[R] comparing two columns of a dataset on a graph

2008-03-10 Thread orkun
hello I want to compare the values of two columns of a dataset on a graph. Which graphic do you recommend ? regards Ahmet Temiz -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __

[R] Problems with installing the rgl package on Linux

2008-03-10 Thread Tim Carnus
HI Paul, I had same problem on ubuntu 7.10. Followed advice here http://help.nceas.ucsb.edu/index.php...ng_R_on_Ubuntu http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu and now it works fine. Something about missing headers for X. Alternatively something like the libx11-dev package

[R] [ca package] access to any x/y in mjca function

2008-03-10 Thread popiel
Hi, I would like to extract x,y from mjca function in ca package to be able to draw other graph types. For example for simple mca function from MASS I can do the following: - anydata.mca - mca(anydata, nf = 2, abbrev = TRUE) x - anydata.mca$rs[,1]#that is what I can 'extract'

[R] Error in extracting monthly observation from a daily time series data

2008-03-10 Thread Megh Dal
Hi all, Suppose I have following dataset : library(zoo) SD = 1 date1 = seq(as.Date(01/01/90, format = %m/%d/%y), as.Date(12/31/08, format = %m/%d/%y), by = 1) len1 = length(date1); data1 = zoo(matrix(rnorm(len1, mean=0, sd=SD*0.5), nrow = len1), date1) Now I want to extract

Re: [R] Bessel functions of complex argument

2008-03-10 Thread Robin Hankin
Hello Baptiste Bessel functions with complex arguments are not supported in R. Neither matlab nor the Gnu Scientific Library support them either. . . . but . . . the pari/gp system (released on the GPL) does: ? besselj(1+I,3) %3 = 0.6919067491368555819808728680 +

Re: [R] R error: Not able to launch R 2.6.2

2008-03-10 Thread Petr PIKAL
Hi Sometimes also helps to start R from elsewhere, load a package which was used in analysis and open .Rdata file. [EMAIL PROTECTED] napsal dne 09.03.2008 17:45:06: Yes. I found one that says to change the extension to RData. Where is the folder located? I tried looking at the R folder but

[R] Odp: comparing two columns of a dataset on a graph

2008-03-10 Thread Petr PIKAL
Hi [EMAIL PROTECTED] napsal dne 10.03.2008 08:12:28: hello I want to compare the values of two columns of a dataset on a graph. Which graphic do you recommend ? It depends on what values you have and what you want to compare. plot(x,y) boxplot(x, y) There are plenty other options in R.

[R] Odp: Help with Error!

2008-03-10 Thread Petr PIKAL
Hi If you bother to look into posting guide it will tell you that providing a reproducible example is a good way to obtain relevant answers to your question. And maybe while constructing reproducible example you will find yourself what is wrong, learn some more from it and need not wait for

[R] hclust graphics - plotting many points

2008-03-10 Thread Karin Lagesen
Hello. I have a distance matrix with lots of distances that I use hclust to organise. I then plot the results using the plot method of hclust. However, the plot itself takes around 20 mins to make due to there being ~700 things in the matrix that I have distances for. I thus would like to dump

[R] plotting hclust dendrograms

2008-03-10 Thread Schulze, Diana
Hallo everybody, I have a question concerning plotting of hclust dendrograms. I created several of those dendrograms and like to plot them in different plots. I'd like to have all plots with the same scaling of the y axis so that they become comparable by eye. That means they should all start

Re: [R] hclust graphics - plotting many points

2008-03-10 Thread michael watson (IAH-C)
I'd recommend outputting either as pdf or as a windows metafile -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Karin Lagesen Sent: 10 March 2008 09:54 To: r-help@r-project.org Subject: [R] hclust graphics - plotting many points Hello. I have a

Re: [R] Problems with installing the rgl package on Linux

2008-03-10 Thread Paul Smith
On Sat, Mar 8, 2008 at 5:33 PM, George N. White III [EMAIL PROTECTED] wrote: I am trying to install the rgl package on R 2.6.1 running on Fedora 8 (Linux), but I am experiencing the following problems: - configure: error: X11 not found but

Re: [R] expression matrix

2008-03-10 Thread Jabez Wilson
Date: Sat, 8 Mar 2008 04:56:58 -0800 (PST) From: Keizer_71 [EMAIL PROTECTED] Subject: [R] expression matrix To: r-help@r-project.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii Hello, I am to run this R script but i keep getting this error. expr-exprs(golubMerge)

[R] aov within subject and contrasts

2008-03-10 Thread guillaume chaumet
Dear R list, again a newbie question here, so I wish I do not exasperated reader. This is example of my data.frame subject length consistency context acc frt 1 1200high scene_c 0.8181818 396.6642 2 2200high scene_c 1.000 595.7778 3

Re: [R] Problems installing packages using the inbuilt facility: Error i n gzfile(file, r) : unable to open connection

2008-03-10 Thread Kauer, Philipp
Thank you Henrik for your response. As I indicated at the end of my e-mail, I only have this problem at work, and was not be able to replicate it at home (ie packages load fine there). I followed the steps you suggested, but unfortunately no luck (below is the output). Essentially, the error

Re: [R] ltm package question

2008-03-10 Thread Dimitris Rizopoulos
the Pearson chi^2 is not directly computed in 'ltm', and the reason is that both the Pearson chi^2 and the likelihood-ratio statistics do not follow the claimed chi-squared distribution, especially as the number of items increases. If you still need to compute it, then you can use the

[R] (no subject)

2008-03-10 Thread Alfons Sutter
Hi all, I am trying to read a text file in R! I have a warning message: In read.table(file = data1.txt, header = T) : uncompleted last line of readTableHeader in 'data1.txt' Could you please tell me why? and how can I deal with missing value when I read this file? all the best Alfons

[R] question for aov and kruskal

2008-03-10 Thread eugen pircalabelu
Hi R users! I have the following problem: how appropriate is my aov model under the violation of anova assumptions? Example: a-c(1,1,1,1,1,1,1,1,1,1,2,2,2,3,3,3,3,3,3,3) b-c(101,1010,200,300,400, 202, 121, 234, 55,555,66,76,88,34,239, 30, 40, 50,50,60) z-data.frame(a, b) fligner.test(z$b,

Re: [R] format a number

2008-03-10 Thread Romain Francois
Hello, sub( ^([- ])?0+, \\1, format(v, digits=2) ) [1] .44 -.22 Cheers, Romain Martin Kaffanke wrote: Hi there! I have i.e. v = c(0.43554, -0.22343), and so on. Now I'd like to make a format like format(v, digits=2) but without the leading 0, so 0.43554 becomes .44, -0.22343

Re: [R] (no subject)

2008-03-10 Thread Alfons Sutter
Thank you! I have the origenal file in MS-Excel, I save the excel file in a txt file. In the excel file there are missing value empty places for these missing value? Do I need to replace the empty places in a symbol for missing value and could you tell me place how can I avoid this warning

[R] format a number

2008-03-10 Thread Martin Kaffanke
Hi there! I have i.e. v = c(0.43554, -0.22343), and so on. Now I'd like to make a format like format(v, digits=2) but without the leading 0, so 0.43554 becomes .44, -0.22343 becomes -.22 How can I do that? runnable example for copy and paste: v = c(0.43554, -0.22343) format(v, digits=2)

Re: [R] (no subject)

2008-03-10 Thread Duncan Murdoch
On 10/03/2008 6:50 AM, Alfons Sutter wrote: Hi all, I am trying to read a text file in R! I have a warning message: In read.table(file = data1.txt, header = T) : uncompleted last line of readTableHeader in 'data1.txt' R is warning you that the file may be incomplete. In Unix, text files

Re: [R] Error in extracting monthly observation from a daily time series data

2008-03-10 Thread Gabor Grothendieck
names(obs) shows the result has been sorted so use %Y instead of %y in the format statement in the split so that 2000 1999; otherwise, 99 00. On Mon, Mar 10, 2008 at 4:10 AM, Megh Dal [EMAIL PROTECTED] wrote: Hi all, Suppose I have following dataset : library(zoo) SD = 1 date1 =

Re: [R] format a number

2008-03-10 Thread jim holtman
You can also use sprintf: v = c(0.43554, -0.22343) sprintf(%.2f, v) [1] 0.44 -0.22 On 3/10/08, Martin Kaffanke [EMAIL PROTECTED] wrote: Hi there! I have i.e. v = c(0.43554, -0.22343), and so on. Now I'd like to make a format like format(v, digits=2) but without the leading 0, so

Re: [R] format a number

2008-03-10 Thread jim holtman
Sorry, I missed the part about not having th leading zero. It is too early yet with daylight savings time and no coffee so far. On 3/10/08, Martin Kaffanke [EMAIL PROTECTED] wrote: Hi there! I have i.e. v = c(0.43554, -0.22343), and so on. Now I'd like to make a format like format(v,

Re: [R] box-constrained

2008-03-10 Thread Paul Smith
On Sun, Mar 9, 2008 at 9:10 PM, Gustave Lefou [EMAIL PROTECTED] wrote: I have another question. I have seen there is a function called constrOptim in R. Is it better than optim, for example to optimize a function f of two parameters belonging to [0,1] and [0,Infinity] ? Do the methods

[R] internet proxy settings (win)

2008-03-10 Thread Thomas Steiner
I cannot access internet through R. My IT-guys told me that I should set the proxy and the port and then everything will be fine. Where can I set them? I use R 2.6.2 under Windows 2000 and these settings are those of the Internet Explorer (no password). I read

Re: [R] Odp: comparing two columns of a dataset on a graph

2008-03-10 Thread Charilaos Skiadas
On Mar 10, 2008, at 5:15 AM, Petr PIKAL wrote: Hi [EMAIL PROTECTED] napsal dne 10.03.2008 08:12:28: hello I want to compare the values of two columns of a dataset on a graph. Which graphic do you recommend ? It depends on what values you have and what you want to compare. plot(x,y)

[R] question

2008-03-10 Thread Svyatkovskiy Alexey
Hello, I have one more question. I looked through MASS.c file but I couldn't find lda(...) function here. I expected that 'lda' function is a part of MASS source code. Where can I find the source code for 'lda' - function? Best wishes, Alexey. __

[R] Weighting data when running regressions

2008-03-10 Thread Elena Wilson
Dear R-Help, I'm new to R and struggling with weighting data when I run regression. I've tried to use search to solve my problem but haven't found anything helpful so far. I (successfully) import data from SPSS (15) and try to run a linear regression on a subset of my data file where

[R] Changing font size of Rcmdr (Linux)

2008-03-10 Thread Paul Smith
Dear All, I have Rcmdr installed on a machine running Fedora 8 (Linux). It works fine, but I find the fonts of the Script window and of Output window very small. How can one increase the size of the font use on those windows? Thanks in advance, Paul

[R] Weird feature in rimage

2008-03-10 Thread Alberto Monteiro
I just noticed a weird feature in rimage. It seems that, when reading an image, the line/colums are transposed. See this reproducible example. The final image should be black - but (as expected) not an absolute black (mean(z) is 0.015, sd(z) is 0.055 but max(z) is 1). Alberto Monteiro #

Re: [R] Weighting data when running regressions

2008-03-10 Thread Chuck Cleland
On 3/10/2008 7:49 AM, Elena Wilson wrote: Dear R-Help, I'm new to R and struggling with weighting data when I run regression. I've tried to use search to solve my problem but haven't found anything helpful so far. I (successfully) import data from SPSS (15) and try to run a linear

[R] A stats question -- about survival analysis and censoring

2008-03-10 Thread Geoff Russell
Dear UseRs, Suppose I have data regarding smoking habits of a prospective cohort and wish to determine the risk ratio of colorectal cancer in the smokers compared to the non-smokers. What do I do at the end of the study with people who die of heart disease? Can I just censor them exactly the

Re: [R] Tinn-R related problem

2008-03-10 Thread Mario Maiworm
david, all I can tell you that I am using TINN-R 1.19.4.7 on a win xp prof sp2 machine and it runs just fine. I also use AutoHotkey, a hotkey (key shortcuts) program which overwrites all program-specific keystrokes. could it be an issue with keystrokes that are assigned elsewhere?? take a look at

Re: [R] internet proxy settings (win)

2008-03-10 Thread Uwe Ligges
Which mirror do you use? Uwe Ligges Thomas Steiner wrote: I cannot access internet through R. My IT-guys told me that I should set the proxy and the port and then everything will be fine. Where can I set them? I use R 2.6.2 under Windows 2000 and these settings are those of the Internet

Re: [R] internet proxy settings (win)

2008-03-10 Thread Thomas Steiner
Which mirror do you use? As I am living in Vienna, I use Austria. Which should I try? Thomas __ 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

[R] build.mim() from the minet package

2008-03-10 Thread Bettina Keller
Hi, I am trying to contstruct a mutual informtation matrix using the function build.mim() from the minet package: build.mim(myData, estimator=empirical) and I have two questions. 1.) The estimator empirical computes the entropy of the empirical probability distribution. This probably means

Re: [R] question for aov and kruskal

2008-03-10 Thread David Winsemius
Subject: Re: question for aov and kruskal Newsgroups: R-help:gmane.comp.lang.r.general To: eugen pircalabelu [EMAIL PROTECTED] On 10 Mar 2008, you wrote in gmane.comp.lang.r.general: Hi R users! I have the following problem: how appropriate is my aov model under the violation of anova

Re: [R] Changing font size of Rcmdr (Linux)

2008-03-10 Thread John Fox
Dear Paul, You can change fonts and font sizes via Rcmdr options, as explained in ?Commander (also accessible via the R Commander Help - Commander help menu). For example, options(Rcmdr=list(default.font=*helvetica-medium-r-normal-*-20*, log.font.size=20)) would change both the GUI elements

Re: [R] relationship between t-test CI and SEM?

2008-03-10 Thread Rob Campbell
Thanks for the replies and apologies for not including code. Bad of me. Chuck Cleland wrote: I get the same confidence intervals with t.test(), lm(), and by hand. We need to see how you calculated the SEM and constructed the interval. Perhaps you constructed the interval using the normal

Re: [R] internet proxy settings (win)

2008-03-10 Thread Uwe Ligges
Thomas Steiner wrote: Which mirror do you use? As I am living in Vienna, I use Austria. Which should I try? Thomas OK, that's perfect. Then the proxy configuration is still wrong. MAybe you want to try the other way given in the R for Windows FAQs and re-check your proxy settings. Uwe

Re: [R] (no subject)

2008-03-10 Thread Petr PIKAL
Hi [EMAIL PROTECTED] napsal dne 10.03.2008 13:00:39: If you have an original file in excel, the way I get such files is to save them as csv (comma-separated), and then to use read.csv. Then Or if you do not have need to save the file just in Excel select data you want to transfer to R

Re: [R] accessing sourcse code; was: question

2008-03-10 Thread Uwe Ligges
Svyatkovskiy Alexey wrote: Hello, I have one more question. I looked through MASS.c file but I couldn't find lda(...) function here. I expected that 'lda' function is a part of MASS source code. Where can I find the source code for 'lda' - function? Not everything has its own C code,

Re: [R] y label perpendicular to the y axis

2008-03-10 Thread Henrique Dallazuanna
Try: par(mar=c(4,6,4,4)) plot(rnorm(100), ylab=) mtext(side=2, text=Label, las=1, line=2) On 10/03/2008, JuanCarlos CorreaMorales [EMAIL PROTECTED] wrote: Hi R-users: We need to place the y label horizontally on a plot. Instead of | l | a | b | e | l |

[R] re moving parentheses/square brackets from data frame numbers

2008-03-10 Thread Thomsen
Dear list, I am importing data consisting of numbers into dataframes. Some of the numbers are flanked by parentheses or square brackets. Thus, they are not recognized as numeric and the corresponding column is of class factor which makes it hard/impossible use in plotting functions. Is there a

[R] How can I sample from a two-dimensional grid of points

2008-03-10 Thread Gregory Gentlemen
Hi everyone, My goal is to sample from a two-dimensional grid. Consider the following example of code: n.grid - 500 muA.grid - seq(-4,4, length=n.grid) muB.grid - seq(-4,4, length=n.grid) mu.p - matrix(NA, nrow=n.grid, ncol=n.grid) for(i in 1:n.grid){ for(j in 1:n.grid){

Re: [R] A stats question -- about survival analysis and censoring

2008-03-10 Thread Max
Geoff, This is a tricky question. Have you done a literature search? -Max Geoff Russell formulated the question : Dear UseRs, Suppose I have data regarding smoking habits of a prospective cohort and wish to determine the risk ratio of colorectal cancer in the smokers compared to the

Re: [R] A stats question -- about survival analysis and censoring

2008-03-10 Thread Matthias Gondan
Hi Geoff, I think the answer to such a problem (overall survival vs. disease free survival) depends on the regulatory environment, for example, in a phase III clinical trial, OS would be used, whereas in an equivalence study, DFS would be used. Best, Matthias Geoff Russell schrieb: Dear

Re: [R] How can I sample from a two-dimensional grid of points

2008-03-10 Thread Dimitris Rizopoulos
you can still use sample(), e.g., n.grid - 500 muA.grid - seq(-4, 4, length = n.grid) muB.grid - seq(-4, 4, length = n.grid) vals - data.matrix(expand.grid(muA.grid, muB.grid)) mu.p - dnorm(vals[, 1]) * dnorm(vals[, 2], sd = 0.5) mu.p - mu.p / sum(mu.p) ind - 1:nrow(vals) samp.ind - sample(ind,

Re: [R] Changing font size of Rcmdr (Linux)

2008-03-10 Thread Paul Smith
On Mon, Mar 10, 2008 at 1:36 PM, John Fox [EMAIL PROTECTED] wrote: You can change fonts and font sizes via Rcmdr options, as explained in ?Commander (also accessible via the R Commander Help - Commander help menu). For example,

Re: [R] sampsize in Random Forests

2008-03-10 Thread Liaw, Andy
Are you sure there are 100 sites in your data? Here's an example: R library(randomForest) randomForest 4.5-23 Type rfNews() to see new features/changes/bug fixes. R f - factor(sample(1:4, nrow(iris), replace=TRUE)) R rf1 - randomForest(iris[1:4], iris[[5]], strata=f, sampsize=rep(5, nlevels(f)))

[R] Mimicking SPSS weighted least squares

2008-03-10 Thread Ben Domingue
Howdy, In SPSS, there are 2 ways to weight a least squares regression: 1. You can do it from the regression menu. 2. You can set a global weight switch from the data menu. These two options have no, in my experience, been equivalent. Now, when I run lm in R with the weights= switch set

Re: [R] Rpart and bagging - how is it done?

2008-03-10 Thread Liaw, Andy
I suppose better late than never: It's possible to get bagging in randomForest by simply setting mtry equal to the number of predictor variables. Note that this is one thing that I changed from Breiman Cutler's Fortran code: They were sampling variables with replacement, so if you use that

Re: [R] Reading microsoft .xls format and openoffice OpenDocument files

2008-03-10 Thread Liaw, Andy
I don't have answer to either of your questions, just some info: 1: Why not try the XLSReadWrite package that can do it natively without using Perl to convert to CSV first? 2: There seems to be an Ooo extension that sounds similar to R-Excel (connecting R to Calc). Not sure if that helps you

Re: [R] Passing function to tapply as a string

2008-03-10 Thread Yuri Volchik
Thanks, match.fun is what i was looking for :-) Or perhaps: myfun - function(fname, ...)match.fun(fname)(...) On 07/03/2008, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Was wondering if it is possible to pass function name as a parameter -- View this message in context:

Re: [R] analysing mixed effects/poisson/correlated data

2008-03-10 Thread Douglas Bates
On Sat, Mar 8, 2008 at 11:00 AM, Manuel Morales [EMAIL PROTECTED] wrote: On Sat, 2008-03-08 at 08:07 -0600, Douglas Bates wrote: On Sat, Mar 8, 2008 at 2:57 AM, Alexandra Bremner [EMAIL PROTECTED] wrote: I am attempting to model data with the following variables: timepoint -

Re: [R] box-constrained

2008-03-10 Thread Gustave Lefou
Hello Paul, It is just a negative log-likelihood with two parameters belonging to [0,1] and [0,Inf]. constrOptim is valid for all linear inequality constraints. My constraints (box-constrained) are as simple as possible, but maybe the methods used by constrOptim are useful too. My question is

Re: [R] Reading microsoft .xls format and openoffice OpenDocument files

2008-03-10 Thread Ajay Shah
1: Why not try the XLSReadWrite package that can do it natively without using Perl to convert to CSV first? I looked at the package (it's http://cran.r-project.org/web/packages/xlsReadWrite/index.html) but it's windows only. So no joy yet. 2: There seems to be an Ooo extension that sounds

Re: [R] Passing function to tapply as a string

2008-03-10 Thread Gabor Grothendieck
Also note that there is match.funfn in the gsubfn package. That allows you to also pass functions defined as formulas: e.g. library(gsubfn) f.at.four - function(f) match.funfn(f)(4) f.at.four(sqrt) # 2 f.at.four(sqrt) # 2 f.at.four(~ x^.5) # 2 - uses function(x) x^.5 See homepage,

[R] caretNWS and training data set sizes

2008-03-10 Thread Tait, Peter
Hi, I am using the caretNWS package to train some supervised regression models (gbm, lasso, random forest and mars). The problem I have encountered started when my training data set increased in the number of predictors and the number of observations. The training data set has 347 numeric

Re: [R] Reading microsoft .xls format and openoffice OpenDocument files

2008-03-10 Thread Gabor Grothendieck
With regards to #1 you could also check out http://tolstoy.newcastle.edu.au/R/help/06/04/25674.html On Fri, Mar 7, 2008 at 7:17 AM, Ajay Shah [EMAIL PROTECTED] wrote: 1. I have used gdata::read.xls() with much happiness. But every now and then it breaks. I have not, as yet, been able to

Re: [R] Tinn-R related problem

2008-03-10 Thread David Hewitt
A few weeks ago all of a sudden the backspace, enter and direction keys were not working. I updated Tinn-R to the newest version but still no sollution. After this I tried reinstalling it (prior to that I removed Tinn-R and deleted all the leftovers manually) and still no change. In every

Re: [R] re moving parentheses/square brackets from data frame numbers

2008-03-10 Thread Charles C. Berry
On Mon, 10 Mar 2008, Thomsen wrote: Dear list, I am importing data consisting of numbers into dataframes. Some of the numbers are flanked by parentheses or square brackets. Thus, they are not recognized as numeric and the corresponding column is of class factor which makes it

[R] 3D projection pursuit

2008-03-10 Thread giovanna menardi
Hi, is there any R function or package aimed at finding 3D projection pursuit solutions? I was able to find only interactive 2D projection pursuit in Rggobi. Thanks in advance, Giovanna _ [[elided Hotmail spam]]

Re: [R] Reading microsoft .xls format and openoffice OpenDocument files

2008-03-10 Thread Liaw, Andy
From: Ajay Shah 1: Why not try the XLSReadWrite package that can do it natively without using Perl to convert to CSV first? I looked at the package (it's http://cran.r-project.org/web/packages/xlsReadWrite/index.html) but it's windows only. So no joy yet. 2: There seems to be an

Re: [R] caretNWS and training data set sizes

2008-03-10 Thread Max Kuhn
What version of caret and caretNWS are you using? Also, what version of the nws server and twisted are you using? What kind of machine (# processors, how much physical memory etc)? I haven't seen any real limitations with one exception: if you are running P jobs on the same machine, you are

Re: [R] draw partition lines

2008-03-10 Thread Greg Snow
Here is one approach (you can adapt as needed): library(TeachingDemos) par(mfrow=c(4,2)) plot(1:10) plot(10:1) plot(c(1:5,5:1)) plot(c(5:1,1:5)) tmp - cnvrt.coords(1,0, input='fig')$usr # get right end coord tmp2 - cnvrt.coords(0,NA, input='tdev')$usr # get left end par(xpd=NA) # turn off

[R] Model confusion

2008-03-10 Thread Christopher De Ang
Hi, I m wondering is there any rules on what variables are used for factor analysis/ loading. For instance, increase reputation lead to increase in volume of post. So is volume need to be calculated in factor loading. InDependent Variable dependent

[R] ML Estimation Differences with R and SAS

2008-03-10 Thread Patrick Richardson
List, I'm working on fitting a logistic model for a well known dataset (which is given below in case anyone wants to try to reproduce). I used both R and SAS to fit the model and have some differences in the parameter estimates. I'm wondering if R calculates the ML estimates differently. I'm

Re: [R] caretNWS and training data set sizes

2008-03-10 Thread Tait, Peter
Hi Max, Thank you for the fast response. Here are the versions of the R packages I am using: caret 3.13 caretNWS 0.16 nws 1.62 Here are the python versions Active Python 2.5.1.1 nws server 1.5.2 for py2.5 twisted 2.5.9 py2.5 The computer I am using has 1 Xeon dual core cpu at 1.86 GHz with 4

[R] reorder x-axis

2008-03-10 Thread stephen sefick
read.table(bug.txt, header=TRUE) plotMeans(bug$tot, bug$station, error.bars=se, main=Total) The plot is ordered in this way HC RM190 RM198 RM202. I would like it to plot in this way HC RM202 RM198 RM190. thanks Stephen Is this okay or would you like the data to be copied and pasted into the

Re: [R] gam - Extraction of nonparametric component

2008-03-10 Thread Wensui Liu
i could remember exactly but it is like something: components - predict(gam.object, type = terms) On Mon, Mar 10, 2008 at 1:36 PM, Michael A. Milligan [EMAIL PROTECTED] wrote: Hello, I am estimating a semiparametric partial linear model using gam of the form y=f1(x1)+f2(x2)+beta*X

Re: [R] caretNWS and training data set sizes

2008-03-10 Thread Max Kuhn
Peter, You are certainly up to date. Can you try replicating this using only two nodes (since you only have two processors)? I'm not sure that specifying 5 really helps. Using 2 nodes on my mac usually gets me about a 30-40% decrease in time. Also, are the processes just hanging or is there an

[R] gam - Extraction of nonparametric component

2008-03-10 Thread Michael A. Milligan
Hello, I am estimating a semiparametric partial linear model using gam of the form y=f1(x1)+f2(x2)+beta*X where y is the dependent variable, f1(x1) and f2(x2) are nonparametric functions of the independent variables x1 and x2, respectively, and beta and X are vectors of coefficients and

[R] When to quote a package name

2008-03-10 Thread Muenchen, Robert A (Bob)
Dear HelpeRs, I'm confused about the role of quotes around package names on the library and detach functions. Books on R use both approaches: library(Hmisc) describe(mydata) detach(package:Hmisc) and library(Hmisc) describe(mydata) detach(package:Hmisc) The help file for detach says quoted or

Re: [R] When to quote a package name

2008-03-10 Thread Uwe Ligges
Muenchen, Robert A (Bob) wrote: Dear HelpeRs, I'm confused about the role of quotes around package names on the library and detach functions. Books on R use both approaches: library(Hmisc) describe(mydata) detach(package:Hmisc) and library(Hmisc) describe(mydata)

[R] plotting multiple lines in 3d

2008-03-10 Thread stephen sefick
I have been looking around for packages that will do this but I am not stumbling on the right one. I would like to make a 3d plot (hopefully an interactive graphic (rgl maybe)) that is simply four 2d graphs stacked next to each other traveling down river. site is the x-axis, bas is the y-axis,

Re: [R] ML Estimation Differences with R and SAS

2008-03-10 Thread Rolf Turner
On 11/03/2008, at 6:09 AM, Patrick Richardson wrote: List, I'm working on fitting a logistic model for a well known dataset (which is given below in case anyone wants to try to reproduce). I used both R and SAS to fit the model and have some differences in the parameter estimates.

Re: [R] Mimicking SPSS weighted least squares

2008-03-10 Thread Rolf Turner
On 11/03/2008, at 4:04 AM, Ben Domingue wrote: Howdy, In SPSS, there are 2 ways to weight a least squares regression: 1. You can do it from the regression menu. 2. You can set a global weight switch from the data menu. These two options have no, in my experience, been equivalent. Now, when

Re: [R] Reading microsoft .xls format and openoffice OpenDocument files

2008-03-10 Thread Gregory Warnes
Hello Ajay, I'm the author of the gdata package. If you send me a copy of an .XLS file that doesn't work with read.xls(), I'll see about fixing the code. -Greg On Mar 7, 2008, at 6:17AM , Ajay Shah wrote: 1. I have used gdata::read.xls() with much happiness. But every now and then

[R] state space model for poisson distribution

2008-03-10 Thread arun kirshna
Hi Rers, I have a poission time series model with 5 parameters. I just wanted to remove two of the lag on response in the model and put it as a system model. I am not sure about the codes to combine these two on R. If anybody has any R example (code), please post it. My original model:

[R] combining/deleting rows

2008-03-10 Thread Suran, Luciana @ Torto Wheaton Research
Hello List, I'm new to R and have some question on combining (and deleting) rows. I have a dataset that looks like this: msa_id base_sf.2002.2 compltns.2002.2 absorption.2002.2 avrate.2002.2 1 AKRON 27918 0 -1420 19 24 ALBUQU 20469 77 -23 9.2 100 ALLENT 41490 0

[R] Help on display of labels

2008-03-10 Thread Murthy S. Vanapalli
Hello all - I am a newbie and trying to figure out how to display all the labels of the regression tree, in a meaningful way. Yes, I have some long labels. # plot tree plot(fit, uniform=TRUE,main=Regression Tree for PVDecayData) text(fit, use.n=TRUE, all=TRUE, cex=.8) Results in the output that

Re: [R] box-constrained

2008-03-10 Thread Paul Smith
On Mon, Mar 10, 2008 at 4:02 PM, Gustave Lefou [EMAIL PROTECTED] wrote: It is just a negative log-likelihood with two parameters belonging to [0,1] and [0,Inf]. constrOptim is valid for all linear inequality constraints. My constraints (box-constrained) are as simple as possible, but maybe

[R] SORT MATRIX

2008-03-10 Thread ermimi
I have a matrix with 2 columns and n row. I need sort the matrix by the first column but the second row must be sort in the same order that the first column. Somebody know how I can sort this matrix. Thanks very much -- View this message in context:

[R] Multiple density plots

2008-03-10 Thread Sean MacEachern
Hi all, I'm interested in doing a multiple density plot on a number of columns in a dataframe. DF lineA.1 lineA.2 lineB.1 lineB.2 r1 5.355354 6.665575 10.288498 11.74750 r2 3.643415 5.427600 11.407112 13.97065 r3 5.813674 6.438502 9.628871 11.57456 r4 5.241340 5.125049 10.456221

Re: [R] Multiple density plots

2008-03-10 Thread Erik Iverson
Where were you reading about that function? simple.densityplot seems to be from a user-supplied package called UsingR. Try install.packages(UsingR) library(UsingR) and then try your simple.densityplot function call. Best, Erik Iverson Sean MacEachern wrote: Hi all, I'm interested in

Re: [R] Multiple density plots

2008-03-10 Thread hadley wickham
On Mon, Mar 10, 2008 at 3:55 PM, Sean MacEachern [EMAIL PROTECTED] wrote: Hi all, I'm interested in doing a multiple density plot on a number of columns in a dataframe. DF lineA.1 lineA.2 lineB.1 lineB.2 r1 5.355354 6.665575 10.288498 11.74750 r2 3.643415 5.427600

Re: [R] Tinn-R related problem

2008-03-10 Thread davidseres
David Hewitt wrote: A few weeks ago all of a sudden the backspace, enter and direction keys were not working. I updated Tinn-R to the newest version but still no sollution. After this I tried reinstalling it (prior to that I removed Tinn-R and deleted all the leftovers manually) and

Re: [R] Mimicking SPSS weighted least squares

2008-03-10 Thread Peter Dalgaard
Rolf Turner wrote: On 11/03/2008, at 4:04 AM, Ben Domingue wrote: Howdy, In SPSS, there are 2 ways to weight a least squares regression: 1. You can do it from the regression menu. 2. You can set a global weight switch from the data menu. These two options have no, in my experience, been

[R] parmat error from MASS?

2008-03-10 Thread john polo
i'm in the midst of using R for a PVA/matrix project. my math skills are lousy and programming skills are worse. to deal with an error that i couldn't solve, i changed a parameter that used a new part of a routine in our PVA package's code: else if (ES == ParDraw) { require(MASS)

Re: [R] Weighting data when running regressions

2008-03-10 Thread Elena Wilson
It works!!! Thanks a lot Chuck! -Original Message- From: Chuck Cleland [mailto:[EMAIL PROTECTED] Sent: Monday, 10 March 2008 11:29 PM To: Elena Wilson Cc: r-help@r-project.org Subject: Re: [R] Weighting data when running regressions On 3/10/2008 7:49 AM, Elena Wilson wrote: Dear

Re: [R] Weighting data when running regressions

2008-03-10 Thread Elena Wilson
It works!!! Thanks a lot Haris! -Original Message- From: Charilaos Skiadas [mailto:[EMAIL PROTECTED] Sent: Monday, 10 March 2008 11:30 PM To: Elena Wilson Cc: r-help@r-project.org Subject: Re: [R] Weighting data when running regressions On Mar 10, 2008, at 7:49 AM, Elena Wilson wrote:

[R] Longitudinal with binary covariates and outcome

2008-03-10 Thread Ted Harding
Hi Folks, I'd be grateful for suggestions about approaching the following kind of data. I'm not sure what general class of models it is best situated in (that's just my ignorance), and in particular if anyone could point me to case studies associated with an R approach that would be most useful.

Re: [R] A stats question -- about survival analysis and censoring

2008-03-10 Thread David Winsemius
Geoff Russell [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Dear UseRs, Suppose I have data regarding smoking habits of a prospective cohort and wish to determine the risk ratio of colorectal cancer in the smokers compared to the non-smokers. What do I do at the end of the study

[R] survreg asking for parameter special

2008-03-10 Thread Chang Liu
Hello Gurus: I'm using basic survival analysis, and trying to use survreg, and I provided the parameter formula= and data=, but I got an error saying: Error in terms.default(formula, special, data = data) : no terms component I'm wondering what it's trying to say. Is it because I

[R] levels() function for a vector

2008-03-10 Thread Chang Liu
Hello: I'm trying to use levels function, but I don't know why it's returning NULL. For example: temp[1] 3 5 5 NA levels(temp)NULL Also, I've tried: list(temp)[[1]][1] 3 5 5 NA levels(list(temp))NULL Is there a specific requirement on the parameter? Karen

Re: [R] Mimicking SPSS weighted least squares

2008-03-10 Thread Rolf Turner
It would appear that the SPSS procedure would then give exactly the same point estimates of the parameters, and change the inference structure by changing the ``denominator degrees of freedom'' from n-p to sum(w) - p. This seems to me to make little sense ... But then, it ***is*** SPSS. :-)

Re: [R] Mimicking SPSS weighted least squares

2008-03-10 Thread JRG
On 11 Mar 2008 at 14:09, Rolf Turner wrote: It would appear that the SPSS procedure would then give exactly the same point estimates of the parameters, and change the inference structure by changing the ``denominator degrees of freedom'' from n-p to sum(w) - p. Well, if that IS what SPSS

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