[R] msm

I am reading the comprehensive on-line documentation about msm. The positive side is that it seems it has been designed for biomedical statistics, like Clinical Trials. The bad side is that it does not seem to model observations sequences that are not independent but instead are autocorrelated, as

[R] choice of an HMM package

We are trying to build a human respiration model. Preliminary analysis of some breathing signals has shown that humans breathe through switching among a finite number of patterns. Hidden Markov seems to be the right approach. Since most of our code is written in R scripting language, finding an R p

Re: [R] PAM: how to get the best number of clusters

). Is this at all possible ? Thank you very much, Maura On Fri, Oct 31, 2008 at 12:18 AM, Dylan Beaudette <[EMAIL PROTECTED] > wrote: > On Thursday 30 October 2008, Maura E Monville wrote: > > I have the book you mentioned. It basically describes the silhouette > > meth

Re: [R] PAM: how to get the best number of clusters

positive silhouette value. This procedure would spare a lot of CPU time. Thank you very much, Maura On Thu, Oct 30, 2008 at 7:25 PM, Dylan Beaudette <[EMAIL PROTECTED]>wrote: > On Thursday 30 October 2008, Maura E Monville wrote: > > I have a pretty big similarity matrix (2870x2870).

[R] PAM: how to get the best number of clusters

I have a pretty big similarity matrix (2870x2870). I will produce even bigger ones soon. I am using PAM to generate clusters. The desired number of output clusters is a PAM input parameter. I do not know a-priopri what is the best clusters layout . I resorted to the silhouette test. It takes forev

[R] FastICA

Is the FastICA R implementation as good as the MatLab Implementation ? I would appreciate talking to someone who has used FastICA for R. Thank you very much. -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing li

[R] How can I display a characters table ?

I would like to generate a graphics text. I have a 67x2 table with 5-character string in col 1 and 2-character string in col 2. Is it possible to make such a table appear on a graphics or a message-box pop-up window ? Thank you so much. -- Maura E.M _

[R] two questions about regression models and clustering routines

I managed to use an example (see attachment) of clever regression routines. I customized it to suit my needs. The initial model I try to fit consists of the first 10 powers of time (time the observation was recorded) and the first 10 powers of the phase. In fact my files record patients' breathing

[R] regsubsets - package(leaps)

Please, can someone suggest me where to find a description for the attributes of the summary of "regsubsets", that is: "which" "rsq""rss""adjr2" "cp" "bic""outmat" "obj" ?? Thank you so much. -- Maura E.M [[alternative HTML version deleted]] _

Re: [R] Cross Spectrum Analysis

R function "spectrum" expects a time series as input. I have attached a compressed archive with two detrended and denoised signals (txt format) whose spectra I would like to compare. I start out trying to generate a multivariate time series. Please, notice the different signals length. Moreover, R

Re: [R] Cross Spectrum Analysis

nd it useful to look at both the no log plot and then the logscale plot > (just remove the log="no") > > plot(x, plot.type="marginal") #this is the default type (the > powerspectrum) > plot(x, plot.type="phase") > plot(x, plot.type="coherency&q

[R] Cross Spectrum Analysis

I am reading some documentation about Cross Spectrum Analysis as a technique to compare spectra. My understanding is that it estimates the correlation strength between quasi-periodic structures embedded in two signals. I believe it may be useful for my signals analysis. I was referred to the R

Re: [R] Graphic text

ch can have nice grahpics > and "pop up's". LaTeX is well supported in R via the Sweave suite and > various other packages such as xtable() and the latex functions in > Hmisc() and many other packages. > > Sorry I've not provided any direct solution, >

[R] How to recognize objects in clusters

I have a set of objects ready for clustering, say {O1,O2,,On} Each such object carries an identifier/label/tag, say {a1,a2, . an}. My goal is to recognize the objects after clustering. That is I'd like to know which cluster object Oi has been assigned to and which are the other objects {Oj,

[R] How to assign identifiers to objects being clustered

I have a number of non-periodic signals , that have been detrended and denoised. Each signal is made up of a variable number of cycles non necessarily of the same length. We can now fit a regression model to each cycle and then use the returned coefficients, together with some other data, to form c

Re: [R] Graphic text

gt; Putting a newline, '\n' works in your main/sub text string works for me > on both *NIX and Windows... > > > > > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Neil Shephard > Sent: Friday, February

[R] Graphic text

Can R handle graphic text ? I mean something like a pop-up message window or a text widget ? Thank you so much. -- Maura E.M __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www

[R] Biomechanics

I serched the R packages list for Biomechanics applications. I am sure there are many. Maybe I did not use the right keywords. Please, any suggestion is welcome. Thank you in advance, -- Maura E.M [[alternative HTML version deleted]] __ R-help

[R] JGR for Linux/SuSE

I apologize for being pedantic. I got JGR working for a very short time yesterday. This morning I realized some patch installed by the on-line SuSE updates had again messed up my monitor. Now the situation seems back to normal as far as the monitor is concerned. But neither JGR nor CrossOver (Windo

[R] R on Mac PRO does anyone have experience with R on such a platform ?

I saw there exists an R version for Mac/OS. I'd like to hear from someone who is running R on a Mac/OS before venturing on getting the following computer system. I am in the process of choosing a powerful laptop 17" MB PRO 2.6GHZ(dual-core) 4GBRAM Thank you so much, -- Maura E.M

[R] R GUI installation on Linux/SuSE 10.3

After a long sufferance I had succeeded in installing R GUI on my Linux/SuSE system. It worked fine. Unluckily a system upgrade patch messed up my monitor so I had to reinstall SuSE 10.3 and every other application on top of it. I have R running back with text interface. I tried to get the nice R

Re: [R] R configuration is not finding the installed f2c cross-compiler

uld be much better off installing your OS's Fortran compiler. > > > > > On Mon, 21 Jan 2008, Maura E Monville wrote: > > > Last Friday my computer monitor was messed up by on-line patches update. > > I had to reinstall everything from the o.s. and all applications

[R] R configuration is not finding the installed f2c cross-compiler

Last Friday my computer monitor was messed up by on-line patches update. I had to reinstall everything from the o.s. and all applications on top of it. I have downloaded R source from the official site. I have uncompressed the archive and ran the configure as root in /usr/local/bin. The configura

Re: [R] R on Linux 64-bit

the problem ? Thank you. Maura On Jan 21, 2008 11:50 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Maura E Monville wrote: > > I have been running R on my Linux/SuSE for over 2 months. I know it > > works. > > Some time ago it aborted as it ran out of memory in spit

Re: [R] R on Linux 64-bit

ches. I am reinstalling all the applications after reinstalling the O.S. Thank you so much, Maura On Jan 21, 2008 8:29 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Maura E Monville wrote: > > I am downloading the latest R source code R-2.6.1.tar.gz > > > > I am instal

[R] R on Linux 64-bit

I am downloading the latest R source code R-2.6.1.tar.gz I am installing ion a 64-bit machine. Is the configuration script the proper one for 64-bin installation ? I mean the compiler and linker options ..? Thanks you, Maura -- Maura E.M [[alternative HTML version deleted]] ___

[R] two plots on the same page

I'd like to know why I cannot get a plot and the QQnorm in the same sheet. The commands are simple but: library(nlme) glmod1 <- gls(upfmla,correlation=corAR1(),method="ML") summary(glmod1) par(mfrow = c(2,1)) plot(glmod1, main="GLS Residuals vs. GLS Fitted") qqnorm(glmod1) No matter what (I

[R] Error: cannot allocate vector of size ... Bcc: Add Cc | Add Bcc

I read the subject message in a number of R archived emails. Since I am experiencing the same problem: > upfmla A ~ T + cosP + cos2P + cos4P + cos5P + sin3P + sin5P + cosP2 + sinP3 + P2 > glmod <- gls(upfmla,correlation=corAR1(),method="ML") Error: cannot allocate vector of size 491.3 Mb > di

[R] package clim.pact

I would like to try the SSA approach with my data. If i am not mistaken there is a package named "clim.pact" in the R repository that does that. I tried to download on my Linux box and it failed as it cannot resolve a dependency that is only needed for Windows platform (that is written in the site

Re: [R] leaps

Thank you very much for the example. I think interactively I could get something. But my obstacle is to write an R script that processes my set of data automatically. My difficulty is to extract the information that appears on the screen, when R is operated interactively, from a scripts. Let me g

[R] R command "leap"

After applying the "step" command to a long list of predictors I came up with the following showing there still are some non significant coefficients. I'd like to try the command "leap". However, I don't quite understand how it returns the spared predicting variables. Can please, someone help ? Ta

Re: [R] package "growth" ... where is it ?

t; command where the package has been already downloaded. I tried different parameters, and repos=NULL, but I could not succeed. What is the pitfall here ? Thank you very much, Maura On Dec 8, 2007 7:12 PM, Marc Schwartz <[EMAIL PROTECTED]> wrote: > On Sat, 2007-12-08 at 18:42 -0600, Maura

[R] package "growth" ... where is it ?

I would like to install the package "growth" as it contains the function "corgram" and some other presumably useful stuff for time series analysis. I can see it is in R standard library list: http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/doc/html/packages.html

[R] fatal error from R function "gls"

I would appreciate some help with the followiing error ... what did I do wrong and what is the woraroud. > library(nlme) > glmod <- gls(A ~ T +cosP +cos2P +cos4P +cos5P +sin3P +sin5P +cosP2 +sinP3 +P2, correlation=corAR1(),method="ML") Error: cannot allocate vector of size 491.3 Mb I have a bunc

[R] Plotting + saving to file on Linux

Thanks to all those of you who answered my question about how to save a plot to a file. But now I have another problem. That is I wish to see / examine the plot on the screen in advance of saving it to a file. If I launch X11() or pdf() or Poscript() the plot does not appear on my screen .. So I ha

[R] How can I save a plot ?

I recently installed R 2.6 on Linux/SuSE When I was running the previous version on Windows I was able to save my plots from a script. There was a command "savePlot" that is no more retrieved in the last version. In this scenario, how can I tell R to save the currently displayed plot to a file ? Th

r-help@r-project.org

I have got R GUI working on SuSE 10.3 The workaround is to set an environment variable that prevents the java related error. See http://en.opensuse.org/Xlib.lock I tried to install 3 packages that I need through the R GUI. When I installed "cluster" I noticed on R console the error messages I'm co

[R] R package "segmented"

Has anyone successfully used R package "segmented" ? I tried on my data and could not get the syntax right. In addition, I wonder whether it only operates with continuous variables as I deal with discrete variables. I was contacted by its author and, upon his request, I forwarded one of my files wh

[R] R GUI for Linux

I have downloaded and tried to install JGR - Java GUI for R - Version 1.5. I followed all the instructions (at least in my best resolution) and installed Java latest version. R installation complete fine. Has anyone succeded in installing JGR on SuSE 10.3 ? In the following I hade detailed the fail

Re: [R] R installation on Linux/SuSE10.3

I am installing in /usr/local/bin where I have to be root even if I changed the access right to some sub directories by chmod. The installation completed fine (all stages: /config, make, make install). But no icon was created on my desktop. It works just typing in on the command line. It has no GU

[R] R installation on SuSE 10.3

I have downloaded the source code for Linux. the ./configure procedure can find gcc but cannot find f77 or f2c I have looked for the above compiler with Test and installed all what pertains to Fortran. Still not even the man pages for f77 anf fc2 work >. Where is f77 and f2c with linux 10.3 ?? Th

[R] Where can I find package "segmented" ?

I tried to install "segmented" from three different repositories but I keep getting the following message on R window: ... Please, advice where to find this package. Thank you in advance. Maura > utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: packag

[R] R segmented package

Most of the data sets I'm dealing with exhibit a time trend. We would like to get rid of the time trend. The plot shows in some cases a monotonic increase of the dependent variable with time. This is the easiest case. In some other cases the plot shows a time trend where the dependent variable chan

[R] Error from lm.fit follow-up

I found myself the reason of the failure. The last row of the matrix input to lm contains all NAs for some reason that I'm going to investigate. I apologize for my previous message. Please, discard it. Sincerely, -- Maura E.M [[alternative HTML version deleted]] ___

[R] doubts about Silhouette

Sorry for the long message. I'm doing my best to try to explain myself. I have fitted a spline to my data, I have fitted a spline, filled in the missing data by replicating the spline coefficients associated to the last node. I obtained a number of dendograms by different combination of distance a

[R] which package does interpSpline belong to ?

I have searched for "interpSpline" and got the following: interpSpline(splines) Create an Interpolation Spline Type 'help(FOO, package = PKG)' to inspect entry 'FOO(PKG) TITLE'. I looked for a package named "splines" executable for Windows but could not find it. Thank you in adavance --

Re: [R] R dynamic memory management

e' would be a lot more efficient). Since we > have no idea of what you loop looks like it is hard to provide more > suggestions. > > On 10/9/07, Maura E Monville <[EMAIL PROTECTED]> wrote: > > I have a loop that processes all the raw data files in agiven directory. &g

[R] R dynamic memory management

I have a loop that processes all the raw data files in agiven directory. It should allocate only the memory to accomodate the filenames list. Each file is loaded into RAM one at a time and saved to another directory after processing. The R script runs fine but it had some memory problems so it was

[R] Clustering techniques using R

Now that I've loaded a file into an R data.frame and played with linear regression until I got a good model, my next step is clustering using the coefficients of the regression model (I have many files) Thanks to some R experts' guidelines I could find plenty of documentation on regression analys

[R] P-P plot

Sorry for my silly questions. I'm a beginner with R and most statistics concepts. I carried out a simple linear regression where the dependent variable is explained through a combination of powers of cos(independent variable). I can see R returned a good R^2 factor (> 0.99) but I have a hard time a

[R] nonlinear regression

I would appreciate some suggestions about nonlinear regression available in R ... possible methods and plenty of worked out examples I have a bunch of noisy curves representing breathing amplitude from medical physics experiments recoding patients' breathing tracks in form of Amplitude, Phase

[R] How can I write routines and scripts in the R environment ?

*I would like to plot some semi-periodic signals as a function of the phase expressed as a value in [0,2PI]* *The problem is that the phase data is reported as the residual of the division by 2PI.* *For instance if the phase is 10.359 rd then:* *15.359 / 6.283185 = 2*6.283185 + 2.79263* *then onl

[R] beginner's questions ... sorry

I have 316 files. Each file represents a patient's breathing track (respiratory signal recorded for a variable number of cycles). All files have the same are made up of a header followed by a variable number of records. Each record contains 7 comma separated fields. The patient ID is recorder in th

[R] Flaw in the installation procedure ?

R printed out the following error messages during the installation of the package "clusterfly": > *install.packages("clusterfly", repos = getOption("repos"),dependencies =TRUE) *--- Please select a CRAN mirror for use in this session --- trying URL ' http://umfragen.sowi.uni-mainz.de/CRAN/bin/win