[R] R project web site

2008-08-24 Thread J Dougherty
Is anyone else encountering trouble viewing the basic www.r-project.org page? Or has it been changed recently so that google hasn't kept up? I find I can access the mirror of the CRAN page at http://www.maths.bris.ac.uk/R/, none of the *.org pages. Nor can I jump to the R homepage from the CR

[R] Extracting formula from an lm object

2008-08-24 Thread Murray Jorgensen
I want to extra the part of the formula not including the response variable from an lm object. For example if the lm object ABx.lm was created by the call ABx.lm <- lm( y ~ A + B + x, ...) Then ACx.lm is saved as part of a workspace. I wish to extract "~ A + B + x". Later in my code I will fi

Re: [R] Extracting formula from an lm object

2008-08-24 Thread Berwin A Turlach
G'day Murray, On Sun, 24 Aug 2008 18:34:39 +1200 Murray Jorgensen <[EMAIL PROTECTED]> wrote: > I want to extra the part of the formula not including the response > variable from an lm object. For example if the lm object ABx.lm was > created by the call > > ABx.lm <- lm( y ~ A + B + x, ...) > >

Re: [R] graphs for pretest data

2008-08-24 Thread Jim Lemon
On Sat, 2008-08-23 at 12:04 -0400, Juliet Hannah wrote: > Is there an easy way to make graphs for the following data. I have > pretest and posttest scores for men and > women. I would like to form a 'titlted segment' plot for the data. > That is, make segments joining the scores, > with different t

Re: [R] R project web site

2008-08-24 Thread Jim Lemon
On Sun, 2008-08-24 at 00:21 -0700, J Dougherty wrote: > Is anyone else encountering trouble viewing the basic www.r-project.org page? > > Or has it been changed recently so that google hasn't kept up? I find I can > access the mirror of the CRAN page at http://www.maths.bris.ac.uk/R/, none of

Re: [R] R project web site

2008-08-24 Thread Peter Dalgaard
J Dougherty wrote: Is anyone else encountering trouble viewing the basic www.r-project.org page? Or has it been changed recently so that google hasn't kept up? I find I can access the mirror of the CRAN page at http://www.maths.bris.ac.uk/R/, none of the *.org pages. Nor can I jump to the R

Re: [R] simple generation of artificial data with defined features

2008-08-24 Thread drflxms
Hi Christoph, perfect! Your code worked out of the box (copy and paste ;-). I had expected at least some lines of code, but this is really easy! So once you get used to command line, this is much more flexible (and comfortable!) than all these coloured windows. Can't tell you how happy I am, that

[R] Plotting 3 way Anova

2008-08-24 Thread Brown, Heidi
Hi I'd really like to get a bar plot showing the means of my anova data. I have looked everywhere and can only seem to find instructions for 2 way anova's. I basically want to look at the mean condition of my subjects spilt by age, sex and year (as a factor rather than a continuous variable,

Re: [R] simple generation of artificial data with defined features

2008-08-24 Thread drflxms
Hello all, beside saying again thank you for your help, I'd like to present the final solution of my problem and the results of the kappa-calculation: > election.2005 <- c(16194,13136,3494,3838,4648,4118) #data obtained via genesis-database of "Statistisches Bundesamt" www.destatis.de #simply cut

Re: [R] R project web site

2008-08-24 Thread George N. White III
On Sun, 24 Aug 2008, J Dougherty wrote: Is anyone else encountering trouble viewing the basic www.r-project.org page? Or has it been changed recently so that google hasn't kept up? I find I can access the mirror of the CRAN page at http://www.maths.bris.ac.uk/R/, none of the *.org pages. Nor c

Re: [R] Extracting formula from an lm object

2008-08-24 Thread Prof Brian Ripley
On Sun, 24 Aug 2008, Berwin A Turlach wrote: G'day Murray, On Sun, 24 Aug 2008 18:34:39 +1200 Murray Jorgensen <[EMAIL PROTECTED]> wrote: I want to extra the part of the formula not including the response variable from an lm object. For example if the lm object ABx.lm was created by the call

Re: [R] clustering and data-mining...

2008-08-24 Thread losemind
Here is some recent update: Any thoughts? I have collected a list of experiment result data. I put them into a table. There are N rows corresponding to N data points. For i-th row, it contains data of the form y_i = f(a_i, b_i, c_i, d_i, e_i, f_i), where f is a possibly stochastic function, a,

Re: [R] R project web site

2008-08-24 Thread ohri2007
Admin please check logs for denial of service attack.the website is anciently designed. Period ajay www.decisionstats.com On 8/24/08, Jim Lemon <[EMAIL PROTECTED]> wrote: > On Sun, 2008-08-24 at 00:21 -0700, J Dougherty wrote: >> Is anyone else encountering trouble viewing the basic www.r-project

[R] Eliminating columns that sum to zero

2008-08-24 Thread Wade Wall
Hi all, I am trying to look for a way to eliminate columns that sum to zero. Any help would be appreciated. Wade [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do r

Re: [R] Eliminating columns that sum to zero

2008-08-24 Thread Ben Bolker
Wade Wall gmail.com> writes: > I am trying to look for a way to eliminate columns that sum to zero. Any > help would be appreciated. x_without_zero_cols <- x[,colSums(x)!=0] If you want to make some return for this helpful advice, you could take this information and add it to the "R tips"

Re: [R] Eliminating columns that sum to zero

2008-08-24 Thread Douglas Bates
On Sun, Aug 24, 2008 at 11:54 AM, Ben Bolker <[EMAIL PROTECTED]> wrote: > > > Wade Wall gmail.com> writes: > >> I am trying to look for a way to eliminate columns that sum to zero. Any >> help would be appreciated. > > x_without_zero_cols <- x[,colSums(x)!=0] Of course, depending on the nature o

Re: [R] Plotting 3 way Anova

2008-08-24 Thread Richard M. Heiberger
Heidi, The interaction2wt function in the HH package does much of what you are looking for. You will probably need to download HH from CRAN. interaction2wt {HH} R Documentation Plot all main effects and twoway interactions in a multifactor design Description The main diagonal displays boxplots

[R] Plotting multiple curves on a plot

2008-08-24 Thread ascentnet
Greetings! I was wondering how to plot multiple equation on the same plot with the data? So if I have three equations: 1.y= 2.31X + -2.2 2.y= 2.27X^2 + 5.63X + 0.52 3.y= -1.53X^3 + 1.92X^2 + -4.72X + 4.57 and a datafram or a 2D matrix. I would also like the equations in different colors,

Re: [R] Plotting multiple curves on a plot

2008-08-24 Thread Rolf Turner
On 25/08/2008, at 4:49 AM, ascentnet wrote: Greetings! I was wondering how to plot multiple equation on the same plot with the data? So if I have three equations: 1.y= 2.31X + -2.2 2.y= 2.27X^2 + 5.63X + 0.52 3.y= -1.53X^3 + 1.92X^2 + -4.72X + 4.57 and a datafram or a 2D matrix. I w

[R] deconvolution: Using the output and a IRF to get the input

2008-08-24 Thread wolf zinke
Hi, Maybe someone could give me some pointers for my problem. So far I have not found a good solution, maybe it is just ill posed? I have a signal that is the result of an input signal convolved with a given impulse response function (IRF) plus noise. I want to use the this signal and the IR

[R] howto optimize operations between pairs of rows in a single matrix like cor and pairs

2008-08-24 Thread Adaikalavan Ramasamy
Hi, I calculating the output of a function when applied to pairs of row from a single matrix or dataframe similar to how cor() and pairs() work. This is the code that I have been using: pairwise.apply <- function(x, FUN, ...){ n <- nrow(x) r <- rownames(x) output <-

[R] problem using cat within Sweave code chunks when fig=TRUE

2008-08-24 Thread Paul.Rustomji
Hello R list I was intending to use a cat statement within Sweave code chunks that generate greaphs to generate a readme.txt file listing all the figures generated with a brief caption along the lines of: desired format of "readme.txt" _ figure1.eps caption for

Re: [R] deconvolution: Using the output and a IRF to get the input

2008-08-24 Thread Moshe Olshansky
Hi Wolf, Without noise you could use FFT, i.e. FFT of a convolution is the product of the individual FFTs and so you get the FFT of your input signal and using inverse FFT you get the signal itself. When there is noise you must experiment. You may want to filter the response before doing FFT.

Re: [R] deconvolution: Using the output and a IRF to get the input

2008-08-24 Thread stephen sefick
remember the the inverse of fft has to be divided by the number of observations. On Sun, Aug 24, 2008 at 8:35 PM, Moshe Olshansky <[EMAIL PROTECTED]> wrote: > Hi Wolf, > > Without noise you could use FFT, i.e. FFT of a convolution is the product of > the individual FFTs and so you get the FFT of

[R] "rval, symbol print name too long"?

2008-08-24 Thread Jan Akko Eleveld
Is there anyone who can tell me what this means (I call a table, that is stores as csv file): Error in do.call("data.frame", rval) : symbol print-name too long Thanks you in advance,Akko Eleveld _ [[alternative HTML versio

[R] Specifying random effects distribution in glmer()

2008-08-24 Thread Robert A. LaBudde
I'm trying to figure out how to carry out a Poisson regression fit to longitudinal data with a gamma distribution with unknown shape and scale parameters. I've tried the 'lmer4' package's glmer() function, which fits the Poisson regression using: library('lme4') fit5<- glmer(seizures ~ time

Re: [R] howto optimize operations between pairs of rows in a single matrix like cor and pairs

2008-08-24 Thread jim holtman
Use Rprof to see where time is being spent. If it is in FUN, then there is probably no way to "optimize" outside of changing the way FUN works. So the first thing is to decide where time is being spent. On Sun, Aug 24, 2008 at 6:35 PM, Adaikalavan Ramasamy <[EMAIL PROTECTED]> wrote: > Hi, > > I

Re: [R] Specifying random effects distribution in glmer()

2008-08-24 Thread Simon Blomberg
Are you trying to fit a Poisson GLMM with Gamma random effects? I don't think you can do that using (g)lmer, which assumes a Gaussian distribution for the random effects. You might have a look at the hnlmix function in Jim Lindsey's repeated package. Or you could use Bayesian methods in JAGS, BUGS

[R] Igraph library: How to calculate APSP (shortest path matrix) matrix for a subset list of nodes.

2008-08-24 Thread dinesh kumar
Dear R Users, I have a network of 25000 total nodes and a list of 500 node which is a subset of all nodes. Now I want to calculate the APSP (all pair shortest path) matrix only for these 500 nodes. I would appreciate any help. Thanks in advance Dinesh -- Dinesh Kumar Barupal Research Associate

Re: [R] Extracting formula from an lm object

2008-08-24 Thread Murray Jorgensen
Thanks to Professors Ripley and Turlach for their help. Brian's solution was simple and elegant but Berwin's was also informative. Murray Jorgensen Prof Brian Ripley wrote: On Sun, 24 Aug 2008, Berwin A Turlach wrote: G'day Murray, On Sun, 24 Aug 2008 18:34:39 +1200 Murray Jorgensen <[EMAIL

Re: [R] [BioC] similarity between two gene lists with varied length

2008-08-24 Thread xie weibo
Hi, Weiwei, I think you can try fisher exact test simply. Take all genes of your organism as sample pool and your question is that: when you selected two gene lists from the sample pool, how to judge the independence of the two gene lists. The fisher exact test worked for this type of question. B

Re: [R] Igraph library: How to calculate APSP (shortest path matrix) matrix for a subset list of nodes.

2008-08-24 Thread Moshe Olshansky
As far as I know/remember, if your graph is connected and contains E edges then you can find the shortest distance from any particular vertex to all other vertices in O(E) operations. You can repeat this procedure starting from every node (out of the 500). If you have 100,000 edges this will req

[R] cbind in data.frame

2008-08-24 Thread Yuan Jian
hi, when I used cbind to combine columns, some contents of columns has been replaced by number. in the script below, column should be aaa,bbb,ccc but I was given 1,2,3. but when I change the column to vector, it gave me correct contents. can you please tell me why?   > d<-read.table("aaa.txt") >

Re: [R] Igraph library: How to calculate APSP (shortest path matrix) matrix for a subset list of nodes.

2008-08-24 Thread Moshe Olshansky
I was too optimistic - the complexity is O(E*log(V)) where V is the number of nodes, but since log(25000) < 20 this is still reasonable. --- On Mon, 25/8/08, Moshe Olshansky <[EMAIL PROTECTED]> wrote: > From: Moshe Olshansky <[EMAIL PROTECTED]> > Subject: Re: [R] Igraph library: How to calculat

Re: [R] cbind in data.frame

2008-08-24 Thread Charles Plessy
Le Sun, Aug 24, 2008 at 10:56:43PM -0700, Yuan Jian a écrit : > hi, > when I used cbind to combine columns, some contents of columns has been > replaced by > number. in the script below, column should be aaa,bbb,ccc but I was given > 1,2,3. > but when I change the column to vector, it gave me cor