[R] [R-pkgs] smacof package for multidimensional scaling

Dear UserR's, The smacof package (see also our PsychoR repository on http://r-forge.r-project.org/projects/psychor/) is uploaded on CRAN. This package provides the following approaches of multidimensional scaling (MDS) based on stress minimization by means of majorization (smacof): - Simple

Re: [R] lsmeans

John Fox mcmaster.ca> writes: > Actually, the effects package does exactly what you suggest for continuous > predictors. But not for lme. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the post

[R] histogram tick labels

Dear Friends, I am doing a rather simple histogram on a vector of data, MR. I set breaks for the intervals: hist(MR,breaks=c(0, 2.9, 5.9, 8.9, 11.9,14.9, 17.9, 20.9)) My question is, how do I change the labels on the tick marks? I have looked at ?hist and can't find a clue... Thanks in advanc

Re: [R] exponential distribution

What do you mean by 'correct' here? If you do manually what glm() does, you would expect to get the same answer, but that is not independent verification. As far as I recall either glm nor survreg are calculation the exact variance in this case -- they are both making use of asymptotic theory

[R] Default Argument Passing in Script

Hi all, Currently I run R script with arguments the following ways $ R --vanilla < myscript.R ARGUMENT1 And in my script it is encoded as: __BEGIN__ args<-commandArgs() do_sth(args[3]) My question is that is there a way to set a default argument inside the R script? In Perl analogically wou

[R] R and C/C++ for loop

I want to call C/C++ in R to do the loops. Is it doable? If my whole code is a big loop, is it better to do the inverse thing, i.e. call R function in C/C++? Whichever is better, is there any online material which guide me the procedure? Thank you! -- View this message in context: http://www.n

[R] Multivariate adaptive regression spline (MARS)

Hi, all!!! I don't know if it is the right place to ask about MARS. I don't learn about statistics, but i have something to do about it. I'm confuse what MARS algorithm do (backward and forward stepwise). when i run 'mars' function from 'mda' library, it produced some outputs, but i don't unde

Re: [R] sample size in bootstrap(boot)

bootstrap() and samp.bootstrap() are part of the S+Resample package, see http://www.insightful.com/downloads/libraries You could modify boot() to allow sampling with size other than n. Use caution when bootstrapping with a sample size other than n. The usual reason for bootstrapping is inference

Re: [R] lsmeans

Dear Hadley, Actually, the effects package does exactly what you suggest for continuous predictors. Regards, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox > -Original Message-

Re: [R] optim, constrOptim: setting some parameters equal to each other

the example I just mailed had an error; it should have been: ## objective function that depends on all parameters, here a, b, c obfun <- function(a,b,c,dd) sum((dd - (exp(a * 1:100) + exp(b * 1:50) + exp(c * 1:25) ))^2) fr <- function(x, eqspec, dd, obfun) { ## assign variables for paramete

Re: [R] Installation of R bindings on Windows

>From within R try this: file.path(R.home(), "bin", "R.dll", fsep = "\\") On Sun, Jun 8, 2008 at 2:19 PM, Axel Etzold <[EMAIL PROTECTED]> wrote: > Dear all, > > I am trying to install a package of R bindings for the Ruby language on > Windows Vista ... > this involves some compilation work with

Re: [R] optim, constrOptim: setting some parameters equal to each other

Here is an example w/optim where you have an objective function F(x) where you have (possibly a few) constraints of form x_i=x_j, and you can specify the constraints flexibly, which is what I _think_ you want. An example from you would have been nice. ## objective function that depends on all para

Re: [R] optim, constrOptim: setting some parameters equal to each other

If 'F' is twice differentiable, this could be done fairly easily by writing 'F' as a function to be maximized with a1 = a + da, etc., and using the 'activePars' argument in maxNR{maxLik} to specify the constraints you want. More specifically, consider the following: Fmax <- f

Re: [R] lsmeans

> Well put Doug. I would add another condition, which I don't know how to > state precisely. The settings for the other terms, which are usually > marginal medians, modes, or means, must make sense when considered jointly. > Frequently when all adjustment covariates are set to overall marginal m

Re: [R] lsmeans

Dear Frank, This point is also correct, but whether this is a serious issue depends upon the structure of the model. With a linear predictor and, in a generalized linear model, expressing fitted values on the scale of the linear predictor, differences are preserved regardless of the "typical" valu

Re: [R] lsmeans

Dear Hadley, Unfortunately, the term "marginal" gets used in two quite different ways, and Searle's "population marginal means" would, I believe, be more clearly called "population conditional means" or "population partial means." This is more or less alternative terminology for "least-squares mea

Re: [R] lsmeans

Dear Doug, Your point is correct, of course, but if people are interested in computing marginal means (or marginal cell means), then they can do so simply and don't need a statistical model. I think that when such a model is fit, interest is typically in conditioning on the other explanatory varia

Re: [R] how to important a date file into R

> Hi: > I have a data file in the following format. The first three digits stand for the ID of a respondent such as 402, 403. Different respondents may have the same ID. Followed the ID are 298 single digit number ranging from 1 to 5. My question is how to read this data file into R. I tried "

[R] optim, constrOptim: setting some parameters equal to each other

Hello, and apologies for the upcoming naive questions. I am a biologist who is trying to teach himself the appropriate areas of math and stats. I welcome pointers to suggested background reading just as much as I do direct answers to my question. Let's say I have a function F() that takes varia

Re: [R] lsmeans

Douglas Bates wrote: On 6/7/08, John Fox <[EMAIL PROTECTED]> wrote: Dear Dieter, I don't know whether I qualify as a "master," but here's my brief take on the subject: First, I dislike the term "least-squares means," which seems to me like nonsense. Second, what I prefer to call "effect disp

Re: [R] lsmeans

On Sun, Jun 8, 2008 at 12:58 PM, Douglas Bates <[EMAIL PROTECTED]> wrote: > On 6/7/08, John Fox <[EMAIL PROTECTED]> wrote: >> Dear Dieter, >> >> I don't know whether I qualify as a "master," but here's my brief take on >> the subject: First, I dislike the term "least-squares means," which seems t

[R] Installation of R bindings on Windows

Dear all, I am trying to install a package of R bindings for the Ruby language on Windows Vista ... this involves some compilation work with Mingw. (The analogous process on Linux Ubuntu went fine, but for the Windows installation, I need to provide the location of the file analogous to the /usr

Re: [R] lsmeans

On 6/7/08, John Fox <[EMAIL PROTECTED]> wrote: > Dear Dieter, > > I don't know whether I qualify as a "master," but here's my brief take on > the subject: First, I dislike the term "least-squares means," which seems to > me like nonsense. Second, what I prefer to call "effect displays" are just

[R] label points on a graph

Hello everyone, I have a plot and I am wanting to label points as 1 through 20 I have the following code for the plot: dat<-read.table(file="C:\\Documents and Settings\\Owner\\My Documents\\colon cancer1.txt",header=T,row.names=1) file.show(file="C:\\Documents and Settings\\Owner\\My Documents\\co

Re: [R] R + Linux

I used Debian, Ubuntu, Mandrake etc., and use FreeBSD now. I like FreeBSD a bit more than Linux. R can run smoothly in FreeBSD as well. On Sat, Jun 7, 2008 at 2:13 AM, steven wilson <[EMAIL PROTECTED]> wrote: > Dear all; > > I'm planning to install Linux on my computer to run R (I'm bored of > W.

Re: [R] multinormality

Dear Hanen, Try also mshapiro.test in the mvnormtest package. HTH, Jorge On Sun, Jun 8, 2008 at 6:01 AM, hanen <[EMAIL PROTECTED]> wrote: > > is there any function under R that allows me to test the normality of my 92 > sumples? > -- > View this message in context: > http://www.nabble.com/mult

Re: [R] how to important a date file into R

Try this. From your printout it seems that there are some extraneous spaces in the file so first we read it in and remove the spaces and just in case remove any completely blank lines. Then we re-read it using read.fwf. Note that the widths= argument in read.fwf can be a list where we specify the

Re: [R] R + Linux

I typically use a Mac (I love it) with Aquamacs, LaTeX, and R, and recently started using Linux Ubuntu as well. Ubuntu is the only distribution I have ever tried, and I really like it. I like it so much that I would have made my switch complete, but cannot find replacement for the PDF cut a

Re: [R] txt file, 14000+ rows, only last 8000 appear

On Fri, Jun 06, 2008 at 02:30:56PM -0700, RobertsLRRI wrote: > when I load my data file in txt format into the R workstation I lose about > 6000 rows, this is a problem. Is there a limit to the display capabilities > for the workstation? is all the information there and I just can't see the > firs

Re: [R] multinormality

For a test of multivariate normality, there is mvnorm.etest in the energy package. Maria Rizzo On Sun, Jun 8, 2008 at 6:01 AM, hanen <[EMAIL PROTECTED]> wrote: > > is there any function under R that allows me to test the normality of my 92 > sumples? > -- > View this message in context: > http:

Re: [R] Adding a Rotated Density Plot to an Existing Plot

Thanks Jim! Thats just what I want. Cheers Rory jim holtman wrote: I forgot to make sure the axis ranges were the same: x <- rnorm(1000) x <- x + exp(-x/2) layout(matrix(rep(c(1,1,2), 2), 2, 3, byrow=TRUE)) boxplot(x, ylim=c(0.5,4)) rug(jitter(x), side=2) y <- density(x) plot(y$y, y$x, type=

[R] AUC steady state calculations

Hi, a collegue has send me an excel sheet with some plasma values, and now he wants to know the AUC steady state. I took a look at the CRAN taskviews, and came up with PK, PKtools, ... The AUC calculation, no problem with that, but how do I calculate the steady state? One way of thinking was wit

[R] exponential distribution

Dear all, I've tried to solve the Es. 12, cap 4 of "Introduction to GLM" by Annette Dobson. It's about the relationship between survival time of leukemia patients and blood cell count. I tried to fit a model with exponential distribution, first by glm (family gamma and then dispersion paramete

[R] multinormality

is there any function under R that allows me to test the normality of my 92 sumples? -- View this message in context: http://www.nabble.com/multinormality-tp17717230p17717230.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-pr

Re: [R] Adding a Rotated Density Plot to an Existing Plot

I forgot to make sure the axis ranges were the same: x <- rnorm(1000) x <- x + exp(-x/2) layout(matrix(rep(c(1,1,2), 2), 2, 3, byrow=TRUE)) boxplot(x, ylim=c(0.5,4)) rug(jitter(x), side=2) y <- density(x) plot(y$y, y$x, type='l',ylim=c(0.5,4)) On Sun, Jun 8, 2008 at 7:07 AM, Rory Winston <[EMAIL

Re: [R] Adding a Rotated Density Plot to an Existing Plot

This gets you close to the solution that you want: x <- rnorm(1000) x <- x + exp(-x/2) layout(matrix(rep(c(1,1,2), 2), 2, 3, byrow=TRUE)) boxplot(x) rug(jitter(x), side=2) y <- density(x) plot(y$y, y$x, type='l') On Sun, Jun 8, 2008 at 7:07 AM, Rory Winston <[EMAIL PROTECTED]> wrote: > Hi > >

Re: [R] eliminating and relabeling the first column

I am not sure exactly what you were trying to do. read.table will read your data into an object with R and you can change the row names: > dat <- read.table(textConnection("H1 H2 H3 + 1 2 3 + 4 54 6 + 6 7 8 + 3 2 1"), header=TRUE) > closeAllConnections() > dat H1 H2 H3 1 1 2 3 2 4 54 6 3

[R] Adding a Rotated Density Plot to an Existing Plot

Hi Consider the following graph: x <- rnorm(1000) x <- x + exp(-x/2) layout(matrix(rep(c(1,1,2), 2), 2, 3, byrow=TRUE)) boxplot(x) rug(jitter(x), side=2) plot(density(x)) What I would really like to do is to have the density plot rotated by 90 degrees so that I can see it line up with the rug

Re: [R] favorite useful tools?

At 15:16 07/06/2008, Carl Witthoft wrote: Hi, I'm relatively new to R, so I don't know the full list of base (or popular add-on packages) functions and tools available. For example, I tripped across mention of rle() in a message about some other problem. rle() turned out to be a handy shortc

[R] SARIMA Model Problem

Hi.. I get a below data from sofeware . For the SARIMA equation should be (1 - 0.991B^{12})z_t + 43.557 = (1+0.37B)(1-0,915B^{12})a_t as somebody advise me .. Then I use it to confrim the forecasting output but it look like this equation is not correct .. because it 's

Re: [R] how to important a date file into R

Hi, ?read.fwf Try, read.fwf("filename.ext",width=c(3,rep(1,298)),header=F) Blay yyan liu wrote: > > Hi: >I have a data file in the following format. The first three digits > stand for the ID of a respondent such as 402, 403. Different respondents > may have the same ID. Followed the I

Re: [R] Need to run R on Fedora 9.

On Sun, Jun 8, 2008 at 9:33 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: >>> I'm in need of a version of R that will run on fedora 9 and haven't been >>> able >>> to find one. I need this in order to run Bioconductor. Any advice? >> >> Why not say (as root) >> yum install R >> ? >> >> Worked for

Re: [R] Need to run R on Fedora 9.

Jonathan Baron wrote: On 06/05/08 09:28, RobertsLRRI wrote: I'm in need of a version of R that will run on fedora 9 and haven't been able to find one. I need this in order to run Bioconductor. Any advice? Why not say (as root) yum install R ? Worked for me. The point is that there