Re: [R] Trying to write a linear regression using MLE and optim()

2005-05-31 Thread Gabor Grothendieck
On 5/30/05, Ajay Shah [EMAIL PROTECTED] wrote: I wrote this: # Setup problem x - runif(100) y - 2 + 3*x + rnorm(100) X - cbind(1, x) # True OLS -- lm(y ~ x) # OLS likelihood function -- ols.lf - function(theta, K, y, X) { beta - theta[1:K] sigma - exp(theta[K+1]) e - (y -

Re: [R] Unique arrangements of a vector

2005-05-31 Thread Uwe Ligges
Tarmo Remmel wrote: Dear List, Running on a PC (Windows 2000) with 256 MB RAM, Version R1.9.1 This one is quite outdated... I have a relatively simple problem, which I can solve for relatively small datasets, but run into difficulties with larger ones. I believe that my approach is a hack

Re: [R] R GUI for Linux?

2005-05-31 Thread Gavin Simpson
White, Charles E WRAIR-Wash DC wrote: John: Thank you for your interest. After more investigation I see that my problem is with linking tcltk to R. tcl 8.4.7-2 and tk 8.4.7-2 are tuned to fc3 (Fedora Core 3) and part of the standard installation. However, required file locations are different

[R] Barplot2 Title

2005-05-31 Thread Navarre Sabine
Hello, I would like to know if it's possible to modify the name of groups of bar because on my barplot2, I have 5 groups of bars and one of them is called User Contributes and when I save the plot User contributes is to big so I don't have it on my plot! Is it pssible to put the name

Re: [R] FANNY function in R package cluster

2005-05-31 Thread Martin Maechler
Aamir == Aamir M [EMAIL PROTECTED] on Mon, 30 May 2005 15:57:29 -0400 writes: Aamir Dear All, I am attempting to use the FANNY fuzzy Aamir clustering function in R (Kaufman Rousseeuw, 1990), Aamir found in the cluster package. I have run into a Aamir variety of

[R] apply the function factor to multiple columns

2005-05-31 Thread Bliese, Paul D LTC USAMH
I have a case where I would like to change multiple columns containing numbers to factors. I can change each column one at a time as in: TEMP.FACT$EXPOS01-factor(TEMP.FACT$EXPOS01,levels=c(1,2,3),labels=c(No ne,Low Impact,MedHigh Imp))

Re: [R] apply the function factor to multiple columns

2005-05-31 Thread Dimitris Rizopoulos
you could try this way: dat - data.frame(V1 = factor(1:3), V2 = factor(1:3), V3 = factor(1:3)) dat[1:3] - lapply(dat[1:3], factor, labels = c(None, Low Impact, MedHigh Imp)) dat I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public

[R] Solved: linear regression example using MLE using optim()

2005-05-31 Thread Ajay Narottam Shah
Thanks to Gabor for setting me right. My code is as follows. I found it useful for learning optim(), and you might find it similarly useful. I will be most grateful if you can guide me on how to do this better. Should one be using optim() or stats4::mle? set.seed(101) #

Re: [R] persp, add lines/highlights

2005-05-31 Thread Robin Hankin
Hello everyone I always cut-n-paste Paul's suggestions and end up learning something! In this case, though, I have a query. I was wondering how the second persp() call dealt with hidden line removal, because pieces of mesh with NA values are see-through. If you replace xi in the code below

[R] How to access to sum of dissimilarities in CLARA

2005-05-31 Thread Amir Safari
Dear Matthias, So many thanks for your answer. Let me please to say I mean the SUM of dissimilarities. For example I want to compare the result of a clustering with k=4 with another clustering with k=5 . How is it possible to compare these two results ? What give us p$diss? ( a lot of

Re: [R] Piecewise Linear Regression

2005-05-31 Thread Achim Zeileis
On Mon, 30 May 2005 19:38:58 -0400 (EDT) Abhyuday Mandal wrote: Hi, I need to fit a piecewise linear regression. x = c(6.25,6.25,12.50,12.50,18.75,25.00,25.00,25.00,31.25,31.25,37.50,37. 50,50.00,50.00,62.50,62.50,75.00,75.00,75.00,100.00,100.00) y =

Re: [R] R GUI for Linux?

2005-05-31 Thread Ernesto Jardim
Sander Oom wrote: Hi Charles, Warm felt sympathies for your struggles. I consider myself a happy GUI user and have also struggled with the 'command line' history and lack of out-of-the-box functionality associated with Linux. However, Linux does have many, many advantages over other OS's, so

[R] How to access to Data within a cluster

2005-05-31 Thread Amir Safari
Dear All , For more process on data resulting clustering, one needs to access data within any cluster. How it is possible in CLARA? $clustering :gives us clustering vector as mixed, so it isn't as separate $clusinfo: gives us dissimilarities, Thanks a lot Amir

[R] LPC

2005-05-31 Thread Stephen Choularton
I want to use the LPC to estimate the vocal tract of various speakers making short utterances. Can anyone point me in the direction of a script that extracts the correct features Stephen -- Internal Virus Database is out-of-date. Checked by AVG Anti-Virus. [[alternative HTML

[R] lm/lme cross-validation

2005-05-31 Thread Arne.Muller
Hello, is there a special package/method to cross-validate linear fixed effects and mixed effects models (from lme)? I've tried cv.glm on an lme (hoping that it may deal with any kind of linear model ...), but it raises an error: Error in eval(expr, envir, enclos) : couldn't find function

Re: [R] R GUI for Linux?

2005-05-31 Thread A.J. Rossini
If you really want something closer to an IDE, add ECB to that mix (Emacs Code Browser). ESS does some minimal connections to it, for code browsing between functions, data.frame creations, and S4 class constructions. On 5/31/05, Jari Oksanen [EMAIL PROTECTED] wrote: On Tue, 2005-05-31 at

[R] Null space (or kernel) and image of a matrix

2005-05-31 Thread Aleš Žiberna
Hello! Does anyone now if there exist a function that would compute a null space (or kernel - Ker) of a matrix and maybe also one that would compute an image (Im) of a matrix. I tried R-site search and google, However I found notnihg useful! Thanks for any sugestions! I am also not sure

Re: [R] How to access to Data within a cluster

2005-05-31 Thread Sean Davis
On May 31, 2005, at 6:04 AM, Amir Safari wrote: Dear All , For more process on data resulting clustering, one needs to access data within any cluster. How it is possible in CLARA? $clustering :gives us clustering vector as mixed, so it isn't as separate Amir, I assume that you want to

[R] Pairs plot

2005-05-31 Thread Frédéric Ooms
Hello, I would like to draw a pair plot with a lot of descriptors (see the attached file) and due to the number of descriptors contained in the file I am not able to view the plot I only end up with really small square in the graphic device. In am working with the windows version of R. Thanks

Re: [R] How to access to sum of dissimilarities in CLARA

2005-05-31 Thread TEMPL Matthias
Hello Amir, You can use e.g. validity measures from the cluster.stats() function from Christian Hennig. It *depends on your data*, which and if a validity criteria of cluster.stats can be used to give an answer to the question, which number of cluster is the right choice. In case of the

[R] X11() and pseudo color

2005-05-31 Thread joerg van den hoff
we are running R under Solaris with SunRay Terminals, which are set to 8 bit color to comply with some other software. In this configuration, X11() opens with colortype=true, i.e., it is not recognized that actually the display is only 8 bit. This leads to error messages (advising to use

[R] lars / lasso with glm

2005-05-31 Thread Bliese, Paul D LTC USAMH
We have been using Least Angle Regression (lars) to help identify predictors in models where the outcome is continuous. To do so we have been relying on the lars package. Theoretically, it should be possible to use the lars procedure within a general linear model (glm) framework - we are

[R] Please help me update my address book on Ringo

2005-05-31 Thread Jean-Luc Allard
undefined [[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

[R] POSIX problem

2005-05-31 Thread David Scott
I am having trouble with creating a POSIXct object. If I create a variable of class Date first out of the date part of my data, I am ok, but if I just paste the date and time parts together and try and create the POSIXct object, I have problems. Here is a toy example created from the actual

Re: [R] Pairs plot

2005-05-31 Thread Uwe Ligges
I guess you (well, in fact do not) want something like pairs(X, gap=0, pch=.) Uwe Ligges Frédéric Ooms wrote: Hello, I would like to draw a pair plot with a lot of descriptors (see the attached file) and due to the number of descriptors contained in the file I am not able to view the

[R] Plot Font Size in Sweave

2005-05-31 Thread Doran, Harold
Dear List I'm working to modify the font size inside of an plot generated using Sweave. I found a thread in the archives addressing this issue from F. Leisch which suggests the solution below. I'm wondering if this is still the best option for this problem or if another solution may exist. Here

[R] Theta and clumping (or aggregation) parameter k

2005-05-31 Thread Johan Kotze
Hi all, in R the glm.nb models return a theta value, the aggregation parameter for negative binomial distributions. Crawly in his S-Plus book talks about the clumping (aggregation) parameter k. Are these two things (theta and k) different, and if so, what would be the relationship between the two?

RE: [R] R GUI for Linux?

2005-05-31 Thread White, Charles E WRAIR-Wash DC
Thanks for the tip. I thought that 'Base' files were installed already but I know better now. Unfortunately, I'm still not up and running yet. Since I don't have access to the subject machine at the moment, I'll be even more vague than usual. I installed the development versions of tcltk and

Re: [R] Barplot2 Title

2005-05-31 Thread Marc Schwartz
On Tue, 2005-05-31 at 10:22 +0200, Navarre Sabine wrote: Hello, I would like to know if it's possible to modify the name of groups of bar because on my barplot2, I have 5 groups of bars and one of them is called User Contributes and when I save the plot User contributes is to big so I don't

Re: [R] R GUI for Linux?

2005-05-31 Thread Bo Peng
ESS looks very good but why should I load more than 30MB on the memory to work on a text file ? and why do I need to lear all the tricks and features of emacs just to edit a text file ? One of the advantages (and disadvantages) of linux applications like emacs is that you can, if you

Re: [R] R GUI for Linux?

2005-05-31 Thread Gavin Simpson
White, Charles E WRAIR-Wash DC wrote: Thanks for the tip. I thought that 'Base' files were installed already but I know better now. Unfortunately, I'm still not up and running yet. Since I don't have access to the subject machine at the moment, I'll be even more vague than usual. Base refers

[R] [DEM01 WD/MV: Virus!]

2005-05-31 Thread DEM01_WatchDog_Demon
GROUP securiQ.Watchdog Server: DEM01 --- This mail item contained attachments which were virus-infected. The attachment(s) has/have been removed and were NOT sent on. Please update your ANTVIRUS program and virus-check

[R] FYI: Problems while loading package class (VR)

2005-05-31 Thread Tuszynski, Jaroslaw W.
Hi, Today, I performed automatic updates of packages and somehow lost class package. I loaded a library that depended on it and got: Error: package 'class' could not be loaded In addition: Warning message: there is no package called 'class' in: library(pkg, character.only = TRUE,

[R] GLM question

2005-05-31 Thread Laetitia Mestdagh
I am unfamiliar with R and I’m trying to do few statistical things like GLM and GAM with it. I hope my following questions will be clear enough: My datas ( y(i,j ))are run off triangles for example : J=1 J=2 J=3 I=1 1 2 3 I=2 4 5 I=3 6 My model is :

Re: [R] FYI: Problems while loading package class (VR)

2005-05-31 Thread Uwe Ligges
Tuszynski, Jaroslaw W. wrote: Hi, Today, I performed automatic updates of packages and somehow lost class package. I loaded a library that depended on it and got: Error: package 'class' could not be loaded In addition: Warning message: there is no package called 'class' in:

Re: [R] Solved: linear regression example using MLE using optim()

2005-05-31 Thread Douglas Bates
Ajay Narottam Shah wrote: Thanks to Gabor for setting me right. My code is as follows. I found it useful for learning optim(), and you might find it similarly useful. I will be most grateful if you can guide me on how to do this better. Should one be using optim() or stats4::mle?

RE: [R] GLM question

2005-05-31 Thread Gesmann, Markus
It appears that you try to do some insurance reserving analysis. Have a look at http://finzi.psych.upenn.edu/R/Rhelp02a/archive/15315.html, this might be helpful. Regards Markus -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Laetitia Mestdagh Sent:

RE: [R] FYI: Problems while loading package class (VR)

2005-05-31 Thread Tuszynski, Jaroslaw W.
What happens after you reinstalling it? After installing VR bundle everything works perfectly. All problems solved. Version of R? platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor

RE: [R] Null space (or kernel) and image of a matrix

2005-05-31 Thread Huntsinger, Reid
The null space or kernel of a matrix A would be the subspace of vectors v such that Av = 0. That is, it's the solution space of a homogeneous linear system of equations whose coefficients are the rows of A. R implements many ways to solve such systems. The image is the set of vectors of the form

[R] A suggestion to improve ifelse behaviour with vector yes/no arguments

2005-05-31 Thread Mäkinen Jussi
Dear All, I luckily found the following feature (or problem) when tried to apply ifelse-function to an ordered data. test - c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE) ifelse(test, 0, 1:4) [1] 0 0 0 4 1 2 3 It roots into the ifelse-syntax: ans[!test !nas] - rep(no, length.out =

Re: [R] A suggestion to improve ifelse behaviour with vector yes/noarguments

2005-05-31 Thread Dimitris Rizopoulos
there is nothing problematic there! According to the help-page of ifelse(), in the Details section you get: If yes or no are too short, their elements are recycled. and this is what you get in your example. Best, Dimitris Dimitris

RE: [R] Null space (or kernel) and image of a matrix

2005-05-31 Thread davidr
help.search(null space) gives Null(MASS) Null Spaces of Matrices PLEASE PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html David Reiner Rho Trading Securities, LLC -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]

Re: [R] Formatting numbers with a limited amount of digits consistently

2005-05-31 Thread Marc Schwartz
On Mon, 2005-05-30 at 23:53 -0400, Gabor Grothendieck wrote: On 5/30/05, Duncan Murdoch [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: On 5/30/05, Duncan Murdoch [EMAIL PROTECTED] wrote: Henrik Andersson wrote: I have tried to get signif, round and format to display numbers

Re: [R] lars / lasso with glm

2005-05-31 Thread Thomas Lumley
On Tue, 31 May 2005, Bliese, Paul D LTC USAMH wrote: We have been using Least Angle Regression (lars) to help identify predictors in models where the outcome is continuous. To do so we have been relying on the lars package. Theoretically, it should be possible to use the lars procedure within

RE: [R] lars / lasso with glm

2005-05-31 Thread Liaw, Andy
From: Thomas Lumley On Tue, 31 May 2005, Bliese, Paul D LTC USAMH wrote: We have been using Least Angle Regression (lars) to help identify predictors in models where the outcome is continuous. To do so we have been relying on the lars package. Theoretically, it should be possible

Re: [R] Scaling data

2005-05-31 Thread Sean Davis
I didn't look at your data, but you might try: help(scale) Sean On May 31, 2005, at 10:46 AM, Frédéric Ooms wrote: Hello, How could I scale and center the data contained in the attached file since I would like to do this before doing a PCA analysis on them as well as drawing boxplot.

[R] jpeg function problem with rterm.exe

2005-05-31 Thread Audouy Jerome \(ext_sub\)
Hello, I'm starting using R and runned a little script. The generated graphic could be exported correctly with RGui.exe (file - save as - jpeg - etc.) But if I try to run the same script with Rterm.exe and followed by: jpeg(file=test.jpeg, quality=90) The created jpeg file is completely white

Re: [R] Scaling data

2005-05-31 Thread Uwe Ligges
Frédéric Ooms wrote: Hello, How could I scale and center the data contained in the attached file since I would like to do this before doing a PCA analysis on them as well as drawing boxplot. DB_molprop.txt __ R-help@stat.math.ethz.ch mailing

Re: [R] jpeg function problem with rterm.exe

2005-05-31 Thread Uwe Ligges
Audouy Jerome (ext_sub) wrote: Hello, I'm starting using R and runned a little script. The generated graphic could be exported correctly with RGui.exe (file - save as - jpeg - etc.) But if I try to run the same script with Rterm.exe and followed by: jpeg(file=test.jpeg, quality=90) The

Re: [R] Formatting numbers with a limited amount of digits consistently

2005-05-31 Thread Duncan Murdoch
Marc Schwartz wrote: Final note to Henrik: Note that the IEEE 754 rounding standard as implemented in R results in: round(18.15, 1) [1] 18.1 formatC(18.15, format = f, digits = 1) [1] 18.1 sprintf(%5.1f, 18.15) [1] 18.1 This is because the rounding method implemented is the go to

Re: [R] FYI: Problems while loading package class (VR)

2005-05-31 Thread Uwe Ligges
Tuszynski, Jaroslaw W. wrote: What happens after you reinstalling it? After installing VR bundle everything works perfectly. All problems solved. Version of R? platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status

Re: [R] lars / lasso with glm

2005-05-31 Thread Wensui Liu
please check the library lasso2. On 5/31/05, Bliese, Paul D LTC USAMH [EMAIL PROTECTED] wrote: We have been using Least Angle Regression (lars) to help identify predictors in models where the outcome is continuous. To do so we have been relying on the lars package. Theoretically, it should

Re: [R] A suggestion to improve ifelse behaviour with vector yes/no arguments

2005-05-31 Thread Duncan Murdoch
Mäkinen Jussi wrote: Dear All, I luckily found the following feature (or problem) when tried to apply ifelse-function to an ordered data. test - c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE) ifelse(test, 0, 1:4) [1] 0 0 0 4 1 2 3 It roots into the ifelse-syntax: ans[!test !nas] -

[R] pdf error msg

2005-05-31 Thread Matt McCall
I get the following error message when trying to start a pdf file: pdf(hi.pdf) Error in PDF(file, old$family, old$encoding, old$bg, old$fg, width, height, : unable to start device pdf In addition: Warning message: cannot open `pdf' file argument `hi.pdf' *** malloc[477]: Deallocation

[R] post hoc kruskal wallis

2005-05-31 Thread amberfer
Hola, Tengo un problema con el post hoc kruskal wallis. No encuentro en el SSPS ningún test estadístico para el post hoc. En el libro de Zar proponen el Turkey-type nonparametric multicomparison. Mi problema es que tengo muchos datos y hacerlo a mano es complicado. El R es un programa que

Re: [R] POSIX problem

2005-05-31 Thread Christoph Buser
Dear David I tried to reproduce your example. It is not exact the same. When I create a dataframe, character are transformed to factors except I use I() to protect them. PeopleData.df - data.frame(StartDate = c(29/10/2001, 7/12/2001, 16/11/2001, 28/11/2001,

[R] plane3d

2005-05-31 Thread Jim Milks
I am attempting to fit a logistic regression plane to a 3-D scatterplot (which was generated using scatterplot3d). I've noticed that the help pages of scatterplot3d include a function titled plane3d. However, when I attempt to use the function, I get the following message: Error: couldn't

Re: [R] A suggestion to improve ifelse behaviour with vector yes/no arguments

2005-05-31 Thread Thomas Lumley
On Tue, 31 May 2005, Duncan Murdoch wrote: Mäkinen Jussi wrote: Dear All, I luckily found the following feature (or problem) when tried to apply ifelse-function to an ordered data. test - c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE) ifelse(test, 0, 1:4) [1] 0 0 0 4 1 2 3 snippage

[R] read.delim2 regarding #

2005-05-31 Thread Hai Lin
Hello R experts: When I tried to read my data into R, it does not take # sign A subset of Exp.txt is: Experiment name assay id Varname (A1)DBA TPA 6h/DBA Acetone rep1(A1) #3 4090A90C1 (A2)DBA TPA 6h/DBA Acetone rep2(A2) #3 4091A91C1 The command is: Exp -

Re: [R] pdf error msg

2005-05-31 Thread Thomas Lumley
On Tue, 31 May 2005, Matt McCall wrote: *** malloc[477]: Deallocation of a pointer not malloced: 0x143cf5c0; This could be a double free(), or free() called with the middle of an allocated block; Try setting environment variable MallocHelp to see tools to help debug And this is a double

[R] is there material about Longitudinal Data Analysis with R?

2005-05-31 Thread ronggui
i am studying Longitudinal Data Analysis and want to carry it with R.anyone knows any materials about Longitudinal Data Analysis with R in the internet which i can download? thank you. __ R-help@stat.math.ethz.ch mailing list

Re: [R] plane3d

2005-05-31 Thread Achim Zeileis
On Tue, 31 May 2005 11:40:09 -0400 Jim Milks wrote: I am attempting to fit a logistic regression plane to a 3-D scatterplot (which was generated using scatterplot3d). I've noticed that the help pages of scatterplot3d include a function titled plane3d. However, when I attempt to use the

Re: [R] read.delim2 regarding #

2005-05-31 Thread Sundar Dorai-Raj
Hai Lin wrote: Hello R experts: When I tried to read my data into R, it does not take # sign A subset of Exp.txt is: Experiment name assay id Varname (A1)DBA TPA 6h/DBA Acetone rep1(A1) #3 4090A90C1 (A2)DBA TPA 6h/DBA Acetone rep2(A2) #3 4091A91C1 The command is: Exp -

[R] Add Columns and Order for Rbind?

2005-05-31 Thread khobson
I am using rbind to add one list with one row to another master list. The problem is that not all columns exist in both lists. What methods would you recommend to reorder one list based on the column names of another? If both sets have the same order and columns, I can then use rbind. I

RE: [R] Errors in Variables

2005-05-31 Thread John Sorkin
I have a routine that corrects regression coefficients for the bias towards zero that occurs when there is error in the measurement of the independent variable. The code only works for a single independent variable, i.e. y~x. At this time the program does not calculate the SE of the

RE: [R] xmlAttrs and problems with reading node attributes of XML file (b ug?)

2005-05-31 Thread Tuszynski, Jaroslaw W.
Duncan, Thanks, that that make sense, I have never encountered namespaces so I did not recognized them. So in my example xmlns=a xmlns:xsi=b are namespace variables, and xsi:schemaLocation=c is a Schema-Related Markup attribute. This last one seemed to be handled strangely, since it is listed as

Re: [R] Add Columns and Order for Rbind?

2005-05-31 Thread Gabor Grothendieck
On 5/31/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I am using rbind to add one list with one row to another master list. The problem is that not all columns exist in both lists. What methods would you recommend to reorder one list based on the column names of another? If both

Re: [R] Formatting numbers with a limited amount of digits consistently

2005-05-31 Thread Gabor Grothendieck
On 5/31/05, Marc Schwartz [EMAIL PROTECTED] wrote: On Mon, 2005-05-30 at 23:53 -0400, Gabor Grothendieck wrote: On 5/30/05, Duncan Murdoch [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: On 5/30/05, Duncan Murdoch [EMAIL PROTECTED] wrote: Henrik Andersson wrote: I have

[R] help

2005-05-31 Thread jose silva
Dear all:   I have this:  A1 B1 C1 D1 E1 A2 B2 C2 D2 E2 A3 B3 C3 D3 E3   And I want this A1 E1 B1 E1 C1 E1 D1 E1 A2 E2 B2 E2 C2 E2 D2 E2 A3 E3 B3 E3 C3 E3 D3 E3   Example:   m-

[R] Shared Frailty in survival package (left truncation, time-dep. covariates)

2005-05-31 Thread Stefan Pohl
Dear list, I want o fit a shared gamma frailty model with the frailty specification in the survival package. I have partly left-truncated data and time-dependent covariates. Is it possible to combine these two things in the frailty function. Or are the results wrong if I use data in the

Re: [R] is there material about Longitudinal Data Analysis with R?

2005-05-31 Thread Tobias Verbeke
On Wed, 01 Jun 2005 00:04:22 +0800 ronggui [EMAIL PROTECTED] wrote: i am studying Longitudinal Data Analysis and want to carry it with R.anyone knows any materials about Longitudinal Data Analysis with R in the internet which i can download? You may have a look at

Re: [R] Shared Frailty in survival package (left truncation, time-dep. covariates)

2005-05-31 Thread Thomas Lumley
On Tue, 31 May 2005, Stefan Pohl wrote: Dear list, I want o fit a shared gamma frailty model with the frailty specification in the survival package. I have partly left-truncated data and time-dependent covariates. Is it possible to combine these two things in the frailty function. Or are

[R] prediction using gls with correlated residuals

2005-05-31 Thread Carlo Fezzi
Dear all, I am a beginner user of R and I tried to fit a gls model with explanatory variables and an AR(1) correlation component using the function gls with: correlation = corAR1 (form = ~ 1) It should mean that the residual follows an AR(1) process, isn't it? The problem is that, if I use the

Re: [R] FYI: Problems while loading package class (VR)

2005-05-31 Thread Duncan Murdoch
Uwe Ligges wrote: Tuszynski, Jaroslaw W. wrote: My email was to inform that there are some problems with instaling package class (VR) by itself. If I go to Menu Packages/Install-package(s)/class(VR) I am still getting: utils:::menuInstallPkgs() dependency 'class (VR)' is not available

Re: [R] A suggestion to improve ifelse behaviour with vector yes/no arguments

2005-05-31 Thread Duncan Murdoch
Thomas Lumley wrote: On Tue, 31 May 2005, Duncan Murdoch wrote: Mäkinen Jussi wrote: Dear All, I luckily found the following feature (or problem) when tried to apply ifelse-function to an ordered data. test - c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE) ifelse(test, 0, 1:4) [1]

[R] RE: Soil texture triangle in R?

2005-05-31 Thread Waichler, Scott R
Sander, has anybody made an attempt to create the soil texture triangle graph in R? See ternaryplot() in package vcd. Its options are quite limited, but it may help. I think you'll need to write your own function to do a ternary plot like the one you point to, perhaps using functions in the

[R] (no subject)

2005-05-31 Thread jatwood
Are there any R packages available that let me directly impose a set of linear parameter restrictions when estimating the simple linear and/or GLS regression model and directly recover the restricted coefficients, predicted values and residuals? Can I do this via the use of contrasts under

[R] FANNY function in R package cluster

2005-05-31 Thread Aamir M
Martin there is no 'm' in the book there, but they talk about the Martin exponent ^ 2 used in some places {but ^ 1 in other places}, Martin notably in 5.2 Why did we choose FANNY? Martin There is no fuzziness parameter defined there, so can you be Martin more specific? Martin Is it the

[R] question regarding new class

2005-05-31 Thread Laura Holt
Hi R people: I have created a new class for a project that I am working on. It works fine. Just one question, please: When I access the slots, is there any way that I could use x$Name instead on [EMAIL PROTECTED], please? Or is it that way by design, please? Thanks. Laura Holt

Re: [R] persp, add lines/highlights

2005-05-31 Thread Paul Murrell
Hi Robin Hankin wrote: Hello everyone I always cut-n-paste Paul's suggestions and end up learning something! In this case, though, I have a query. I was wondering how the second persp() call dealt with hidden line removal, because pieces of mesh with NA values are see-through. If you

[R] simple predict question

2005-05-31 Thread sms13+
Excuse the simple question... I'm not sure what I'm doing wrong with predict, but let me use this example: Suppose I do: dat-matrix(c(0,0,10,20),2,byrow=T) lm1-lm(dat[,2]~dat[,1]) Suppose I want to generate the linearly-interpolated y-values between the point (0,0) and (0,20) at every unit

[R] Increasing Console Paste Buffer

2005-05-31 Thread Manuel Morales
Hello list. I'm using R from the gnome-terminal in Fedora. My preference is to write programs in VIM, and then source the file from R, or copy and paste the lines into the console. I'm wondering if there is a way to increase the paste buffer as an alternative to sourcing large analyses. As was

Re: [R] simple predict question

2005-05-31 Thread Gabor Grothendieck
On 5/31/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Excuse the simple question... I'm not sure what I'm doing wrong with predict, but let me use this example: Suppose I do: dat-matrix(c(0,0,10,20),2,byrow=T) lm1-lm(dat[,2]~dat[,1]) Suppose I want to generate the linearly-interpolated

[R] subset-analogue removing fed in indexes?

2005-05-31 Thread Johannes Graumann
Hello, Here's my issue: I want to plot the following vectors: x - c(0.0, 2.0, 15.0, 100.0, 105.0, 105.1, 110.0, 120.0, 120.1, 130.0) data - c(8.75, 8.75, 16.25, 38.75, 61.25, 8.75, NA, 8.75, NA, NA) and avoid the line discontinuations caused by 'NA'. plot_data - na.omit(data) will clean up

Re: [R] subset-analogue removing fed in indexes?

2005-05-31 Thread Gabor Grothendieck
On 5/31/05, Johannes Graumann [EMAIL PROTECTED] wrote: Hello, Here's my issue: I want to plot the following vectors: x - c(0.0, 2.0, 15.0, 100.0, 105.0, 105.1, 110.0, 120.0, 120.1, 130.0) data - c(8.75, 8.75, 16.25, 38.75, 61.25, 8.75, NA, 8.75, NA, NA) and avoid the line

[R] Loading matrices and other things

2005-05-31 Thread Mike Schuler
Hi all, I'm new to R, so needless to say I have a couple questions (which I hope I haven't missed through the documentation). I have several files in lower triangular matrix form. For each of these matrices, I want to perform some form of hierarchical clustering on each matrix and capture the

Re: [R] subset-analogue removing fed in indexes?

2005-05-31 Thread Johannes Graumann
Jebus, you guys are fast! Thanks so much, Joh On Tue, 2005-05-31 at 17:38 -0400, Gabor Grothendieck wrote: On 5/31/05, Johannes Graumann [EMAIL PROTECTED] wrote: Hello, Here's my issue: I want to plot the following vectors: x - c(0.0, 2.0, 15.0, 100.0, 105.0, 105.1, 110.0,

[R] Why does summary show number of NAs as non-integer?

2005-05-31 Thread Earl F. Glynn
Example: set.seed(19) summary( c(NA, runif(10,1,100), NaN) ) Min. 1st Qu. MedianMean 3rd Qu.Max.NA's 7.771 24.850 43.040 43.940 63.540 83.830 2.000 Why isn't the number of NA's just 2 instead of the 2.000 shown above? efg

[R] FW: why is it numeric(0)?

2005-05-31 Thread luan_sheng
hello,everyone. I have one question: example 1 x=numeric(0) y=5 print(x+y) numeric(0) example 2 x=numeric(1) y=5 print(x+y) [1] 5 why the print(x+y) is numeric(0) at the first example, but the result is 0 at the second example? __

RE: [R] FW: why is it numeric(0)?

2005-05-31 Thread luan_sheng
yea, I have read the help. But some one tell me that i f you want use a vector that you don't know it's length, you should use xx=numric(0) , is it not right? If it isn't right, how can I do? thanks -Original Message- From: Douglas Grove [mailto:[EMAIL PROTECTED] Sent: Wednesday, June

RE: [R] Why does summary show number of NAs as non-integer?

2005-05-31 Thread Berton Gunter
summary() is an S3 generic that for your vector dispatches summary.default(). The output of summary default has class table and so calls print.table (print is another S3 generic). Look at the code of print.table() to see how it formats the output. -- Bert Gunter Genentech Non-Clinical Statistics

RE: [R] FW: why is it numeric(0)?

2005-05-31 Thread Berton Gunter
?numeric Hint: Type numeric(0) and numeric(1) at the prompt and see what you get. What is the sum of anything and a zero length vector? -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. -

Re: [R] Increasing Console Paste Buffer

2005-05-31 Thread Gavin Simpson
Manuel Morales wrote: Hello list. I'm using R from the gnome-terminal in Fedora. My preference is to write programs in VIM, and then source the file from R, or copy and paste the lines into the console. I'm wondering if there is a way to increase the paste buffer as an alternative to sourcing

Re: [R] Problem going back to a viewport with gridBase

2005-05-31 Thread Paul Murrell
Hi Gabor Grothendieck wrote: I am setting up base plots -- one in viewport A and and one in B. This part works fine. But if I go back to A after having done B and add horizontal lines it seems to not use the correct coordinates. How do I tell it to resume using A's coordinates? I am

Re: [R] Formatting numbers with a limited amount of digits consistently

2005-05-31 Thread Marc Schwartz
On Tue, 2005-05-31 at 11:11 -0400, Duncan Murdoch wrote: Marc Schwartz wrote: Final note to Henrik: Note that the IEEE 754 rounding standard as implemented in R results in: round(18.15, 1) [1] 18.1 formatC(18.15, format = f, digits = 1) [1] 18.1 sprintf(%5.1f,

Re: [R] Why does summary show number of NAs as non-integer?

2005-05-31 Thread Marc Schwartz
On Tue, 2005-05-31 at 17:14 -0500, Earl F. Glynn wrote: Example: set.seed(19) summary( c(NA, runif(10,1,100), NaN) ) Min. 1st Qu. MedianMean 3rd Qu.Max.NA's 7.771 24.850 43.040 43.940 63.540 83.830 2.000 Why isn't the number of NA's just 2 instead of the 2.000

[R] Tiger problems

2005-05-31 Thread Thomas Davidoff
I get the following when I try to run R from the terminal (I think ok from the gui, but not what I want to do): dyld: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/

Re: [R] FW: why is it numeric(0)?

2005-05-31 Thread Thomas Lumley
On Wed, 1 Jun 2005, luan_sheng wrote: hello,everyone. I have one question: example 1 x=numeric(0) y=5 print(x+y) numeric(0) example 2 x=numeric(1) y=5 print(x+y) [1] 5 why the print(x+y) is numeric(0) at the first example, but the result is 0 at the second example? numeric(0) is a

Re: [R] Problem going back to a viewport with gridBase

2005-05-31 Thread Paul Murrell
Hi Gabor Grothendieck wrote: On 5/31/05, Paul Murrell [EMAIL PROTECTED] wrote: Hi Gabor Grothendieck wrote: I am setting up base plots -- one in viewport A and and one in B. This part works fine. But if I go back to A after having done B and add horizontal lines it seems to not use the

Re: [R] FW: why is it numeric(0)?

2005-05-31 Thread Duncan Murdoch
luan_sheng wrote: yea, I have read the help. But some one tell me that i f you want use a vector that you don't know it's length, you should use xx=numric(0) , is it not right? If it isn't right, how can I do? It depends on the context. Why do you need a vector, but don't know its length?

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