+Sex)), data=locomotor.tab) 3. Include SEX inside the Error Term (inside Single parentheses): >My.aov = aov(Locomotor.Response~(Age*AcousticCond*Sex) + Error (Subject/(Timepoint*Acx.Cond)+Sex), data=locomotor.tab) note: Placing SEX inside the single parentheses (as shown above in #3) generates no main effect of Sex. Thus, I'm fairly confident that option #3 is incorrect. Scenarios 1,2, and 3 yield different results in the aov summary. Thanks for your help! Alex -- Alexander T Baugh Institute for Neuroscience Univ. of Texas at Austin Austin, TX 78712 512.475.6164 [[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] factanal frustration!
Hi. It seems that nearly every time I try to use factanal I get the following response: >faa2db1<-factanal(mretdb1,factors=2,method="mle",control=list(nstart=25)) Error in factanal(mretdb1, factors = 2, method = "mle", control = list(nstart = 25)) : unable to optimize from these starting value(s) > In the case cited above, mretdb1 is synthetic data created from two factors, that is, mretdb1 has dimensions 3050*1000, and each of the thousand columns has the form c[i]=a1[i]*f1 + a2[i]*f2 + a3[i]*fn[,i] where a1, a2, a3 are each vectors of length 1000, f1 and f2 are vectors of length 3050, and fn is a matrix of dimension 3050*1000, such that f1, f2, and all the columns of fn are mutually uncorrelated. I wanted to see how closely the factors returned by factanal are to the ones that generated the data. But, as you can see, factanal hasn't cooperated! I would greatly appreciate advice from factanal users, especially those who have experienced the same error. Thanks! -- TMK -- 917-656-5351cell 212-460-5430home __ 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] Clustering nested data
Hi all, I am interested in performing a cluster analysis on ecological data from forests in Pennsylvania. I would like to develop definitions for forest types (red maple forests, upland oak forests, etc.(AH AR in attached table)) based on measured attributes in each forest type. To do this, I would like to 'draw clusters' around forest types based on information from various tree species (red maple, red oak, etc.(837, 832 in attached table)) occurring in those forests. Each row of data includes mean values on a particular species occurring within a forest type at a particular site. In other words, if we monitored 10 sites in red maple forests, we would only have 10 rows of data for the tree species 'red maple', even though we measured 100 trees. I have used classification trees to examine this data, which I like because of it's predictive abilities for later 'unknown' datasets. However, my concern is that the mean species attributes (columns Diameter:Avgnumtrees in attached table) are associated with the tree species (nested?)(column Treespecies in attached table) and are not independent attributes, but are directly associated with the species listed in that row. My question is, what is the best way to conduct a clustering (I have also tried hclust, cclust and flexclust) or CART model with this sort of nested data? Also, what is the preferrable method for predicting a new dataset once these clusters or CART models have been developed? Any help would be greatly appreciated. Kind regards, Scott PS-Due to r-help email size restrictions, I cannot post the table. Please let me know if you would like me to forward an example to you. Scott L. Bearer, Ph.D. Forest Ecologist [EMAIL PROTECTED] (570) 321-9092 (Office) (570) 321-9096 (Fax) (570) 460-0778 (Mobile) The Nature Conservancy in Pennsylvania Community Arts Center 220 West Fourth Street, 3rd Floor Williamsport, PA 17701 nature.org [[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] character string to name
Jim Lemon wrote:
> Hi folks,
>
> I thought I recalled a request for turning a character string into an
> object name as in:
>
> x$as.name("y")<-1:4
> ...
Thanks to those who replied to this eminently dumb question.
OT:
I put this down to the Euthermic Model of Cognitive Efficiency. This
model, recently developed in Sydney, Australia, proposes that cognitive
efficiency is maximized at the most comfortable ambient temperature for
the thinker. Thus after riding home in the cold Sydney rain last night,
I was unable to think of the simplest answer:
names(x)<-"y"
until I had gone to bed and warmed up. Then I awoke in the early morning
and thought of Gabor's suggestion:
x[["y"]]<-...
I felt compelled to arise and publish this amazing theory, that not only
explains why the rate of intellectual and technical innovation is
greatest in the temperate climes, but more importantly, gives me an
excuse for asking the question.
Jim
__
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[R] Clustering nested data
My apologies for cross-postings Hi all, I am interested in performing a cluster analysis on ecological data from forests in Pennsylvania. I would like to develop definitions for forest types (red maple forests, upland oak forests, etc.(AH AR in attached table)) based on measured attributes in each forest type. To do this, I would like to 'draw clusters' around forest types based on information from various tree species (red maple, red oak, etc.(837, 832 in attached table)) occurring in those forests. Each row of data includes mean values on a particular species occurring within a forest type at a particular site. In other words, if we monitored 10 sites in red maple forests, we would only have 10 rows of data for the tree species 'red maple', even though we measured 100 trees. I have used classification trees to examine this data, which I like because of it's predictive abilities for later 'unknown' datasets. However, my concern is that the mean species attributes (columns Diameter:Avgnumtrees in attached table) are associated with the tree species (nested?)(column Treespecies in attached table) and are not independent attributes, but are directly associated with the species listed in that row. My question is, what is the best way to conduct a clustering (I have also tried hclust, cclust and flexclust) or CART model with this sort of nested data? Also, what is the preferrable method for predicting a new dataset once these clusters or CART models have been developed? Any help would be greatly appreciated. Kind regards, Scott > head(data_hal_dom, 15) ForestType COMMON_NAME BasalArea TreesperAcreDeadperAcre VolumeperAcre BiomassperAcre AverageDiameter STDERRDIAM AVGHT STDERRHT AVGNUMTREES AH blackoak50 31.525.1NA 950.9 47955 15.1 1.1 86.815.24 AH chestnutoak 50 11.212 NA 231.9 16713.8 13.1 0.3 55 4.2 2 AH northernoak 50 45.337.6NA 1319.7 82508.2 14.70.9 81.57 6 AH redmaple50 51.966.2NA 1564.4 60960.9 12 0.2 70.32.5 3 AH redpine 50 8.8 9.3 NA 189.4 8106.9 13.20 42 0 1 AH scarletoak 50 41.227.9NA 121167645.6 16.3 1.5 80.312.43 AH whiteoak50 10.49.2 NA 264.1 15738.6 14.4 0.3 73.30 1.3 AR northernoak 50 47.230.112 1506.4 93490 16.90.9 84.210.75 AR paperbirch 50 7.5 6 NA 243.7 963715.1 0 77 0 1 AR redmaple50 7.1 6 6 226.7 9102.2 14.6 0 75 0 1 AR sweetbirch 50 4.7 6 NA 146.3 6676.2 12 0 75.50 1 AR whiteash50 6.8 6 NA 261.5 9474.5 14.4 0 106 0 1 AR yellow-poplar 50 23.818.1NA 962.1 28302.8 15.3 2.1 99.36.8 3 AR easternhemlock 70 16.66 NA 512.6 17125.8 22.5 0 94 0 1 AR northernoak 70 16.26 12 583.4 38060.4 22.20 110 0 1 Scott Bearer Forest Ecologist The Nature Conservancy in Pennsylvania Community Arts Center 220 West Fourth Street, 3rd Floor Williamsport, PA 17701 __ 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] When is the periodogram is consistent with white noise?
Hello everyone, This is my first time posting to the list, thanks in advance. I am calculating the smoothed periodogram for the residuals of an AR model that I fit to EEG data. The autocorrelation plot of the residuals shows the series is now approximately white (i.e. ACF = 1 at lag 0, and close to 0 for all other lags). I would like to show that the spectrum of the series is also approximately white. When I calculate the periodogram using spec.pgram, what I get indeed looks white, but I would like to add horizontal threshold lines between which one can be 95% confident the spectrum is white. Thanks, -Andre [[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] similar limma's contrasts.fit() for lme (mixed effect model)object
Shirley, Well, you picked the type of contrast that proves my statement wrong. The interface in the contrast package (and the Design package) may not be well suited for the type that you are interested in (or other types, such as SAS's "lsmeans" type contrasts). The good news is that the function contrast:::contrastCalc currently does most of the work for all types of models. A modified version of that function can be used for your situation. The top part of the function works to generate two objects: xa and xb. Looking at the limma documentation, this might correspond to vectors given for WT.SvsU and Mu.SvsU. I'll attach the modified version in an off-list email with an lme example. (and I'll think about how to let the contrasts be specified by the coefficient vectors for a future release) Max -Original Message- From: shirley zhang [mailto:[EMAIL PROTECTED] Sent: Monday, July 09, 2007 11:50 AM To: Kuhn, Max Cc: R-help@stat.math.ethz.ch Subject: Re: [R] similar limma's contrasts.fit() for lme (mixed effect model)object Hi Max, Thanks for your prompt reply. Actually I have already checked contrast package, but I still could not figure out how to set the contrast matrix for a 2x2 factorial design. I would like to set a contrast exactly similar to the limma's user guide, 8.7 Factorial Designs (page 45). For example, after a mixed linear model fit with the default contr.treatment, I want to compute an estimated coefficient as the sum of the third and fourth coefficients of the original lme model (2x2 factorial design). Could you give me an example how to implement this using the contrast package? Thanks, Shirley On 7/9/07, Kuhn, Max <[EMAIL PROTECTED]> wrote: > Shirley, > > The contrast package can do this. The method of specifying the contrast > conditions/coefficients is different (and I think easier). > > Max > > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of shirley zhang > Sent: Monday, July 09, 2007 11:16 AM > To: R-help@stat.math.ethz.ch > Subject: [R] similar limma's contrasts.fit() for lme (mixed effect > model)object > > Dear R help, > > In limma package, contrasts.fit() function is very useful. I am > wondering whether there is a similar function for lme object, which > means given a mixed linear model fit, compute estimated coefficients > and standard errors for a given set of contrasts. > > Thanks, > Shirley > > __ > 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. > > -- > LEGAL NOTICE > Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Reshape version 0.8
Reshape version 0.8 http://had.co.nz/reshape Reshape is an R package for flexibly restructuring and aggregating data. It's inspired by Excel's pivot tables, and it (hopefully) makes it very easy to get your data into the shape that you want. You can find out more at http://had.co.nz/reshape This version brings a few minor changes to make the output more attractive and less surprising. If you have any code that relies on the exact output structure you might need to tweak it a little. * preserve.na renamed to na.rm to be consistent with other R functions * Column names are no longer automatically converted to valid R names. You may need to use `` (those are backticks) to access these names. * Margins now displayed with (all) instead of NA * melt.array can now deal with cases where there are partial dimnames - Thanks to Roberto Ugoccioni * Added the Smiths dataset to the package * Fixed a bug when displaying margins with multiple result variables Regards, Hadley ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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-pkgs] CRANberries -- An RSS feed about New and Updated CRAN packages
Dirk Eddelbuettel wrote: > but the easiest way may just be to subscribe to Elijah's wonderful 'Planet R' > feed aggregator My favourite RSS reader at the moment is the RSS cat caption generator: http://lol.ianloic.com/feed/dirk.eddelbuettel.com/cranberries/index.rss Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] CRANberries -- An RSS feed about New and Updated CRAN packages
Announcing CRANberries -- An RSS feed about New and Updated CRAN packages A new RSS feed [1] is now available that summarizes uploads to CRAN. This makes it possibly to quickly obtain concise information about which (of the now over one thousand !!) packages were added or updated at CRAN and its mirrors. To this end, two basic variants are provided: - a feed for new packages where we display the DESCRIPTION file - a feed for updated packages where we display the output of diffstat(1) between the old and new source tar archives. As the URLs for these are in a hierarchy, one can subscribe to both or individual feeds. The URLs are as follows: Everything http://dirk.eddelbuettel.com/cranberries/index.rss Just CRAN (so far the same as All) http://dirk.eddelbuettel.com/cranberries/cran/index.rss New CRAN packages http://dirk.eddelbuettel.com/cranberries/cran/new/index.rss Updated CRAN packages http://dirk.eddelbuettel.com/cranberries/cran/updated/index.rss but the easiest way may just be to subscribe to Elijah's wonderful 'Planet R' feed aggregator which already sources the 'Everything' variant above. Beside giving you lots of other R information, it also points to a more reliable back-end than my small server at home. Lastly, I could add other repositories. However, to provide updates in the current format, my code relies on some CRAN features not available on all other repos (i.e an Archive/ section with old tarballs, and the various Descriptions/$package.DESCRIPTION files). For the technically inclined, this is implemented using a few lines of R executed by littler [2] storing data via R/DBI in a SQLite db and writing simple text files that are then aggregated by the Blosxom [3] blog engine. Comments, questions, criticism most welcome. Best regards, Dirk [1] See the Wikipedia entry at http://en.wikipedia.org/wiki/Rss if that term is unfamiliar. RSS feeds can be read in web browsers, numerous stand-alone applications, or web-services such as Google Reader. [2] See http://dirk.eddelbuettel.com/code/littler.html [3] See http://blosxom.sourceforge.net/ and http://blosxom.sourceforge.net/ but not that Blosxom development seems to have ceased. There are many alternatives such as PyBlosxom and Nanoblogger. -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculating p-values of columns in a dataframe
Uwe- thanks. After a little trial and error, I created these two very simple
custom functions that calculate the t.stat and p.value of columns in a
dataframe.
I "think" they work correctly and as intended. I welcome comments & critiques.
myfn.t.stat <- function(df) { apply(df,2,function(x) if(fn.count(x)==0) NA else
t.test(x)$statistic) }
myfn.p.val <- function(df) { apply(df,2,function(x) if(fn.count(x)==0) NA else
t.test(x)$p.value) }
Uwe Ligges <[EMAIL PROTECTED]> wrote:
Thomas Pujol wrote:
> I have a dataframe ("mydf") that contains "differences of means".
> I wish to test whether these differences are significantly different from
> zero.
>
> Below, I calculate the t-statistic for each column.
>
> What is a "good" method to calculate/look-up the p-value for each column?
>
>
> mydf=data.frame(a=c(1,-22,3,-4),b=c(5,-6,-7,9))
>
> mymean=mean(mydf)
> mysd=sd(mydf)
> mynn=sapply(mydf, function(x) {sum ( as.numeric(x) >= -Inf) })
> myse=mysd/sqrt(mynn)
> myt=mymean/myse
> myt
You can do the whole lot with
L <- lapply(mydf, t.test)
or if you only want the t statistics and p-values now:
sapply(L, "[", c("statistic", "p.value"))
If you want to follow your initial approach quickly, you can calculate
the probability function of the t distribution with 3 degrees of freedom
(for your data) with
2 * pt(-abs(myt), df = nrow(mydf) - 1)
Uwe Ligges
>
>
> -
> Food fight? Enjoy some healthy debate
>
> [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-
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Re: [R] Writing Excel (.xls) files on non-Windows OSs using Perl
Gabor Grothendieck wrote: > Note that there already is a function, read.xls, in gdata that uses Perl. Note that Marc talked about *writing* in his original message. Uwe Ligges > On 7/9/07, Marc Schwartz <[EMAIL PROTECTED]> wrote: >> On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote: >>> Hi, >>> >>> 2007/7/8, Marc Schwartz <[EMAIL PROTECTED]>: [snip] There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which is restricted to Windows, since it utilizes the non-FOSS MS Office API to write the Excel formats. >>> The non-FOSS API is not the problem(#) but its implementation is: >>> >>> The 3rd party library I use is written in Pascal and supports Delphi >>> and Kylix. Kylix would allow to port the package to Linux but as Kylix >>> has unfortunately been abandoned by CodeGear (Borland) I am not >>> ready/interested to spend my time on this dead road. Though it >>> probably could be done quickly. >>> >>> A much more interesting way is to port the package using FreePascal. >>> --> I plan to do this since long but... >>> --> Maybe someone fluent on Linux and FreePascal could have a look at >>> the pascal header files (treetron.googlepages.com) and make the demos >>> run on Linux..., that would be great and speed up an eventual >>> xlsReadWrite port! >> Thanks for the clarification. >> >> However, I think that if you are going to pursue a cross-platform >> solution, providing source code requiring compilation (as opposed to a >> pre-compiled Windows binary), you should consider what the installation >> requirements for your package would then be. >> >> If you are going to take the step of requiring a prospective end-user to >> have a particular Pascal compiler in place, you may as well have the >> requirement for a Perl interpreter and associated packages. Since Perl >> is widely available and you are more likely to find Perl-fluent coders >> as opposed to Pascal-fluent coders (eg. I have not used Pascal since the >> late 80's), I would urge you to consider Perl as a future substrate for >> your functions. >> >> While compiled code will run faster than interpreted code, for these >> types of file I/O functions, I am not sure that you lose much with Perl >> from a performance standpoint and you certainly gain the eyes of a wider >> audience with respect to use, debugging and enhancements. >> >> To that end, you (or any other interested parties) are free to utilize >> my code in any way you deem appropriate. I did not state this in my >> original post, but I make the code available under GPL(v2), freeing you >> from any restrictions in its use, including your "Pro" version, as long >> as you make the source available in a fashion consistent with the GPL >> requirements. >> >> Regards, >> >> 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. >> > > __ > 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] similar limma's contrasts.fit() for lme (mixed effect model)object
Hi Max, Thanks for your prompt reply. Actually I have already checked contrast package, but I still could not figure out how to set the contrast matrix for a 2x2 factorial design. I would like to set a contrast exactly similar to the limma's user guide, 8.7 Factorial Designs (page 45). For example, after a mixed linear model fit with the default contr.treatment, I want to compute an estimated coefficient as the sum of the third and fourth coefficients of the original lme model (2x2 factorial design). Could you give me an example how to implement this using the contrast package? Thanks, Shirley On 7/9/07, Kuhn, Max <[EMAIL PROTECTED]> wrote: > Shirley, > > The contrast package can do this. The method of specifying the contrast > conditions/coefficients is different (and I think easier). > > Max > > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of shirley zhang > Sent: Monday, July 09, 2007 11:16 AM > To: R-help@stat.math.ethz.ch > Subject: [R] similar limma's contrasts.fit() for lme (mixed effect > model)object > > Dear R help, > > In limma package, contrasts.fit() function is very useful. I am > wondering whether there is a similar function for lme object, which > means given a mixed linear model fit, compute estimated coefficients > and standard errors for a given set of contrasts. > > Thanks, > Shirley > > __ > 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. > > -- > LEGAL NOTICE > Unless expressly stated otherwise, this message is confidential and may be > privileged. It is intended for the addressee(s) only. Access to this E-mail > by anyone else is unauthorized. If you are not an addressee, any disclosure > or copying of the contents of this E-mail or any action taken (or not taken) > in reliance on it is unauthorized and may be unlawful. If you are not an > addressee, please inform the sender immediately. > __ 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] similar limma's contrasts.fit() for lme (mixed effect model)object
Shirley,
The contrast package can do this. The method of specifying the contrast
conditions/coefficients is different (and I think easier).
Max
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of shirley zhang
Sent: Monday, July 09, 2007 11:16 AM
To: R-help@stat.math.ethz.ch
Subject: [R] similar limma's contrasts.fit() for lme (mixed effect
model)object
Dear R help,
In limma package, contrasts.fit() function is very useful. I am
wondering whether there is a similar function for lme object, which
means given a mixed linear model fit, compute estimated coefficients
and standard errors for a given set of contrasts.
Thanks,
Shirley
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
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Re: [R] No convergence using ADAPT
Since the covariance is zero (i.e. you have independent normals), you can
simplify your problem so that you just need to perform one-dimensional
integration. Here is how you can do it:
trial2 <- function(input) {
#pmvnorm(lower = c(0,0), upper = c(10, 10), mean = input, sigma =
matrix(c(.01, 0, 0, .01), nrow = 2, ncol = 2, byrow = FALSE))
pnorm(q=10, mean = input, sd = sqrt(.01)) - pnorm(q=0, mean = input, sd =
sqrt(.01))
}
bottomB <- -5*sqrt(.01)
topB <- 10 + 5*sqrt(.01)
areaB <- (topB - bottomB)^2
new.ans <- 1/areaB * (integrate(f=trial2, lo = bottomB, up = topB)$val)^2
> new.ans
[1] 0.8264463
Hope this is helpful,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Philip Turk
Sent: Saturday, July 07, 2007 3:20 PM
To: r-help@stat.math.ethz.ch
Subject: [R] No convergence using ADAPT
I am trying calculate a probability using numerical integration. The first
program I ran spit out an answer in a very short time. The program is below:
## START PROGRAM
trial <- function(input)
{
pmvnorm(lower = c(0,0), upper = c(2, 2), mean = input, sigma = matrix(c(.1,
0,
0, .1), nrow = 2, ncol = 2, byrow = FALSE))
}
require(mvtnorm)
require(adapt)
bottomB <- -5*sqrt(.1)
topB <- 2 + 5*sqrt(.1)
areaB <- (topB - bottomB)^2
unscaled.Po.in.a <- adapt(2, lo = c(bottomB, bottomB), up = c(topB, topB),
minpts = 1000, eps = 1e-4, functn = trial)
(1/areaB)*unscaled.Po.in.a$value
## FINISH PROGRAM
I tried to run the program again changing a.) sigma in the trial function,
b.)
upper in the trial function, and c.) the bounds of integration; that is,
bottomB and topB. The new program is below:
## START PROGRAM
trial <- function(input)
{
pmvnorm(lower = c(0,0), upper = c(10, 10), mean = input, sigma =
matrix(c(.01,
0, 0, .01), nrow = 2, ncol = 2, byrow = FALSE))
}
require(mvtnorm)
require(adapt)
bottomB <- -5*sqrt(.01)
topB <- 10 + 5*sqrt(.01)
areaB <- (topB - bottomB)^2
unscaled.Po.in.a <- adapt(2, lo = c(bottomB, bottomB), up = c(topB, topB),
minpts = 1000, eps = 1e-4, functn = trial)
(1/areaB)*unscaled.Po.in.a$value
## FINISH PROGRAM
Now, the program just runs and runs (48 hours at last count!). By playing
around with the program, I have deduced the program is highly sensitive to
changing the upper option in the trial function. For example, using a
vector
like (4, 4) causes no problems and the program quickly yields an answer. I
have a couple of other programs where I can easily obtain a simulation-based
answer, but I would ultimately like to know what's up with this program
before
I give up on it so I can learn a thing or two. Does anyone have any clues
or
tricks to get around this problem? My guess is that it will simply be very
difficult (impossible?) to obtain this type of relative error (eps = 1e-4)
and
I will have no choice but to pursue the simulation approach.
Thanks for any responses ([EMAIL PROTECTED])!
-- Phil
Philip Turk
Assistant Professor of Statistics
Northern Arizona University
Department of Mathematics and Statistics
PO Box 5717
Flagstaff, AZ 86011
Phone: 928-523-6884
Fax: 928-523-5847
E-mail: [EMAIL PROTECTED]
Web Site: http://jan.ucc.nau.edu/~stapjt-p/
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[R] about scagnostics
Hi Hadley, thank you for providing this "scagnostics" primer I was trying to do some basic testing, and I see that I probably missed some points : first it's not clear for me if the argument of "scagnostics" should be raw data or "processed" data (results of calling "splom" or whatever...). If the first, I thought (from Wilkinson & al.) that if taking as an example variables x and y being the coordinates of a circle, I should find in scagnostics(x,y)$s : Skinny = 0 and Convex =1. I get Skinny = 1 and Convex =0 What am I missing ? (My God, I'm feeling myself going to be "Ripleyed" !.) Regards, Olivier -- Olivier ETERRADOSSI Maître-Assistant CMGD / Equipe "Propriétés Psycho-Sensorielles des Matériaux" Ecole des Mines d'Alès Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9 tel std: +33 (0)5.59.30.54.25 tel direct: +33 (0)5.59.30.90.35 fax: +33 (0)5.59.30.63.68 http://www.ema.fr __ 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] similar limma's contrasts.fit() for lme (mixed effect model) object
Dear R help, In limma package, contrasts.fit() function is very useful. I am wondering whether there is a similar function for lme object, which means given a mixed linear model fit, compute estimated coefficients and standard errors for a given set of contrasts. Thanks, Shirley __ 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] using the function unique(), but asking it to ignore a column of a data.frame
Thanks, this works perfectly.
On 7/9/07, Prof Brian Ripley <[EMAIL PROTECTED]> wrote:
> On Mon, 9 Jul 2007, Andrew Yee wrote:
>
> > Thanks. But in this specific case, I would like the output to include
> > all three columns, including the "ignored" column (in this case, I'd
> > like it to ignore column a).
>
> sample.data.frame[!duplicated(sample.data.frame[-1]), ]
>
> (index to exclude columns as you wish).
>
> > Thanks,
> > Andrew
> >
> > On 7/9/07, hadley wickham <[EMAIL PROTECTED]> wrote:
> >> On 7/9/07, Andrew Yee <[EMAIL PROTECTED]> wrote:
> >>> Take for example the following data.frame:
> >>>
> >>> a<-c(1,1,5)
> >>> b<-c(3,2,3)
> >>> c<-c(5,1,5)
> >>> sample.data.frame<-data.frame(a=a,b=b,c=c)
> >>>
> >>> I'd like to be able to use unique(sample.data.frame), but have
> >>> unique() ignore column a when determining the unique elements.
> >>>
> >>> However, I figured that this would be setting for incomparables=, but
> >>> it appears that this funcationality hasn't been incorporated. Is
> >>> there a work around for this, i.e. to be able to get unique to only
> >>> look at selected columns of a data frame?
> >>
> >> unique(df[,c("a","c")]) ?
> >>
> >> Hadley
> >>
> >
> > __
> > R-help@stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
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Re: [R] Writing Excel (.xls) files on non-Windows OSs using Perl
Note that there already is a function, read.xls, in gdata that uses Perl. On 7/9/07, Marc Schwartz <[EMAIL PROTECTED]> wrote: > On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote: > > Hi, > > > > 2007/7/8, Marc Schwartz <[EMAIL PROTECTED]>: > > > [snip] > > > There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which > > > is restricted to Windows, since it utilizes the non-FOSS MS Office API > > > to write the Excel formats. > > > > The non-FOSS API is not the problem(#) but its implementation is: > > > > The 3rd party library I use is written in Pascal and supports Delphi > > and Kylix. Kylix would allow to port the package to Linux but as Kylix > > has unfortunately been abandoned by CodeGear (Borland) I am not > > ready/interested to spend my time on this dead road. Though it > > probably could be done quickly. > > > > A much more interesting way is to port the package using FreePascal. > > --> I plan to do this since long but... > > --> Maybe someone fluent on Linux and FreePascal could have a look at > > the pascal header files (treetron.googlepages.com) and make the demos > > run on Linux..., that would be great and speed up an eventual > > xlsReadWrite port! > > Thanks for the clarification. > > However, I think that if you are going to pursue a cross-platform > solution, providing source code requiring compilation (as opposed to a > pre-compiled Windows binary), you should consider what the installation > requirements for your package would then be. > > If you are going to take the step of requiring a prospective end-user to > have a particular Pascal compiler in place, you may as well have the > requirement for a Perl interpreter and associated packages. Since Perl > is widely available and you are more likely to find Perl-fluent coders > as opposed to Pascal-fluent coders (eg. I have not used Pascal since the > late 80's), I would urge you to consider Perl as a future substrate for > your functions. > > While compiled code will run faster than interpreted code, for these > types of file I/O functions, I am not sure that you lose much with Perl > from a performance standpoint and you certainly gain the eyes of a wider > audience with respect to use, debugging and enhancements. > > To that end, you (or any other interested parties) are free to utilize > my code in any way you deem appropriate. I did not state this in my > original post, but I make the code available under GPL(v2), freeing you > from any restrictions in its use, including your "Pro" version, as long > as you make the source available in a fashion consistent with the GPL > requirements. > > Regards, > > 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. > __ 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] Planet R - a weblog aggregator for statistical computing
Announcing... Planet R - a weblog aggregator for statistical computing Q: What is it? A: An aggregator for weblog posts about statistical computing topics, focused primarily around the R community. Q2: Where is it? A2: For now, at http://planetr.stderr.org Q3: What's it good for? A3: Hopefully, collecting resources and weblog posts from people who might otherwise not know about each other. Community-building, you see? Q4: How do I get my stuff on there? A4: Send mail to [EMAIL PROTECTED], with a representative subject line (e.g. 'please add to planet r' will be fine..); I'll need the link to the RSS feed of your blog or other resource. If you'd like a personal icon in the style of Planet Debian or Planet Gnome (or one of those other planetplanet-based sites..) feel free to send along a smallish picture or icon as well. (Think 80-by-80 pixels...) Q5: What sort of things are there? A5: A selection of weblogs about statistical computing, a feed from omegahat, some bioconductor-related content, feeds from a couple of journals (including JoSS content, as a subset of the J Computational and Graphical Statistics, as well as Royal Statistical Society content sourced from IngentaConnect...), the changes feed from the R Wiki, and a few other things of great utility to the R community. Please feel free to contact me directly with further content, media, suggestions, et cetera, that you think would enhance the utility of this site as a resource to the community. thanks, --elijah wright indiana university bloomington school of library and information science __ 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] Writing Excel (.xls) files on non-Windows OSs using Perl
On Mon, 2007-07-09 at 16:42 +0300, Hans-Peter wrote: > Hi, > > 2007/7/8, Marc Schwartz <[EMAIL PROTECTED]>: > > [snip] > > There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which > > is restricted to Windows, since it utilizes the non-FOSS MS Office API > > to write the Excel formats. > > The non-FOSS API is not the problem(#) but its implementation is: > > The 3rd party library I use is written in Pascal and supports Delphi > and Kylix. Kylix would allow to port the package to Linux but as Kylix > has unfortunately been abandoned by CodeGear (Borland) I am not > ready/interested to spend my time on this dead road. Though it > probably could be done quickly. > > A much more interesting way is to port the package using FreePascal. > --> I plan to do this since long but... > --> Maybe someone fluent on Linux and FreePascal could have a look at > the pascal header files (treetron.googlepages.com) and make the demos > run on Linux..., that would be great and speed up an eventual > xlsReadWrite port! Thanks for the clarification. However, I think that if you are going to pursue a cross-platform solution, providing source code requiring compilation (as opposed to a pre-compiled Windows binary), you should consider what the installation requirements for your package would then be. If you are going to take the step of requiring a prospective end-user to have a particular Pascal compiler in place, you may as well have the requirement for a Perl interpreter and associated packages. Since Perl is widely available and you are more likely to find Perl-fluent coders as opposed to Pascal-fluent coders (eg. I have not used Pascal since the late 80's), I would urge you to consider Perl as a future substrate for your functions. While compiled code will run faster than interpreted code, for these types of file I/O functions, I am not sure that you lose much with Perl from a performance standpoint and you certainly gain the eyes of a wider audience with respect to use, debugging and enhancements. To that end, you (or any other interested parties) are free to utilize my code in any way you deem appropriate. I did not state this in my original post, but I make the code available under GPL(v2), freeing you from any restrictions in its use, including your "Pro" version, as long as you make the source available in a fashion consistent with the GPL requirements. Regards, 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] possible bug in ggplot2 v0.5.2???
On 7/6/07, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Wed, 4 Jul 2007, hadley wickham wrote: > > > On 7/4/07, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > >> On Tue, 3 Jul 2007, hadley wickham wrote: > >> > >> > Hi Stephane, > >> > > >> > The problem is that the windows graphics device doesn't support > >> > transparent colours. You can get around this in two ways: > >> > >> It certainly does! Try col="transparent" (and perhaps consult your > >> dictionary). It was news to me that the windows() graphics device worked > >> on > >> Linux i586. > > > > Well my dictionary defines transparent as "allowing light to pass > > through so that objects behind can be distinctly seen" which I believe > > applies here (ie. stained glass windows and blue points with alpha 0.5 > > are both transparent). What does your dictionary say? > > Not quite the same, but even by your definition col="transparent" is > transparent. In this context > > http://en.wikipedia.org/wiki/Transparency_%28graphic%29 > > seems more pertinent. col="transparent" is transparent by any reasonable definition, but does it make sense to claim that a graphics device "supports" transparency? How can you tell the difference between a transparent object and nothing? > >> What it does not support as yet is translucent colours, and that is a > >> restriction imposed by Windows (translucency support was introduced for > >> Windows XP, and we still try to support older versions of Windows, unlike > >> the MacOS people). I have been working on a workaround, so translucency > >> support is likely to be implemented in R 2.6.0 for users of XP or later. > > > > I am confused by your implication that windows (prior to XP) does not > > support translucency. Perhaps it is not supported at the operating > > system level, but it has certainly been available at the application > > level for a very long time. > > Really? It's hard to reply to unspecific assertions. But remember XP has > been out since 2001, almost as long as PDF has supported translucency. Yes, I agree, and thank you for providing some support to your statements. Java has supported transparency since 1.2 (with the Graphics2D class), and was released on Dec 4, 1998, so certainly some applications were drawing transparent graphics on windows. > >> Given that neither of the two main screen devices and neither of the > >> standard print devices support translucency, the subject line looks > >> correct to me: the problem surely lies in the assumptions made in ggplot2. > > > > The features of the windows and X11 devices clearly lag behind the > > quartz and pdf devices. I can program for the lowest common > > denominator or I can use modern features that support the tasks I am > > working on. I choose the later, and it is certainly your prerogative > > to declare that a bug in me. > > I think to make undocumented assumptions about the environment is unkind > to your would-be users. Ideally the graphics devices would detect and I have tried to point that out in most places where I used alpha-blending in the documentation, but I did miss a few. I think part of my job is to educate users about what is possible with R, even though it might be currently available for their default set up. > report that, but that is not how support for semi-transparency was added. > As a by-product of adding limited translucency support on the windows() > family of devices, they do now warn. That's great news. > You also need to check that the extra features work correctly. I found > some problems with all the devices I tried that support translucency (or > at least with device+viewer combinations for pdf and svg). Issues include > whether translucent fills are rendered at all, blending translucent > colours with transparent backgrounds, and the model used (is it the light > intensity or the perceptual colours that are being blended?). Could you provide more details about these bugs so that I can look into the implications for my code? I haven't seen any problems with preview or acrobat on the mac. Regards, Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using the function unique(), but asking it to ignore a column of a data.frame
On Mon, 9 Jul 2007, Andrew Yee wrote:
> Thanks. But in this specific case, I would like the output to include
> all three columns, including the "ignored" column (in this case, I'd
> like it to ignore column a).
sample.data.frame[!duplicated(sample.data.frame[-1]), ]
(index to exclude columns as you wish).
> Thanks,
> Andrew
>
> On 7/9/07, hadley wickham <[EMAIL PROTECTED]> wrote:
>> On 7/9/07, Andrew Yee <[EMAIL PROTECTED]> wrote:
>>> Take for example the following data.frame:
>>>
>>> a<-c(1,1,5)
>>> b<-c(3,2,3)
>>> c<-c(5,1,5)
>>> sample.data.frame<-data.frame(a=a,b=b,c=c)
>>>
>>> I'd like to be able to use unique(sample.data.frame), but have
>>> unique() ignore column a when determining the unique elements.
>>>
>>> However, I figured that this would be setting for incomparables=, but
>>> it appears that this funcationality hasn't been incorporated. Is
>>> there a work around for this, i.e. to be able to get unique to only
>>> look at selected columns of a data frame?
>>
>> unique(df[,c("a","c")]) ?
>>
>> Hadley
>>
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] using the function unique(), but asking it to ignore a column of a data.frame
On 7/9/07, Peter Dalgaard <[EMAIL PROTECTED]> wrote:
> Andrew Yee wrote:
> > Thanks. But in this specific case, I would like the output to include
> > all three columns, including the "ignored" column (in this case, I'd
> > like it to ignore column a).
> >
> df[!duplicated(df[,c("a","c")]),]
>
> or perhaps
>
> df[!duplicated(df[-2]),]
Yes - of course. I was momentarily confused about unique vs. duplicated. Oops!
Hadley
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Re: [R] about scagnostics
Hi Olivier, You can call scagnostics either with two vectors, or a data.frame (in which case it computes all pairwise scagnostics). I just double checked to make sure I didn't accidentally misname the vector of scagnostics in R, and it doesn't look like I did, so could you please send me a reproducible example so I can look into it more closely. Thanks, Hadly On 7/9/07, Olivier ETERRADOSSI <[EMAIL PROTECTED]> wrote: > Hi Hadley, > thank you for providing this "scagnostics" primer > I was trying to do some basic testing, and I see that I probably missed > some points : > first it's not clear for me if the argument of "scagnostics" should be > raw data or "processed" data (results of calling "splom" or whatever...). > If the first, I thought (from Wilkinson & al.) that if taking as an > example variables x and y being the coordinates of a circle, I should > find in scagnostics(x,y)$s : > Skinny = 0 and Convex =1. > I get Skinny = 1 and Convex =0 What am I missing ? > (My God, I'm feeling myself going to be "Ripleyed" !.) > Regards, Olivier > > -- > Olivier ETERRADOSSI > Maître-Assistant > CMGD / Equipe "Propriétés Psycho-Sensorielles des Matériaux" > Ecole des Mines d'Alès > Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9 > tel std: +33 (0)5.59.30.54.25 > tel direct: +33 (0)5.59.30.90.35 > fax: +33 (0)5.59.30.63.68 > http://www.ema.fr > > __ 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] character string to name
On Mon, 9 Jul 2007, Jim Lemon wrote:
> Hi folks,
>
> I thought I recalled a request for turning a character string into an
> object name as in:
Yes. It's a FAQ.
-thomas
> x$as.name("y")<-1:4
>
> OR
>
> x<-data.frame(as.name("y")=1:4)
>
> However, as.name and a few other uninformed attempts didn't even come
> close. A search of "character to name" produced no helpful functions.
> This isn't a very urgent request, but if anyone knows some trick to
> perform this transformation, I would like to hear about it. Thanks.
>
> Jim
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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[R] [R-pkgs] New package "proxy" for distances and similiarities
Dear useRs, a new package for computing distance and similarity matrices made it to CRAN, and will propagate to the mirrors soon. It includes an enhanced version of "dist()" with support for more than 40 popular similarity and distance measures, both for auto- and cross-distances. Some important ones are implemented in C. The proximity measures are stored in a registry which can easily be queried and extended by users at run-time. For adding a new measure, the simplest way is to provide the distance measure as a small R function, the package code will do the loops on the C code level to create the proximity matrix. It is of course also possible to use more efficient C implementations---either for the distance measure alone, or the whole matrix computation. Input data is not restricted to matrices: provided the proximity measure can handle it, lists and data frames are also accepted. The formulas for binary proximities can conveniently be specified in the a/b/c/d/n format, where the number of concordant/discordant pairs is precomputed on the C code level. We are currently working on support for sparse data. This is also a "Call for Measures": if you feel that a particular similarity of distance measure is missing, please send the formula and a reference (or, ideally, the whole registry entry) to one of the package maintainers who will happily add it. David and Christian. ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] using the function unique(), but asking it to ignore a column of a data.frame
Andrew Yee wrote:
> Thanks. But in this specific case, I would like the output to include
> all three columns, including the "ignored" column (in this case, I'd
> like it to ignore column a).
>
df[!duplicated(df[,c("a","c")]),]
or perhaps
df[!duplicated(df[-2]),]
> Thanks,
> Andrew
>
> On 7/9/07, hadley wickham <[EMAIL PROTECTED]> wrote:
>
>> On 7/9/07, Andrew Yee <[EMAIL PROTECTED]> wrote:
>>
>>> Take for example the following data.frame:
>>>
>>> a<-c(1,1,5)
>>> b<-c(3,2,3)
>>> c<-c(5,1,5)
>>> sample.data.frame<-data.frame(a=a,b=b,c=c)
>>>
>>> I'd like to be able to use unique(sample.data.frame), but have
>>> unique() ignore column a when determining the unique elements.
>>>
>>> However, I figured that this would be setting for incomparables=, but
>>> it appears that this funcationality hasn't been incorporated. Is
>>> there a work around for this, i.e. to be able to get unique to only
>>> look at selected columns of a data frame?
>>>
>> unique(df[,c("a","c")]) ?
>>
>> Hadley
>>
>>
>
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> and provide commented, minimal, self-contained, reproducible code.
>
--
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
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Re: [R] Speeding up
Dear Bjorn,
Do you know that mean(xy*ind)+mean(xy*!ind) yields the same value for
all i? Maybe you meant mean(xy[ind]) + mean(xy[!ind])
sapply(xord, function(xordi, xy = x){
ind <- xy < xordi
mean(xy*ind)+mean(xy*!ind)
})
Cheers,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research 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 Van Campenhout Bjorn
> Verzonden: maandag 9 juli 2007 15:12
> Aan: r-help@stat.math.ethz.ch
> Onderwerp: [R] Speeding up
>
> Hi R-helpers,
>
> I am new in programming and R, so this may be basic. I need
> to speed up a procedure where I minimize some function on
> different partitions of the data. I can do this with a loop,
> as for instance in:
>
> i<-1
> meanmin<-Inf
> while (i ind<-x if (some function to be minimized meanmin<-some function to be minimized
> indmin<-xord[i]
> }
> i<-i+1
> }
> print(indmin)
>
> I learned that I should avoid loops, so I found the following
> alternative:
>
> dmat<-outer(x,xord,"<")*1
> ss<-apply(dmat,2,function (z) some function to be minimized)
> indmin<-xord[which.min(ss)]
> print(indmin)
>
> But this does not lead to spectacular improvements
> (obviously, this is dependent on the function and the length
> of x, and this dmat does not seem to be an elegant solution
> to me). Is there scope for substantial improvement? Any
> pointers will be greatly appreciated. Below an example with
> some timings.
>
>
> > set.seed(12345)
> > x <- rnorm(1000, mean = 5, sd = 2)
> > xord<-x[order(x)]
> >
> > system.time({i<-1
> + meanmin<-Inf
> + while (i + ind<-x + if ((mean(x*ind)+mean(x*!ind)) + meanmin<-mean(x*ind)+mean(x*!ind)
> + indmin<-xord[i]
> + }
> + i<-i+1
> + }
> + print(indmin)})
> [1] 3.826595
>user system elapsed
>0.140.000.14
> >
> >
> >
> > system.time({dmat<-outer(x,xord,"<")*1
> + ss<-apply(dmat,2,function (z) mean(x*z)+mean(x*!z))
> + indmin<-xord[which.min(ss)]
> + print(indmin)})
> [1] 3.826595
>user system elapsed
>0.420.060.49
> >
> >
>
> __
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> 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.
>
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Re: [R] Several quick questions
Thanks all of you guys for your help. It will most helpful.
[EMAIL PROTECTED] a écrit :
> On 7/7/07, Sébastien <[EMAIL PROTECTED]> wrote:
>> Dear R users,
>>
>> Here is a couple a quick questions, for which I was unable to not find
>> any answer in the list archives and in the help:
>
> [...]
>
>> 2- When a log scale is called in a graph, the label takes a format like
>> 10^n.
>
> That's true for lattice, but not traditional graphics, as far as I know.
>
>> Is there a way to come back to a regular number format like 1, 10,
>> 100... without having to create a custom axis ?
>
> Depends on what you mean by "custom axis". You don't need to manually
> choose the tick positions etc, but you still need to define the rules
> that determine how they are calculated. See example(axis.default) for
> an example where the tick positions remain the same (as the defaults),
> but the labels change. The slightly different rule used in
> traditional graphics is available through the axTicks() function,
> which basically boils down to this:
>
> logTicks <- function (lim, loc = c(1, 5))
> {
>ii <- floor(log10(range(lim))) + c(-1, 2)
>main <- 10^(ii[1]:ii[2])
>r <- as.numeric(outer(loc, main, "*"))
>r[lim[1] <= r & r <= lim[2]]
> }
>
> where 'lim' is the limits in the original scale. So we have
>
>> logTicks(c(1, 100))
> [1] 1 5 10 50 100
>> logTicks(c(1, 100), loc = c(2, 5, 10))
> [1] 1 2 5 10 20 50 100
>
>> 3- In lattice graphics, how does the default value of the "axs" argument
>> influence the values of "limits" ?
>> This question should be considered in the following context. The help
>> states that a 4% extension is applied by default to the axis range in
>> base graphics. So, I have tried to apply this 4 % extension to create
>> some custom lattice graphics. I worked on a dataset in which the
>> independent variable ranged from 0 to 120, so I basically customized my
>> axis using limits=c(-4.8,124.8). The results of the graphics with and
>> without the limits command were not identical...
>
> The extension is user-settable in lattice, and defaults to 7% (I think
> this value came from Trellis specs, but I don't remember the exact
> details).
>
>> lattice.getOption("axis.padding")
> $numeric
> [1] 0.07
>
> $factor
> [1] 0.6
>
> -Deepayan
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[R] HTML.data.frame
I can't use the HTML.data.frame function maybe because the good package should however be charged I charged R2HTML and HTMLapplets could you indicate to me in which package this function is? _ [[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] Writing Excel (.xls) files on non-Windows OSs using Perl
Hi, 2007/7/8, Marc Schwartz <[EMAIL PROTECTED]>: > [snip] > There exists the xlsReadWrite package on CRAN by Hans-Peter Suter, which > is restricted to Windows, since it utilizes the non-FOSS MS Office API > to write the Excel formats. The non-FOSS API is not the problem(#) but its implementation is: The 3rd party library I use is written in Pascal and supports Delphi and Kylix. Kylix would allow to port the package to Linux but as Kylix has unfortunately been abandoned by CodeGear (Borland) I am not ready/interested to spend my time on this dead road. Though it probably could be done quickly. A much more interesting way is to port the package using FreePascal. --> I plan to do this since long but... --> Maybe someone fluent on Linux and FreePascal could have a look at the pascal header files (treetron.googlepages.com) and make the demos run on Linux..., that would be great and speed up an eventual xlsReadWrite port! -- Regards, Hans-Peter (#) at least for people who are not in principle opposed to run a package which contains a non-FOSS code part. __ 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] using the function unique(), but asking it to ignore a column of a data.frame
Thanks. But in this specific case, I would like the output to include
all three columns, including the "ignored" column (in this case, I'd
like it to ignore column a).
Thanks,
Andrew
On 7/9/07, hadley wickham <[EMAIL PROTECTED]> wrote:
> On 7/9/07, Andrew Yee <[EMAIL PROTECTED]> wrote:
> > Take for example the following data.frame:
> >
> > a<-c(1,1,5)
> > b<-c(3,2,3)
> > c<-c(5,1,5)
> > sample.data.frame<-data.frame(a=a,b=b,c=c)
> >
> > I'd like to be able to use unique(sample.data.frame), but have
> > unique() ignore column a when determining the unique elements.
> >
> > However, I figured that this would be setting for incomparables=, but
> > it appears that this funcationality hasn't been incorporated. Is
> > there a work around for this, i.e. to be able to get unique to only
> > look at selected columns of a data frame?
>
> unique(df[,c("a","c")]) ?
>
> Hadley
>
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] using the function unique(), but asking it to ignore a column of a data.frame
On 7/9/07, Andrew Yee <[EMAIL PROTECTED]> wrote:
> Take for example the following data.frame:
>
> a<-c(1,1,5)
> b<-c(3,2,3)
> c<-c(5,1,5)
> sample.data.frame<-data.frame(a=a,b=b,c=c)
>
> I'd like to be able to use unique(sample.data.frame), but have
> unique() ignore column a when determining the unique elements.
>
> However, I figured that this would be setting for incomparables=, but
> it appears that this funcationality hasn't been incorporated. Is
> there a work around for this, i.e. to be able to get unique to only
> look at selected columns of a data frame?
unique(df[,c("a","c")]) ?
Hadley
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[R] using the function unique(), but asking it to ignore a column of a data.frame
Take for example the following data.frame: a<-c(1,1,5) b<-c(3,2,3) c<-c(5,1,5) sample.data.frame<-data.frame(a=a,b=b,c=c) I'd like to be able to use unique(sample.data.frame), but have unique() ignore column a when determining the unique elements. However, I figured that this would be setting for incomparables=, but it appears that this funcationality hasn't been incorporated. Is there a work around for this, i.e. to be able to get unique to only look at selected columns of a data frame? Thanks, Andrew __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Speeding up
Hi R-helpers,
I am new in programming and R, so this may be basic. I need to speed up
a procedure where I minimize some function on different partitions of
the data. I can do this with a loop, as for instance in:
i<-1
meanmin<-Inf
while (i set.seed(12345)
> x <- rnorm(1000, mean = 5, sd = 2)
> xord<-x[order(x)]
>
> system.time({i<-1
+ meanmin<-Inf
+ while (i
>
>
> system.time({dmat<-outer(x,xord,"<")*1
+ ss<-apply(dmat,2,function (z) mean(x*z)+mean(x*!z))
+ indmin<-xord[which.min(ss)]
+ print(indmin)})
[1] 3.826595
user system elapsed
0.420.060.49
>
>
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] transform excel data into graph
I am not sure exactly what you want but see if this will work. It will give you a dotchart. Assume your data.frame is dat First give the lessons column a name. See ?names convert numbers in data.frame to a matrix for dotchart dmat <- as.matrix(dat[,2:4]) Draw dotchart using dat$lessons as a dotchart(dmat, labels = dat[,1]) --- cross123 <[EMAIL PROTECTED]> wrote: > > Hello everyone, > I have a set of data in the following form, which > are stored in an Excel > file: > nick john peter > > lesson1 0.465 0.498 0.473 > lesson2 0.422 0.44 0.134 > lesson3 0.45 0.35 0.543 > > lesson4 0.590 0.64 0.11 > > lesson5 0.543 0.50.32 > > > What I want to do is a 2d-graph plot where I will > have the name of the > student in the X-axis and the name of the lesson in > the Y-axis and the > number from each pair will be used to construct the > plot. > I am newbie with R and I don't know which package > shall I use nor the > commands with which I will import my data in R so > that the plot will be > created... > > Any help would be greatly appreciated. __ 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] character string to name
Is one of these alternatives what you want?
# 1
x <- list()
x[["y"]] <- 1:4
x <- as.data.frame(x)
x
# 2
x <- data.frame(1:4)
names(x) <- "y"
x
# 3
x <- as.data.frame(sapply("y", function(x, y) y, 1:4, simplify = FALSE))
x
On 7/9/07, Jim Lemon <[EMAIL PROTECTED]> wrote:
> Hi folks,
>
> I thought I recalled a request for turning a character string into an
> object name as in:
>
> x$as.name("y")<-1:4
>
> OR
>
> x<-data.frame(as.name("y")=1:4)
>
> However, as.name and a few other uninformed attempts didn't even come
> close. A search of "character to name" produced no helpful functions.
> This isn't a very urgent request, but if anyone knows some trick to
> perform this transformation, I would like to hear about it. Thanks.
>
> 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.
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] why function 'sum' within 'aggregate' need an 'index'?
On Mon, 2007-07-09 at 20:14 +0800, jingjiang yan wrote: > Hi, people. > I am using R-2.5.0 now, when tried the function aggregate with sum, it > showed an error as following: > > a <- gl(3,10) > > b <- rnorm(30) > > aggregate(b,list(a),sum) > # here is the error message, it complained that an error in FUN(X[[1L]], > missing "INDEX", and no defaults value. > > but the tapply function will be okay. > > tapply(b,list(a),sum) > 1 2 3 > 2.113349 -5.972195 4.854731 > > furthermore, when I was using the R-2.5.0 pre-release version before. > it could work well. > > a <- gl(3,10) > > b <- rnorm(30) > > aggregate(b,list(a),sum) # it works well > Group.1 x > 1 1 -1.0330482 > 2 2 0.1235796 > 3 3 -1.0086930 > > tapply(b,list(a),sum)# so does tapply > 1 2 3 > -1.0330482 0.1235796 -1.0086930 > > So, who can tell what should I do to overcome this? > thanks a lot. Update to R 2.5.1 as your first example works for me [version info below]. If that is not possible, just use the tapply version for now. G > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major 2 minor 5.1 year 2007 month 07 day05 svn rev42131 language R version.string R version 2.5.1 Patched (2007-07-05 r42131) -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] character string to name
Hi folks,
I thought I recalled a request for turning a character string into an
object name as in:
x$as.name("y")<-1:4
OR
x<-data.frame(as.name("y")=1:4)
However, as.name and a few other uninformed attempts didn't even come
close. A search of "character to name" produced no helpful functions.
This isn't a very urgent request, but if anyone knows some trick to
perform this transformation, I would like to hear about it. Thanks.
Jim
__
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and provide commented, minimal, self-contained, reproducible code.
[R] why function 'sum' within 'aggregate' need an 'index'?
Hi, people. I am using R-2.5.0 now, when tried the function aggregate with sum, it showed an error as following: > a <- gl(3,10) > b <- rnorm(30) > aggregate(b,list(a),sum) # here is the error message, it complained that an error in FUN(X[[1L]], missing "INDEX", and no defaults value. but the tapply function will be okay. > tapply(b,list(a),sum) 1 2 3 2.113349 -5.972195 4.854731 furthermore, when I was using the R-2.5.0 pre-release version before. it could work well. > a <- gl(3,10) > b <- rnorm(30) > aggregate(b,list(a),sum) # it works well Group.1 x 1 1 -1.0330482 2 2 0.1235796 3 3 -1.0086930 > tapply(b,list(a),sum)# so does tapply 1 2 3 -1.0330482 0.1235796 -1.0086930 So, who can tell what should I do to overcome this? thanks a lot. [[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] Problem with Sweave and pdf version 1.4
Dear useRs,
I'm trying to use ggplot2 in Sweave (R 2.5.1). The plots use the alpha
channel, so I need to use pdf version 1.4. Search the mailinglist
archive I found two solutions: \SweaveOpts{echo = FALSE,
pdf.version=1.4} and explicit writing to a pdf 1.4 file. The latter
works but the first doesn't. Probably I'm doing something wrong (see the
Rnw file below). The file tmp_tmp.pdf is generated but is corrupt.
Using the second option, is there a way to create the filename based on
some variable. Something like
x <- "sometext"
filename <- paste(x, ".pdf", sep = "")
pdf(file=filename, version="1.4")
But how can I pass the filename to \includegraphics?
The Rnw file
\documentclass[11pt]{report}
\usepackage{Sweave}
\SweaveOpts{echo = FALSE, pdf.version=1.4, eps = FALSE}
\begin{document}
\begin{figure}
\centering
<>=
library(ggplot2)
x <- runif(100)
dataset <- data.frame(x = x, y = 5 * x + rnorm(100))
ggplot(dataset, aes(y = y, x = x)) + stat_smooth() + geom_jitter()
@
\caption{Here comes a caption.}
\label{fig:tmp}
\end{figure}
\begin{figure}
\centering
<>=
pdf(file="foo.pdf", version="1.4")
ggplot(dataset, aes(y = y, x = x)) + stat_smooth() + geom_jitter()
dev.off()
@
\incudegraphics{foo}
\caption{Here comes a caption.}
\label{fig:foo}
\end{figure}
\end{document}
Thanks in advance,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research 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
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] a little problem on selecting a subset from dataset A accordingto dataset B?
> AB <- with(B, subset(A, coords.x1 %in% X1)) > AB coords.x1 coords.x2 0 542250.9 3392404 7 541512.5 3394722 8 541479.3 3394878 9 538903.4 3395943 18 543274.0 3389919 19 543840.8 3392012 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of zhijie zhang Sent: Monday, 9 July 2007 2:43 AM To: R-help@stat.math.ethz.ch Subject: [R] a little problem on selecting a subset from dataset A accordingto dataset B? Dear Friends, I want to extract the records from A according to B, but the results are not correct because R says : The length of long object is not integer times on the length of short object. Anybody have met the same problem? How to do it correctly? length(A)=47 length(B)=6 A[A$coords.x1==B$X1,] #the program for the above task. I should get 6 records, but i only get former 4 records for the above reason. Thanks. The folloing shows dataset A and B. > A coords.x1 coords.x2 0 542250.89 3392404.1 1 538813.87 3388339.0 2 536049.19 3385821.6 3 533659.62 3383194.2 4 530642.30 3376834.9 5 529573.15 3378177.8 6 530853.82 3394838.8 7 541512.51 3394721.6 8 541479.33 3394877.8 9 538903.39 3395942.5 10 536019.95 3396286.1 11 538675.23 3384213.2 12 535127.95 3381255.4 13 533852.24 3378660.4 14 531360.91 3379273.8 15 539289.14 3375759.8 16 543410.51 3384353.1 17 543089.27 3388170.1 18 543274.03 3389919.2 19 543840.77 3392012.4 20 553383.55 3402401.8 21 554621.51 3397938.9 22 564096.42 3397524.4 23 567529.64 3398702.9 24 561798.76 3404864.0 25 562868.34 3405502.2 26 563145.22 3403192.1 27 562419.87 3404090.4 28 558321.85 3403879.9 29 567050.74 3404973.1 30 570609.70 3408742.4 31 556777.57 3397858.0 32 531353.38 3368596.6 33 533513.50 3372749.3 34 537543.19 3364284.8 35 538779.41 3368224.8 36 525930.09 3374067.7 37 522990.85 3369213.1 38 528826.37 3359019.0 39 533865.85 3362595.4 40 531200.25 3365053.0 41 551054.10 3377181.3 42 546974.19 3369284.8 43 572315.59 3359541.1 44 562703.63 3355173.4 45 558959.31 3357804.4 46 558531.39 3361741.1 > B X1X2 1 542250.89 3392404.1 2 541512.51 3394721.6 3 541479.33 3394877.8 4 538903.39 3395942.5 5 543274.03 3389919.2 6 543840.77 3392012.4 -- With Kind Regards, oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [*** ] Zhi Jie,Zhang ,PHD Tel:86-21-54237149 Dept. of Epidemiology,School of Public Health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 Email:[EMAIL PROTECTED] Website: www.statABC.com [*** ] oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [[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] rpart weight prior
On Sun, 8 Jul 2007, Aurélie Davranche wrote: Hi! Could you please explain the difference between "prior" and "weight" in rpart? It seems to be the same. But in this case why including a weight option in the latest versions? For an unbalanced sampling what is the best to use : weight, prior or the both together? The 'weight' argument (sic) has been there for a decade, and is not the same as the 'prior' param. The help file (which you seem unfamiliar with) says weights: optional case weights. parms: optional parameters for the splitting function. Anova splitting has no parameters. Poisson splitting has a single parameter, the coefficient of variation of the prior distribution on the rates. The default value is 1. Exponential splitting has the same parameter as Poisson. For classification splitting, the list can contain any of: the vector of prior probabilities (component 'prior'), the loss matrix (component 'loss') or the splitting index (component 'split'). The priors must be positive and sum to 1. The loss matrix must have zeros on the diagonal and positive off-diagonal elements. The splitting index can be 'gini' or 'information'. The default priors are proportional to the data counts, the losses default to 1, and the split defaults to 'gini'. The rpart technical report at http://mayoresearch.mayo.edu/mayo/research/biostat/upload/61.pdf may help you understand 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__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a little problem on selecting a subset from dataset A according to dataset B?
zhijie zhang wrote: > Dear Friends, >I want to extract the records from A according to B, but the results are > not correct because R says : > The length of long object is not integer times on the length of short > object. > Anybody have met the same problem? How to do it correctly? > > length(A)=47 > length(B)=6 > > A[A$coords.x1==B$X1,] #the program for the above task. I should get 6 > records, but i only get former 4 records for the above reason. > > Thanks. A[A$coords.x1 %in% B$X1,] coords.x1 coords.x2 1 542250.9 3392404 8 541512.5 3394722 9 541479.3 3394878 10 538903.4 3395943 19 543274.0 3389919 20 543840.8 3392012 ?is.element > The folloing shows dataset A and B. > > >> A >coords.x1 coords.x2 > 0 542250.89 3392404.1 > 1 538813.87 3388339.0 > 2 536049.19 3385821.6 > 3 533659.62 3383194.2 > 4 530642.30 3376834.9 > 5 529573.15 3378177.8 > 6 530853.82 3394838.8 > 7 541512.51 3394721.6 > 8 541479.33 3394877.8 > 9 538903.39 3395942.5 > 10 536019.95 3396286.1 > 11 538675.23 3384213.2 > 12 535127.95 3381255.4 > 13 533852.24 3378660.4 > 14 531360.91 3379273.8 > 15 539289.14 3375759.8 > 16 543410.51 3384353.1 > 17 543089.27 3388170.1 > 18 543274.03 3389919.2 > 19 543840.77 3392012.4 > 20 553383.55 3402401.8 > 21 554621.51 3397938.9 > 22 564096.42 3397524.4 > 23 567529.64 3398702.9 > 24 561798.76 3404864.0 > 25 562868.34 3405502.2 > 26 563145.22 3403192.1 > 27 562419.87 3404090.4 > 28 558321.85 3403879.9 > 29 567050.74 3404973.1 > 30 570609.70 3408742.4 > 31 556777.57 3397858.0 > 32 531353.38 3368596.6 > 33 533513.50 3372749.3 > 34 537543.19 3364284.8 > 35 538779.41 3368224.8 > 36 525930.09 3374067.7 > 37 522990.85 3369213.1 > 38 528826.37 3359019.0 > 39 533865.85 3362595.4 > 40 531200.25 3365053.0 > 41 551054.10 3377181.3 > 42 546974.19 3369284.8 > 43 572315.59 3359541.1 > 44 562703.63 3355173.4 > 45 558959.31 3357804.4 > 46 558531.39 3361741.1 > > >> B > X1X2 > 1 542250.89 3392404.1 > 2 541512.51 3394721.6 > 3 541479.33 3394877.8 > 4 538903.39 3395942.5 > 5 543274.03 3389919.2 > 6 543840.77 3392012.4 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Message Acknowledgement
This is just a quick confirmation to let you know that we received your message below at [EMAIL PROTECTED] Your input is important to us and we will get back to you as soon as we can. If you have any other questions please feel free to send us email or call our customer service department at 1-800-651-1415. Email customer service is availible 8:00 AM - 5:00 PM Central Time, Monday through Friday. Sincerely, Customer Service HomeVisions www.HomeVisions.com Your Message: -- CI:00864890 Your message was not delivered due to the following reason(s): Your message was not delivered because the destination computer was unreachable within the allowed queue period. The amount of time a message is queued before it is returned depends on local configura- tion parameters. Most likely there is a network problem that prevented delivery, but it is also possible that the computer is turned off, or does not have a mail system running right now. Your message was not delivered within 1 days: Mail server 178.23.220.84 is not responding. The following recipients did not receive this message: <[EMAIL PROTECTED]> Please reply to [EMAIL PROTECTED] if you feel this message to be in error. File attachment: homevisions.com A file attached to this email was removed because it was infected with a virus. Virus Name: [EMAIL PROTECTED] Virus ID:34256 __ 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] a little problem on selecting a subset from dataset A according to dataset B?
Dear Friends, I want to extract the records from A according to B, but the results are not correct because R says : The length of long object is not integer times on the length of short object. Anybody have met the same problem? How to do it correctly? length(A)=47 length(B)=6 A[A$coords.x1==B$X1,] #the program for the above task. I should get 6 records, but i only get former 4 records for the above reason. Thanks. The folloing shows dataset A and B. > A coords.x1 coords.x2 0 542250.89 3392404.1 1 538813.87 3388339.0 2 536049.19 3385821.6 3 533659.62 3383194.2 4 530642.30 3376834.9 5 529573.15 3378177.8 6 530853.82 3394838.8 7 541512.51 3394721.6 8 541479.33 3394877.8 9 538903.39 3395942.5 10 536019.95 3396286.1 11 538675.23 3384213.2 12 535127.95 3381255.4 13 533852.24 3378660.4 14 531360.91 3379273.8 15 539289.14 3375759.8 16 543410.51 3384353.1 17 543089.27 3388170.1 18 543274.03 3389919.2 19 543840.77 3392012.4 20 553383.55 3402401.8 21 554621.51 3397938.9 22 564096.42 3397524.4 23 567529.64 3398702.9 24 561798.76 3404864.0 25 562868.34 3405502.2 26 563145.22 3403192.1 27 562419.87 3404090.4 28 558321.85 3403879.9 29 567050.74 3404973.1 30 570609.70 3408742.4 31 556777.57 3397858.0 32 531353.38 3368596.6 33 533513.50 3372749.3 34 537543.19 3364284.8 35 538779.41 3368224.8 36 525930.09 3374067.7 37 522990.85 3369213.1 38 528826.37 3359019.0 39 533865.85 3362595.4 40 531200.25 3365053.0 41 551054.10 3377181.3 42 546974.19 3369284.8 43 572315.59 3359541.1 44 562703.63 3355173.4 45 558959.31 3357804.4 46 558531.39 3361741.1 > B X1X2 1 542250.89 3392404.1 2 541512.51 3394721.6 3 541479.33 3394877.8 4 538903.39 3395942.5 5 543274.03 3389919.2 6 543840.77 3392012.4 -- With Kind Regards, oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [***] Zhi Jie,Zhang ,PHD Tel:86-21-54237149 Dept. of Epidemiology,School of Public Health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 Email:[EMAIL PROTECTED] Website: www.statABC.com [***] oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [[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] [R-pkgs] ggplot 0.5.4
ggplot2 === ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics. Find out more at http://had.co.nz/ggplot2, and check out the over 500 examples of ggplot in use. Changes in version 0.5.4 -- * border now drawn on top of geoms, instead of below - this results in better appearance when adjusting scale limits * ggplot() + aes() now modifies existing default aesthetic mapping, rather than overwriting * polished examples in facet_grid Changes in version 0.5.3 -- * added experimental scatterplot matrix, see ?plotmatrix * added new border.colour and grid.minor.colour options for better control over plot appearance * updated theme_bw to do better when drawing a plot with white background * better default colour choices for gradients (and more discussion in examples) * fixed bug in ScaleGradient2 where scales with different positive and negative ranges were not scaled correctly * allow expressions as result from strip.text * fixed rare bug in geom_vline and geom_hline * fixed example in geom_abline * tweaked display of multiline axis labels Regards, Hadley ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] adding latex, html docs. to new packag
Edna Bell wrote: > Hi again! > > How do I create the Latex and HTML files for documentation for a new > package, please? > > Is there something in the R CMD stuff that would do it, or do I need > to produce by hand, pleaes? As the manual "Writing R Extensions" suggests, please write your documentation in the Rd format. Those files are converted automatically to latex and html (among other format) when the package is installed. Skeletons for the help files can be generated using prompt() or for a whole package, see ?package.skeleton. Uwe Ligges > thanks, > eb > > __ > 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] EM algorithm for Missing Data.
On 09-Jul-07 02:20:47, Marcus Vinicius wrote: > Dear all, > I need to use the EM algorithm where data are missing. > Example: > x<- c(60.87, NA, 61.53, 72.20, 68.96, NA, 68.35, 68.11, NA, 71.38) > > May anyone help me? > > Thanks. > > Marcus Vinicius The Dempster, Laird & Rubin reference given by Simon Blomberg is the classical account of the EM Algorithm for incomplete information, though there has been a lot more published since. However, more to the point in the present case: If the above is typical of your data, you had better state what you want to do with the data. Do you want to fit a distribution by estimating parameters? Are they observations of a "response" variable with covariates and you want to fit a linear model estimating the coefficients? Are they data from a time-series and you need to interpolate at the missing values? Etc.?? Depending on what you want to do, the way you apply the general EM Algorithm procedure may be very different; and a lot of applications are not covered by Dempster, Laird & Rubin (1977). And there may possibly be no point anyway: If all you want to do is estimate the mean of the distribution of the data, then the best procedure may simply be to ignore the missing data. Best wishes, Ted. E-Mail: (Ted Harding) <[EMAIL PROTECTED]> Fax-to-email: +44 (0)870 094 0861 Date: 09-Jul-07 Time: 09:18:56 -- 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] random sampling with some limitive conditions?
Dear Jian, This came up on R-help recently; I haven't got time to find the thread for you, but it shouldn't take too much hunting out. I suggested the following approach, based on the swap method of Roberts and Stone (1990) Island-sharing by archipelago species. Oecologia 85: 560-567. The code for this is appended at the end of this message. Below is an example: > dat <- matrix(scan(), ncol = 8, byrow = TRUE) 1: 1 0 0 0 1 1 0 0 9: 0 1 1 1 0 1 0 1 17: 1 0 0 0 1 0 1 0 25: 0 0 0 1 0 1 0 1 33: 1 0 1 0 0 0 0 0 41: 0 1 0 1 1 1 1 1 49: 1 0 0 0 0 0 0 0 57: 0 0 0 1 0 1 0 1 65: Read 64 items > dat ## your data [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,]10001100 [2,]01110101 [3,]10001010 [4,]00010101 [5,]10100000 [6,]01011111 [7,]10000000 [8,]00010101 rBinMat is the function appended below. We search for elements of dat that that are diagonal: 10 or 01 01 10 We do this by randomly selecting two rows and columns to find a 2x2 sub-matrix of dat. We check if it is diagonal, and if it is, we swap the 1's and 0's. This retains the row and column sums. If the sub-matrix is non-diagonal, we simply leave it as it is. This process is repeated many times in a "burn in" period, after which, random binary matrices can be produced. In the line below we use a burn in of 3 swaps - which takes about 9 seconds to prime the matrix. (in fact this matrix is achieved after making a further 1000 swaps as per argument skip = 1000) > system.time(ran.mat1 <- rBinMat(dat, burn.in = 3)) user system elapsed 9.556 0.104 9.683 > ran.mat1 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,]01001001 [2,]01101110 [3,]10110000 [4,]00010101 [5,]10010000 [6,]10011111 [7,]00000100 [8,]10000101 > rowSums(ran.mat1) [1] 3 5 3 3 2 6 1 3 > colSums(ran.mat1) [1] 4 2 2 4 3 5 2 4 Having primed our random matrix, we can use this matrix and produce a new random matrix from it by making a smaller number of swaps (default 1000), by setting the burn in to be 0. > ran.mat2 <- rBinMat(ran.mat1, burn.in = 0) > ran.mat2 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,]10001100 [2,]10110101 [3,]10100010 [4,]00011001 [5,]01000001 [6,]01011111 [7,]00000100 [8,]10010100 > rowSums(ran.mat2) [1] 3 5 3 3 2 6 1 3 > colSums(ran.mat2) [1] 4 2 2 4 3 5 2 4 > As you can see, the row and column sums are as per your original matrix. There are other methods to achieve these random binary matrices - some of which were mentioned in the recent thread. HTH G Ps: I cooked this up over lunch in response to the earlier thread. It could no doubt be improved upon. ### ## ## ## rBinMat() ## ## ## ## Function: ## ## = ## ## Generates random binary matrices that preserve row and column ## ## sums using the swap method of Roberts and Stone (1990) Island-## ## sharing by archipelago species. Oecologia 85: 560-567.## ## ## ## Arguments:## ## ==## ## x : Species presence/absence matrix (binary, 1/0s) ## ## burn.in : The "burn in" period required --- how many swaps to ## ## make to 'x' before a random matrix can be generated?## ## skip: The number of swaps to skip before drawing a matrix.## ## Once a matrix is burned in, it can be used in sub- ## ## sequent calls to rBinMat() [using "burn.in = 0"] for## ## generating further random matrices. In such cases, one ## ## might wish to skip n swaps before drawing the next ## ## matrix. ## ## ## ## Author : Gavin L. Simpson## ## Date:
[R] display data.frame with lines and colimns
hello,
to display a data.frame I use this syntax
dir.create(file.path(tempdir(),"R2HTML"))
target <- HTMLInitFile(file.path(tempdir(),"R2HTML"),filename="sample",
BackGroundColor="#EE")
HTML("Don't forget to use the CSS file in order to benefit from fixed-width
font",file=target)
tmp <- as.data.frame(matrix(rnorm(100),ncol=10))
HTML(tmp,file=target)
HTMLEndFile()
I obtain a good result but I'd like to display my data.frame with lines and
columns and when I use the syntax FOR R don't display all the data.frame just
for the last boucle (for).
Can you help me please?
thanks.
_
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] help on fisher.test(stats)?
Original Message Subject: [R] help on fisher.test(stats)? From: zhijie zhang <[EMAIL PROTECTED]> To: R-help@stat.math.ethz.ch Date: 09.07.2007 09:03 > Dear friends, > My dataset have many zeros, so i must use fisher exact test . > Unfortunately, the fisher.test(stats) function fail to do it. > Anybody knows how to do the fisher exact test with many zeros in the > dataset? > My dataset is: > a<-matrix(c(0,1,0,0,0,0,1,0,1,0,0,0,0,1,0,1,1,0,2,1,5,1,1,6,4,4,1,17,2,8,5,7,1,1,24,3,6,1,1,3,2,16,7,4,0,2,4,0,17,0,1,0,0,0,1,2),nrow=8,byrow=TRUE) > data.frame(a) > b<-a[,-7] > as.matrix(b) > c<-as.matrix(b) > > >> c >> > [,1] [,2] [,3] [,4] [,5] [,6] > [1,]010000 > [2,]010000 > [3,]011021 > [4,]116441 > [5,]285711 > [6,]361132 > [7,]740240 > [8,]010001 > >> fisher.test(c,workspace=20) >> > ŽíÎóÓÚfisher.test(c, workspace = 2e+17) : > ÍâœÓº¯Êýµ÷ÓÃʱ²»ÄÜÓÐNA(arg10) > ŽËÍâ: Warning message: > Ç¿Öƞıä¹ý³ÌÖвúÉúÁËNA > > Any suggestion or help are greatly appreciated. > Your workspace is by far to large. I have done it with > fisher.test(c,workspace=4000) Fisher's Exact Test for Count Data data: c p-value = 0.01548 alternative hypothesis: two.sided (btw. it took half an hour...) Simulation would also be an alternative approach: > fisher.test(c,simulate=T) Fisher's Exact Test for Count Data with simulated p-value (based on 2000 replicates) data: c p-value = 0.01349 alternative hypothesis: two.sided As you see the p-value is not that different, you could use more replications: > fisher.test(c,simulate=T,B=100) Fisher's Exact Test for Count Data with simulated p-value (based on 1e+06 replicates) data: c p-value = 0.01514 alternative hypothesis: two.sided and it is still much faster... Stefan -=-=- ... The most incomprehensible thing about the world is that it is comprehensible. (A. Einstein) __ 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] transform excel data into graph
Hello everyone, I have a set of data in the following form, which are stored in an Excel file: nick john peter lesson1 0.465 0.498 0.473 lesson2 0.422 0.44 0.134 lesson3 0.45 0.35 0.543 lesson4 0.590 0.64 0.11 lesson5 0.543 0.50.32 What I want to do is a 2d-graph plot where I will have the name of the student in the X-axis and the name of the lesson in the Y-axis and the number from each pair will be used to construct the plot. I am newbie with R and I don't know which package shall I use nor the commands with which I will import my data in R so that the plot will be created... Any help would be greatly appreciated. -- View this message in context: http://www.nabble.com/transform-excel-data-into-graph-tf4046056.html#a11493073 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rpart weight prior
Hi! Could you please explain the difference between "prior" and "weight" in rpart? It seems to be the same. But in this case why including a weight option in the latest versions? For an unbalanced sampling what is the best to use : weight, prior or the both together? Thanks a lot. Aurélie Davranche. __ 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] Calling R function in C
Hi R Users! Thanks in advance. I am using R-2.5.1 on Windows XP and I have installed all necessary tools such as perl and tools.exe. I am trying to use sample(1:100, 3, rep=F) in C. How can I use this R function in C? Once again thank you very much for your time. Regards, Debabrata (Deb) Statistician NSW Department of Commerce Sydney, Australia. - [[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] boot.ci
Dear boot.ers,
I ran a small program for training purposes and ended with problems in
boot.ci
bush <- c(rep(1, 840), rep(0, 660))
> f.mean <- function(y, id) {mean(y[id])}
> bushB <- boot(bush, f.mean, 1000)
> boot.ci(bushB, conf = 0.95, type = c('perc', 'bca'))
Error in bca.ci(boot.out, conf, index[1], L = L, t = t.o, t0 = t0.o, h =
h, :
estimated adjustment 'a' is NA
>
What's wrong in my setup? boot appears to work OK
Sincerly Fredrik Lundgren
PS. By the way - anyone who has "Resampling stats, standalone" for sale?
DS
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] help on fisher.test(stats)?
Dear friends, My dataset have many zeros, so i must use fisher exact test . Unfortunately, the fisher.test(stats) function fail to do it. Anybody knows how to do the fisher exact test with many zeros in the dataset? My dataset is: a<-matrix(c(0,1,0,0,0,0,1,0,1,0,0,0,0,1,0,1,1,0,2,1,5,1,1,6,4,4,1,17,2,8,5,7,1,1,24,3,6,1,1,3,2,16,7,4,0,2,4,0,17,0,1,0,0,0,1,2),nrow=8,byrow=TRUE) data.frame(a) b<-a[,-7] as.matrix(b) c<-as.matrix(b) > c [,1] [,2] [,3] [,4] [,5] [,6] [1,]010000 [2,]010000 [3,]011021 [4,]116441 [5,]285711 [6,]361132 [7,]740240 [8,]010001 > fisher.test(c,workspace=20) ´íÎóÓÚfisher.test(c, workspace = 2e+17) : Íâ½Óº¯Êýµ÷ÓÃʱ²»ÄÜÓÐNA(arg10) ´ËÍâ: Warning message: Ç¿ÖƸıä¹ý³ÌÖвúÉúÁËNA Any suggestion or help are greatly appreciated. -- With Kind Regards, oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [***] Zhi Jie,Zhang ,PHD Tel:86-21-54237149 Dept. of Epidemiology,School of Public Health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 Email:[EMAIL PROTECTED] Website: www.statABC.com [***] oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [[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.
