[R] problem installing R packages in Windows Vista
** High Priority **
I have recently installed the R program in Windows Vista. However, I am
experiencing problem installing some of the packages. Specifically, I wanted to
install BRugs package running R as an administrator. I issued the following
command in R and received the following error message.
install.packages(BRugs)
Warning in install.packages(BRugs):
argument 'lib' is missing: 'C\Users\norman\Documents/R/win-library/2.8'
Warning: unable to access index for repository
http://cran-za.r-project.org/bin/windows/contrib/2.8
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8
Warning message: package 'BRugs' is not available
Your prompt response will be greatly appreciated.
Disclaimer\ \ This message is confidential and may be co...{{dropped:20}}
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Re: [R] problem installing R packages in Windows Vista
This is not a problem in R, but with Internet access from your system.
It is an FAQ, see
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-Internet-download-functions-fail_002e
Another possibility is to download the file
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8/BRugs_0.4-2.zip
and use the menu item to install from a local zip file.
On Wed, 24 Dec 2008, norman Maiwashe wrote:
** High Priority **
Please make it a high priority to read the posting guide and rw-FAQ: see
the footer to this message.
I have recently installed the R program in Windows Vista. However, I am
experiencing problem installing some of the packages. Specifically, I
wanted to install BRugs package running R as an administrator. I issued
the following command in R and received the following error message.
I don't see an *error* message here. (warning != error .) It is warning
you of a problem on your machine or, possibly, the system you are
accessing.
install.packages(BRugs)
Warning in install.packages(BRugs):
argument 'lib' is missing: 'C\Users\norman\Documents/R/win-library/2.8'
Warning: unable to access index for repository
http://cran-za.r-project.org/bin/windows/contrib/2.8
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8
Warning message: package 'BRugs' is not available
Your prompt response will be greatly appreciated.
Disclaimer\ \ This message is confidential and may be co...{{dropped:20}}
__
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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.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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] filling values in a vector using smaller vector
I believe the following does what is wanted: desired - large desired[large] - small Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Milton Huang wrote: Dear list members: I am looking for an elegant (or efficient) way to accomplish the following: take a large boolean vector and fill the TRUE values with the values from a smaller boolean vector that has a length that is the number of TRUE values of the large vector. Example: large- c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE) small- c(TRUE, FALSE, TRUE) desired output = c(FALSE, FALSE, FALSE, *TRUE*, FALSE, FALSE, *FALSE*, FALSE, FALSE, FALSE, *TRUE*, FALSE) (without the asterisks! ) my first thought as someone new to R was ifelse(large,small, large) but that returns: c(FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE) because small is cycled to match the size of large instead of the size of the TRUE subset of large. I am guessing that there is probably a way to do this without writing a loop, but I just don't know the syntax. -mph __ R-help@r-project.org 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@r-project.org 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] filling values in a vector using smaller vector
Wacek Kusnierczyk wrote: Milton Huang wrote: Dear list members: I am looking for an elegant (or efficient) way to accomplish the following: take a large boolean vector and fill the TRUE values with the values from a smaller boolean vector that has a length that is the number of TRUE values of the large vector. Example: large- c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE) small- c(TRUE, FALSE, TRUE) desired output = c(FALSE, FALSE, FALSE, *TRUE*, FALSE, FALSE, *FALSE*, FALSE, FALSE, FALSE, *TRUE*, FALSE) replace(large, which(large), small) in fact, this will do: replace(large, large, small) vQ __ R-help@r-project.org 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] 4 questions regarding hypothesis testing, survey package, ts on samples, plotting
Ben Bolker wrote: Khawaja, Aman wrote: I need to answer one of the question in my open source test is: What are the four questions asked about the parameters in hypothesis testing? Please check the posting guide. * We don't answer homework questions (open source doesn't mean that other people answer the questions for you, it means you can find the answers outside your own head -- and in any case, we don't have any of way of knowing that the test is really open). * this is not an R question but a statistics question * please don't post the same question multiple times Besides, this is really unanswerable without access to your teaching material, which probably has a list of four questions somewhere... It is a bit like the History question: Who was what in what of whom? (Answer: King Gustav Adolf was a thorn in the eye of Christian IV) -- 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 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org 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] selecting a subset of a matrix based on a value occurring in 5 records
mat[,colSums(mat!=0)=5] Jacques VESLOT CEMAGREF - UR Hydrobiologie Route de Cézanne - CS 40061 13182 AIX-EN-PROVENCE Cedex 5, France Tél. + 0033 04 42 66 99 76 fax+ 0033 04 42 66 99 34 email jacques.ves...@cemagref.fr -Message d'origine- De : r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] De la part de Bob Green Envoyé : mercredi 24 décembre 2008 13:17 À : r-help@r-project.org Objet : [R] selecting a subset of a matrix based on a value occurring in 5 records Hello, I am hoping for some advice as to how I might create a subset of a matrix. The matrix is 176 x 3530. The rows are individual records and the columns words. I want to create a new matrix that only consists of words which occur in at least 5 records. For example, if column 7 is charges and this only appears in 4 records/rows this variable would not be included, whereas if column 109 was the word monitor and occurred in 95 records it would be saved into the new matrix. Values in the matrix are numbers, such that if a word does not occur in a record the cell contains a zero, whereas if it occurs 7 times there is a value of 7 for that record. It is the number of records rather than the than the column total that is the criteria for determing inclusion into the matrix. Any suggestions on how I might reduce the size of this matrix so as to include only those columns in which a word occurs at least in 5 records is much appreciated, regards Bob __ R-help@r-project.org 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@r-project.org 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 'cat' on data frame
On Dec 24, 2008, at 2:35 AM, Gundala Viswanath wrote: Dear all, I have the following data frame: raw.count Var1 Freq 1 AA 707 2 AC14 3 AT 3 But why when printint it using 'cat', it doesn't print the desired string AAA ? cat(raw.count$Var1, \n) 1 2 3 What's wrong with my cat command above. What's wrong is that Var1 is a factor rather than a character vector. Veslot's answers provide the proper method for dealing with that situation. -- David Winsemius - Gundala Viswanath __ R-help@r-project.org 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@r-project.org 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] Viewing code
How do you view the code for a built-in R command (i.e., if I want to see what R is doing when I run a glm() statement)? Regards, Stephen [[alternative HTML version deleted]] __ R-help@r-project.org 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] Fata; error:
Hi Antonio, Sounds like your .RData file might be corrupt. Did you try deleting it (or renaming it) and starting R again? The .RData file should be in the directory where you started R. HTH, Brian -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Antonio Paredes Sent: Wednesday, December 24, 2008 12:45 PM To: r-help@r-project.org Subject: [R] Fata; error: I just installed R 2.8.1 for windows. When I try to start the software I get the following: Fatal error: unable to restore saved data in .RData. Note that on my previous section I tried to read a large dataset and I got a message stating that no enough memory was avaliable (I don't have the complete log for that section) I wanted to ask how can I go about solving this problem, or do I need to remove and then reinstall R in order to solve the problem. I also wanted to know if someone can provide me with a reference (pdf, published book, or article) about the difference aspects of dealing with memory in R. -- -Tony [[alternative HTML version deleted]] __ R-help@r-project.org 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. -- This message w/attachments (message) may be privileged, confidential or proprietary, and if you are not an intended recipient, please notify the sender, do not use or share it and delete it. Unless specifically indicated, this message is not an offer to sell or a solicitation of any investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Merrill Lynch. Subject to applicable law, Merrill Lynch may monitor, review and retain e-communications (EC) traveling through its networks/systems. The laws of the country of each sender/recipient may impact the handling of EC, and EC may be archived, supervised and produced in countries other than the country in which you are located. This message cannot be guaranteed to be secure or error-free. This message is subject to terms available at the following link: http://www.ml.com/e-communications_terms/. By messaging with Merrill Lynch you consent to the foregoing. -- __ R-help@r-project.org 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] Tick and Label Color in Plot
Dear All, I would like to plot two quantities using two different scales along the two vertical y axes. On top of this, I would like to use two different colors (let us say red and blue) for the two vertical axes, their labels, their ticks and the text for each tick. I paste below a code snippet x - c(4,10,50,98) temp - c(1.3e-1,4.92e-2,9.48e-3,4.84e-3) conc - c(1.92,5.08,26.35,51.56) conc2 - c(7.5e-1,1.14,2.12,4.7) b - diff(range(temp))/diff(range(conc)) a - min(temp) - b*min(conc) pdf(D_k_and_R_mobility.pdf) par(mar=c(4.5,5,2,4.2)+0.1) plot(x, temp, type=b,lwd=2,col=transparent,lty=2,xlab=expression(paste(k)) ,ann=FALSE,yaxt=none, ylim=range(c(0.,1.4e-1)), xaxt=none, xlim=range(c(0,100)),cex.lab=1.4,cex.axis=1.2) lines(x, temp, col=blue,type=b,lwd=2,lty=1,pch=2) ticks -c(0, 0.035,0.07,0.105, 0.14) axis(side=2,at=ticks,labels=FALSE, col = blue,cex.lab=1.4,cex.axis=1.2) mtext(side = 2, text = ticks, at = ticks, col = blue, line = 1,cex.lab=1.4,cex.axis=1.2) mtext(side = 2, text = expression(paste(D[k])), line = 3,cex.lab=2.4,cex.axis=6.2, col=blue) ticks -c(0, 25,50,75, 100) axis(side=1,at=ticks, labels = ticks, col = black,cex.lab=1.4,cex.axis=1.2) lines(x, a + b*conc, col=red,type=b,lwd=2,lty=1,pch=4) lines(x, a + b*conc2, col=red,type=b,lwd=2,lty=1,pch=6) ticks -c(0,10,20,30,40,50) axis(4, at=a + b*ticks, labels=ticks,cex.lab=1.4,cex.axis=1.2, col=red) #this controls the 4th axis and what I want to do there! mtext(expression(paste(R[g(m)])),cex=1.4, 4, 3, col=red) legend(50,0.1, c(expression(paste(D[k])), expression(paste(R[m])),expression(paste(R[g]))), lwd=c(2,2,2),lty=c(2,1,1),pch = c(1,4,6),col=c(blue, red,red),box.lwd=1,box.lty=1, ,xjust = 1, yjust = 1) dev.off() The result is NOT what I am looking for, since I am having a lot of troubles in tuning both the color and the size of the labels, tick locations and so on. Can anyone fix this example? I had a look at http://tolstoy.newcastle.edu.au/R/help/03b/2708.html and http://www.mail-archive.com/r-h...@stat.math.ethz.ch/msg07033.html but obviously I am not quite there yet. Kind Regards and merry Xmas Lorenzo __ R-help@r-project.org 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] Viewing code
since 'glm' is an object, just type its name at the command prompt:
glm
function (formula, family = gaussian, data, weights, subset,
na.action, start = NULL, etastart, mustart, offset, control =
glm.control(...),
model = TRUE, method = glm.fit, x = FALSE, y = TRUE, contrasts = NULL,
...)
{
call - match.call()
if (is.character(family))
family - get(family, mode = function, envir = parent.frame())
if (is.function(family))
family - family()
if (is.null(family$family)) {
print(family)
stop('family' not recognized)
}
...
On Wed, Dec 24, 2008 at 12:49 PM, Stephen Collins
stephen_coll...@aon.com wrote:
How do you view the code for a built-in R command (i.e., if I want to see
what R is doing when I run a glm() statement)?
Regards,
Stephen
[[alternative HTML version deleted]]
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Non-finite finite difference error
Ravi, thank you for the explanation - that makes perfect sense, and it wouldn't have occurred to me to suspect a negative parameter based on the error. Using the elaborated syntax from the help page yields a lovely fit. Regards, Jason On Wed, Dec 24, 2008 at 10:57 AM, Ravi Varadhan rvarad...@jhmi.edu wrote: Hi Jason, The error message indicates that there was problem in estimating the gradient of objective function. It has nothing to do with your second data point. This could happen for a variety of reasons, but the most proximate cause of the problem seems due to a parameter being negative during the iteration. The best solution, most often, is to provide a better (or atleast a different) starting value. Look at the example in the help page for fitdistr: fitdistr(x, dgamma, list(shape = 1, rate = 0.1), lower = 0.01) Note that the above command specifies lower bounds on both the shape and the rate parameter (hence a different optimziation algorithm will be used in optim). Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: js.augus...@gmail.com Date: Tuesday, December 23, 2008 11:27 pm Subject: [R] Non-finite finite difference error To: r-help@r-project.org Hello, I'm trying to use fitdistr() from the MASS package to fit a gamma distribution to a set of data. The data set is too large (1167 values) to reproduce in an email, but the summary statistics are: Min. 1st Qu. Median Mean 3rd Qu. Max. 116.7 266.7 666.7 1348.0 1642.0 16720.0 The call I'm trying to make is: fitdistr(x,gamma) and the error is: Error in optim(x = c(3466.676842, 1666.749002, 2500.067852, 1200.053892, : non-finite finite-difference value [2] In addition: Warning message: In dgamma(x, shape, scale, log) : NaNs produced I found a couple of other posts from folks who were getting the same error from optim(), but did not find any useful tips for my situation. The error seems to indicate a problem with value 2 in my data set (1666.749002), but nothing seems odd about that value. I'm willing to pass along the full data set as an attachment if it would help. Thank you in advance! Jason S. Augustyn, Ph.D. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org 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] filling values in a vector using smaller vector
Milton Huang wrote:
Thank you both for such beautiful solutions. Just what I was looking for! I
love the Internet, R, and the R-list! There is so much opportunity to learn.
In fact, looking at the replace function, I see the two solutions are the
same:
replace
function (x, list, values)
{
x[list] - values
x
}
environment: namespace:base
not exactly. an application of replace generates a local copy of the
data, and whatever you pass to replace as x will not be modified, while
if you do the assignment yourself, you'll modify the data.
Thanks again. You made my day. Have a happy holiday season.
you too! meRRy chRistmas and a happy new yeaR to all subscRibeRs.
vQ
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[R] statistical significance, nonlinear regression
I am using nonlinear regression to fit a couple of variables to a set of measurements. I would like to do some significance tests for the estimated parameters. I am able to check the confidence intervals using the Jacobian coming out of nonlinear regression. I do see in a paper which shows t-value (it says estimated by White method??), f-value, f-test, and j-test, are these available in matlab, or I could code them myself but I need details about these tests. I would be glad if you could provide a reference... Thanks -- View this message in context: http://www.nabble.com/statistical-significance%2C-nonlinear-regression-tp21156969p21156969.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to skip re-installing CRAN packages when updating R?
Dear R-helpers: I am new to R and would like to seek your expert opinion on installation tip. Many thanks in advance. I want to update my R to the newest version and wonder the following two questions: Question 1: How can I install R and its contributed packages in a way so when updating R in the future, I do NOT need to re-install contributed packages used by R of last version. Question 2: Is it an ok-practice to just install all the CRAN packages (i.e., install.packages(available.packages()[,1]) ). Does someone do so? The reason I ask the second question is that if installing all available packages does Not consume too much time (say less than 2 hours), too much computer resource (I have big harddrive, so harddrive is probably not a concern. I guess computing speed will not be affected but not sure...) then, I do not need to bother Question 1 and will just install all available packages when updating R. Many Thanks in advance. Merry Christmas! -Sean [[alternative HTML version deleted]] __ R-help@r-project.org 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] snowfall sfInit error
Dear Mr. Ripley, snowfall 1.7 is finished, and is now working on Windows as intended - sorry for my oversight of that error. The given example now runs (as a sidenote: snow does not have to loaded explicitely, snowfall will do that). Also the NWS startup is fixed now (thanks to M. Schmidtberger for a small patch) and an error in sfSapply is fixed. Otherwise minor things were corrected or added. I uploaded the package to CRAN yesterday and beside it is downloadable from our site http://www.imbi.uni-freiburg.de/parallel Greetings, Jochen Knaus On Sat, 6 Dec 2008, chi...@gmail.com wrote: Dear all, I am trying to execute the simple example in snowfall http://cran.r-project.org/web/packages/snowfall/vignettes/snowfall.pdf ... require(snow) require(snowfall) sfInit( parallel=TRUE, cpus=2 ) sfLapply( 1:10, exp ) sfStop() I have installed the snow and snowfall packages in R on a machine with windows xp, however, after running the sfInit( parallel=TRUE, cpus=2 ) line I get an error ... Error in system(whoami, intern = TRUE, ignore.stderr = TRUE) : whoami not found Error in paste(sep = _, R, uname, format(Sys.time(), %H%M%S_%m%d%y)) : object uname not found I am the only (administrator) user of the computer. It has a dual core processor, and is not networked. I would be greatful if someone could tell me how to proceed. Follow the posting guide (see the footer of this message) and talk to the maintainer of 'snowfall'. Most likely it is not intended to be used on Windows, but has not declared that. 'whoami' and 'uname' are Unix programs, not Windows ones, but R's Sys.info() provides equivalent information. Kind regards Chibisi [[alternative HTML version deleted]] __ R-help@r-project.org 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@r-project.org 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] Implementing a linear restriction in lm()
Dear All! I want to test a coeffcient restriction beta=1 in a univariate model lm (y~x). Entering lm((y-x)~1) does not help since anova test requires the same dependent variable. What is the right way to proceed? Thank you for your help and marry xmas, Serguei Kaniovski Austrian Institute of Economic Research (WIFO) P.O.Box 91 Tel.: +43-1-7982601-231 1103 Vienna, AustriaFax: +43-1-7989386 Mail: serguei.kaniov...@wifo.ac.at http://www.wifo.ac.at/Serguei.Kaniovski [[alternative HTML version deleted]] __ R-help@r-project.org 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] command Polygenic gives error message concerning dimensions of data
Dear Sir/Madam, Since a few day now I try to use the command polygenic from the GenAbel package. However, I keep bumping up against an error message: Error in polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and kinship.matrix do not match. My data exists of 1240 individuals with 74 markers. It mainly consists of small families (2 or more brothers, father and mother; otherwise only the brothers are given). Genotypes are provided for the largest part of the members, whereas the phenotype is only given for the male individuals. I imported the data using the convert.snp.ped and load.gwaa.data commands. The kinship table was constructed with makekinship. When I look at the dimensions of the kinship table, it is exactly the same as the number of individuals in my dataset. I also provide you with the following information because maybe that gives a clue on where things are going wrong. When using the genetic control method via the qtscore command, I get the following message: data1.qt-qtscore(Testo~age+BMI,data1) Warning messages: 1: In qtscore(Testo ~ age + BMI, data1) : 265 observations deleted due to missingness 2: In qtscore(Testo ~ age + BMI, data1) : Number of observations 100, Lambda estimate is unreliable. Results for only a few SNPs are returned. Can you tell me what I'm missing? Thank you in advance, Kindest Regards, Veerle Bogaert Ghent University Hospital Veerle Bogaert Ghent University Hospital Department of Endocrinology 6K12 I.E. De Pintelaan 185 9000 Ghent Belgium Tel +32 9 332 34 13 Fax +32 9 332 38 86 __ R-help@r-project.org 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] overwrite title
Hi, useRs- I have a plot with a title generated automatically. I need to overwrite the title, but I can't figure out how to do that. I've tried the following: title( abc, bg='white') But, that does not set the title background as white. Now I am stuck and need your help. Thanks- -- View this message in context: http://www.nabble.com/overwrite-title-tp21156936p21156936.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] overwrite title
Lacking specifics about what you actually did, one can only guess. Have you yet tried setting ..., main = , within the plot call, whatever that might have been? Failing that, the way to specify the color of the main argument to title() is not bg (which is an argument for the plot device), but rather col.main At least that is how I read the par() help page. plot(1:10) title(main = test) #... now title(main=test, col.main=white) Doesn't completely white it out on my screen display. -- David Winsemius On Dec 24, 2008, at 2:27 PM, whizvast wrote: Hi, useRs- I have a plot with a title generated automatically. I need to overwrite the title, but I can't figure out how to do that. I've tried the following: title( abc, bg='white') But, that does not set the title background as white. Now I am stuck and need your help. Thanks- -- View this message in context: http://www.nabble.com/overwrite-title-tp21156936p21156936.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] statistical significance, nonlinear regression
Tests of statistical significance and/or confidence intervals for individual parameters in nonlinear regression are often meaningless and misguided. Nonlinear regression is **inherently** different than linear regression. It may make no physical sense whatever to eliminate *any* of the parameters describing, say, a series of interrelated chemical interactions. Determining what sequence of nested models to consider (which is the only thing that makes sense) is typically difficult and subject specific. Finally, statistical inference for nonlinear models is almost never exact, and the standard (e.g. likelihood based) approximations can be way off for small samples and certain data configurations. As for references -- are you kidding?! There are tons of books and papers out there. As you did not provide your identity, we have no idea what line of work you're in -- but you might start by looking for tutorials on the subject pitched to your profession and level of statistical understanding. Google is your friend here. -- Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of adam99 Sent: Wednesday, December 24, 2008 3:21 PM To: r-help@r-project.org Subject: [R] statistical significance, nonlinear regression I am using nonlinear regression to fit a couple of variables to a set of measurements. I would like to do some significance tests for the estimated parameters. I am able to check the confidence intervals using the Jacobian coming out of nonlinear regression. I do see in a paper which shows t-value (it says estimated by White method??), f-value, f-test, and j-test, are these available in matlab, or I could code them myself but I need details about these tests. I would be glad if you could provide a reference... Thanks -- View this message in context: http://www.nabble.com/statistical-significance%2C-nonlinear-regression-tp211 56969p21156969.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] statistical significance, nonlinear regression
On Dec 24, 2008, at 6:20 PM, adam99 wrote: I am using nonlinear regression to fit a couple of variables to a set of measurements. I would like to do some significance tests for the estimated parameters. I am able to check the confidence intervals using the Jacobian coming out of nonlinear regression. I do see in a paper which shows t-value (it says estimated by White method??), f-value, f-test, and j-test, are these available in matlab, or I could code them myself but I need details about these tests. I would be glad if you could provide a reference... Gosset WS, On the Probable Error of the Mean. (1908), Biometrika, 6:1. Fisher RA, The Distribution of the Partial Correlation Coefficient, (1924), Metron, 3: 329. -- David Winsemius Thanks -- View this message in context: http://www.nabble.com/statistical-significance%2C-nonlinear-regression-tp21156969p21156969.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] statistical significance, nonlinear regression
See ?confint2 in the nlrwr package for confidence intervals and for more info on hypothesis testing in nonlinear regression focused on R see the book associated with that package. On Wed, Dec 24, 2008 at 6:20 PM, adam99 adamquest...@gmail.com wrote: I am using nonlinear regression to fit a couple of variables to a set of measurements. I would like to do some significance tests for the estimated parameters. I am able to check the confidence intervals using the Jacobian coming out of nonlinear regression. I do see in a paper which shows t-value (it says estimated by White method??), f-value, f-test, and j-test, are these available in matlab, or I could code them myself but I need details about these tests. I would be glad if you could provide a reference... Thanks -- View this message in context: http://www.nabble.com/statistical-significance%2C-nonlinear-regression-tp21156969p21156969.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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@r-project.org 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] Class and object problem
Dear all, I have a problem with accessing class attributes. I was unable to solve this yet, but someone may know how to solve it. I'm trying to extract some information from the summary, and Akaike weight has the desired value. Object for a model fitted using the glmmML function from the glmmML package: result - glmmML(cbind (y, n-y)~ x+a+b+c, family = binomial, data, cluster$B!K(B library(MASS) stepAIC(result) Then calculated the delta AIC by hand (following is the best four). model1 - 0.0 model2 - 1.8 model3 - 4.2 model4 - 6.2 Then followed equation as below: *W - exp(-0.5 * Delta) / sum(exp(-0.5 * Delta))* However, result was always same value as [1] even each delta AIC is different values. I don't know why happened. I've also tried Ben's AIC tab in the bbmle package under the Ben's suggestion: summary - stepAIC(result) AICtab(summary) When I try to run the code from within a package, error came up as UseMethod(logLik) no method to use logLik. I've tried adding slot -summary (result) slotName (slot) but it didn't help, slotName is NULL. Thanks for any kind of suggestions! Odette r-help@r-project.org [[alternative HTML version deleted]] __ R-help@r-project.org 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.
