[R] extract t-values from pairwise.t.test

2005-08-08 Thread Guido Parra Vergara
Hi, how can I extract the t-values after running a pairwise.t.test? The output just list the p-values. Many thanks for your help. Cheers Guido Guido J. Parra School of Tropical Environment Studies and Geography James Cook University Townsville Queensland

Re: [R] R-help Digest, Vol 30, Issue 6

2005-08-08 Thread David Duffy
On Fri, 5 Aug 2005 Julia Reid wrote: Subject: [R] GAP pointer I am trying to do a simple segregation analysis using the GAP package. I have the documentation for pointer but I desperately need an example so that I can see how to format the datfile and the jobfile. For each individual, I

[R] chisq.test

2005-08-08 Thread Stephen Choularton
Hi I am trying to use this function. Can anyone show me how I would input the following example? Chi-Squared = (40-30)^2 + (20-30)^2 + (30-30)^2 30 30 30 = 3.333 + 3.333 + 0 = 6.666 (p value = 0.036) I want to be able to use different

[R] Alerte Virus

2005-08-08 Thread avscan
Le mail envoye a [EMAIL PROTECTED] le lundi 08 août contient un virus __ 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

Re: [R] extract t-values from pairwise.t.test

2005-08-08 Thread Petr Pikal
Hallo My output lists more than p-values ttt-t.test(rnorm(10), rnorm(10), paired=T) ttt Paired t-test data: rnorm(10) and rnorm(10) t = 1.7508, df = 9, p-value = 0.1139 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -0.1750263

Re: [R] extract t-values from pairwise.t.test

2005-08-08 Thread Simon Blomberg
I think the questioner was interested in pairwise.t.test. See ?pairwise.t.test. From looking at the source, pairwise.t.test calls t.test if sd's are not pooled, or calculates its own t.val if sds are pooled. It looks very easy to hack to return the t values instead of the p values. Simon. At

Re: [R] extract t-values from pairwise.t.test

2005-08-08 Thread Peter Dalgaard
Guido Parra Vergara [EMAIL PROTECTED] writes: Hi, how can I extract the t-values after running a pairwise.t.test? The output just list the p-values. Many thanks for your help. It's not a very complicated function. Why not just modify it to your needs? -- O__ Peter Dalgaard

Re: [R] chisq.test

2005-08-08 Thread Peter Dalgaard
Stephen Choularton [EMAIL PROTECTED] writes: Hi I am trying to use this function. Can anyone show me how I would input the following example? Chi-Squared = (40-30)^2 + (20-30)^2 + (30-30)^2 30 30 30 = 3.333 + 3.333 + 0 = 6.666 (p

[R] Searchable Mailing List Archives Down

2005-08-08 Thread Ido M. Tamir
Hi, I was a user of the searchable Mail Archives which you have linked from somewhere on your homepage. http://maths.newcastle.edu.au/~rking/R/ This link is out of order. I know there is a search at GMANE and MARC, but the results were not that nice. Is it possible to recreate this searchable

Re: [R] extract t-values from pairwise.t.test

2005-08-08 Thread Guido Parra Vergara
Hi, I am not familiar with changing R functions. I can see in the code that t-values get calculated as t. val, however when I modified the code to include t.val under ans and then run the modified function I get Object t.val not found. How do I properly modify the function to list t. val in

[R] nested logit with latent classes

2005-08-08 Thread Agnieszka Prokopowicz
Hi Everybody, I am interested in estimating nested logit with latent classes at the lower level. I have seen the codes for conditional logit and latent class analysis but I haven’t found anything about nested logit all the more nested logit with latent classes. Could you help me with

[R] installing problems about randomForest

2005-08-08 Thread Xiao Jianfeng
Hi all, When I tried to install package randomForest, it gave out the following error message: install.packages(randomForest, dependencies = TRUE) trying URL 'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz' Content type 'application/x-gzip' length 82217 bytes opened

Re: [R] installing problems about randomForest

2005-08-08 Thread Uwe Ligges
Xiao Jianfeng wrote: Hi all, When I tried to install package randomForest, it gave out the following error message: install.packages(randomForest, dependencies = TRUE) trying URL 'http://www.lmbe.seu.edu.cn/CRAN/src/contrib/randomForest_4.5-12.tar.gz' Content type

Re: [R] extract t-values from pairwise.t.test

2005-08-08 Thread Petr Pikal
Hallo I am not sure but this could be what you want. You has to change function compare.levels not only add t.val in ans. If you want t- values AND p-values together in one table it probably is not so simple. my.pairded.t.test - function (x, g, p.adjust.method = p.adjust.methods, pool.sd =

Re: [R] Searchable Mailing List Archives Down

2005-08-08 Thread Adaikalavan Ramasamy
The site by Robert King is now working again. I admit that I had problems accessing it too few times last week. By adding the phrase site:https://stat.ethz.ch/pipermail/r-help/; in my google search, I got something that resembled that output but it did specify from which archive and month the

Re: [R] installing problems about randomForest

2005-08-08 Thread Prof Brian Ripley
On Mon, 8 Aug 2005, Uwe Ligges wrote: Xiao Jianfeng wrote: Hi all, When I tried to install package randomForest, it gave out the following error message: install.packages(randomForest, dependencies = TRUE) trying URL

[R] help on regression by subsets in dataset

2005-08-08 Thread Krishna
Hi Everyone May I request for a small help while performing the regression analysis. I would like to know is there any possibility of conducting the regression for different data subsets (in the same data file), classified on the basis of grouping variable. The alternative for this is running

[R] R: cbind

2005-08-08 Thread Clark Allan
hi all are we able to combine column vectors of different lengths such that the result appears in matrix form? e.g. a=1 b=1:3 d=1:4 then z=CBIND(a,b,d) 1 1 1 2 2 3 3 4 i stil want the following! z[,1]=1 z[,2]=1:3 z[,3]=1:5 i made up the name of this function. we could use cbind

[R] R: matrix sizes

2005-08-08 Thread Clark Allan
hi all assume that one is doing a simulation. in each iteration one produces a vector of results. this vectors length might change for each different iteration. how can one construct a matrix that contains all of the interation results in a matrix where each of the columns are the outputs from

Re: [R] R: matrix sizes

2005-08-08 Thread Uwe Ligges
Clark Allan wrote: hi all assume that one is doing a simulation. in each iteration one produces a vector of results. this vectors length might change for each different iteration. how can one construct a matrix that contains all of the interation results in a matrix where each of the

Re: [R] R: cbind

2005-08-08 Thread Uwe Ligges
Clark Allan wrote: hi all are we able to combine column vectors of different lengths such that the result appears in matrix form? e.g. a=1 b=1:3 d=1:4 then z=CBIND(a,b,d) 1 1 1 2 2 3 3 4 i stil want the following! z[,1]=1 z[,2]=1:3 z[,3]=1:5 i made up

Re: [R] R: cbind

2005-08-08 Thread Sundar Dorai-Raj
Clark Allan wrote: hi all are we able to combine column vectors of different lengths such that the result appears in matrix form? e.g. a=1 b=1:3 d=1:4 then z=CBIND(a,b,d) 1 1 1 2 2 3 3 4 i stil want the following! z[,1]=1 z[,2]=1:3 z[,3]=1:5 i made

[R] Groups in histograms?

2005-08-08 Thread Fredrik Karlsson
Dear list, I would like to create histograms for up to three groups, with distincive colour/pattern, in a trellis panel. However, I have not been able to find a way to do this. histogram does not seem to have a group argument. Please help. /Fredrik

Re: [R] R: cbind

2005-08-08 Thread Gabor Grothendieck
On 8/8/05, Clark Allan [EMAIL PROTECTED] wrote: hi all are we able to combine column vectors of different lengths such that the result appears in matrix form? e.g. a=1 b=1:3 d=1:4 then z=CBIND(a,b,d) 1 1 1 2 2 3 3 4 i stil want the following! z[,1]=1

Re: [R] R: cbind

2005-08-08 Thread Gabor Grothendieck
On 8/8/05, Gabor Grothendieck [EMAIL PROTECTED] wrote: On 8/8/05, Clark Allan [EMAIL PROTECTED] wrote: hi all are we able to combine column vectors of different lengths such that the result appears in matrix form? e.g. a=1 b=1:3 d=1:4 then z=CBIND(a,b,d) 1 1 1

Re: [R] help on regression by subsets in dataset

2005-08-08 Thread Dimitris Rizopoulos
you could use function lmList() from the nlme package, i.e., dat - data.frame(y = rnorm(120), x = runif(120, -3, 3), g = rep(1:3, each = 40)) library(nlme) m - lmList(y ~ x | g, data = dat) m summary(m) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student

Re: [R] help on regression by subsets in dataset

2005-08-08 Thread Gabor Grothendieck
On 8/8/05, Krishna [EMAIL PROTECTED] wrote: Hi Everyone May I request for a small help while performing the regression analysis. I would like to know is there any possibility of conducting the regression for different data subsets (in the same data file), classified on the basis of

Re: [R] Groups in histograms?

2005-08-08 Thread Fredrik Karlsson
Hi Gary, I have found this, but it is not exactly what I am looking for. What I need is the groups to be inside of a single panel, not in different panels. Kind of like an histogram version of the xyplot(Y ~ X1, groups=X2,panel=panel.superpose) command. (I hope this is correct). /Fredrik On

Re: [R] installing problems about randomForest

2005-08-08 Thread Xiao Jianfeng
Prof Brian Ripley wrote: On Mon, 8 Aug 2005, Uwe Ligges wrote: Xiao Jianfeng wrote: Hi all, When I tried to install package randomForest, it gave out the following error message: install.packages(randomForest, dependencies = TRUE) trying URL

[R] selecting outliers

2005-08-08 Thread alessandro carletti
Hi everybody, I'd like to know if there's an easy way for extracting outliers record from a dataset, in order to perform further analysis on them. Thanks Alessandro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] linkage disequilibrium

2005-08-08 Thread David Duffy
Date: Thu, 4 Aug 2005 19:36:35 +0200 From: Cristian [EMAIL PROTECTED] Subject: [R] linkage disequilibrium To: r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 I'm using the package Genetics, and I'm interested in the computation of D'

Re: [R] selecting outliers

2005-08-08 Thread Christian Hennig
Hi Alessandro, On Mon, 8 Aug 2005, alessandro carletti wrote: Hi everybody, I'd like to know if there's an easy way for extracting outliers record from a dataset, in order to perform further analysis on them. The answer is no. The reasons are not technical. There are some quite easy outlier

Re: [R] selecting outliers

2005-08-08 Thread Søren Højsgaard
Perhaps what Alessandro is after is simpler than that: Making a plot of data in a data frame, being able to click on 'suspicious points', getting the corresponding rows of a data out in a new data frame (for further inspection) while keeping the 'good points' in the plot (and perhaps redoing

Re: [R] selecting outliers

2005-08-08 Thread Christian Hennig
Hi, if Soren is right, why not take a look on the identify help page? Christian On Mon, 8 Aug 2005, Søren Højsgaard wrote: Perhaps what Alessandro is after is simpler than that: Making a plot of data in a data frame, being able to click on 'suspicious points', getting the corresponding

[R] coefficient of polynomial expansion

2005-08-08 Thread Peter Yang
Hi, I would like to get the coefficient of polynomial expansion. For example, (1+ x)^2 = 1 + 2x + x^2, and the coefficients are 1, 2 and 1. (1 + x + x^2)^3 = 1 + 3*x + 6*x^2 + 7*x^3 + 6*x^4 + 3*x^5 + x^6, and the coefficients are 1, 3, 6, 7, 6, 3, and 1. I know that we can use polynom library.

Re: [R] installing problems about randomForest

2005-08-08 Thread Liaw, Andy
From: Prof Brian Ripley On Mon, 8 Aug 2005, Uwe Ligges wrote: Xiao Jianfeng wrote: Hi all, When I tried to install package randomForest, it gave out the following error message: install.packages(randomForest, dependencies = TRUE) trying URL

[R] xyplot with 2 y-axes

2005-08-08 Thread Nathan Weisz
Dear R-helpers, I'm trying to get xyplot to plot 2 y-axes. I looked at the examples and googled around. This is how far I got so far. test-data.frame(a=rnorm(100),b=rnorm(100)*10,ind=rep(1:10,10),con=rep (1:10,rep(10,10))) xyplot(a+b~con|ind,data=test,allow.multiple=T) This however puts a+b

Re: [R] installing problems about randomForest

2005-08-08 Thread Xiao Jianfeng
Liaw, Andy wrote: Thanks for catching that! It must have slipped when I was going back and forth between C and Fortran... Update should appear on CRAN this week, I hope. Best, Andy Thanks for your quick replay. I just want you to know that I have tried R 2.1.0 on my pc running Debian

[R] heatmap -- invisible list?

2005-08-08 Thread Jacob Michaelson
Hi all, In heatmap's documentation, it mentions that the output value is actually an invisible list...how would one access this list? Thanks, Jake __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] coefficient of polynomial expansion

2005-08-08 Thread Gabor Grothendieck
On 8/8/05, Peter Yang [EMAIL PROTECTED] wrote: Hi, I would like to get the coefficient of polynomial expansion. For example, (1+ x)^2 = 1 + 2x + x^2, and the coefficients are 1, 2 and 1. (1 + x + x^2)^3 = 1 + 3*x + 6*x^2 + 7*x^3 + 6*x^4 + 3*x^5 + x^6, and the coefficients are 1, 3, 6, 7,

Re: [R] R: matrix sizes

2005-08-08 Thread Adaikalavan Ramasamy
1) If the output at each iteration gives a fixed number of elements, then you can pre-define the matrix. For example mat - matrix( NA, nr=6, nc=500 ) for(i in 1:500 ){ x - rnorm(13) mat[ , i] - summary(x) } 2) If the length of the output varies at each iteration, then it is

Re: [R] heatmap -- invisible list?

2005-08-08 Thread Sean Davis
On 8/8/05 9:45 AM, Jacob Michaelson [EMAIL PROTECTED] wrote: Hi all, In heatmap's documentation, it mentions that the output value is actually an invisible list...how would one access this list? Mylist - heatmap() __ R-help@stat.math.ethz.ch

[R] INDVAL and mvpart

2005-08-08 Thread astrzelczak
Hi, I'd like to perform Dufrene-Legendre Indicator Species Analysis for a multivariate regression tree. However I have problems with arguments of duleg(veg,class,numitr=1000)function. How to obtain a vector of numeric class memberships for samples, or a classification object returned from

[R] using - with a changing variable name (substitute?)

2005-08-08 Thread Tamas K Papp
I have a matrix r and a scalar d, and I would like to apply the following functions to each of its elements: 1. if r 0, no change 2. if 0 = r d, replace element by zero 3. if d = r, replace element by r-d I wrote a small function for this m - function(b) {sapply(b, function(bb) { if (bb

Re: [R] coefficient of polynomial expansion

2005-08-08 Thread Martin Maechler
Peter == Peter Yang [EMAIL PROTECTED] on Mon, 8 Aug 2005 09:11:47 -0400 writes: Peter Hi, I would like to get the coefficient of polynomial Peter expansion. For example, Peter (1+ x)^2 = 1 + 2x + x^2, and the coefficients are 1, Peter 2 and 1. (1 + x + x^2)^3 = 1 + 3*x +

Re: [R] using - with a changing variable name (substitute?)

2005-08-08 Thread Prof Brian Ripley
On Mon, 8 Aug 2005, Tamas K Papp wrote: I have a matrix r and a scalar d, and I would like to apply the following functions to each of its elements: 1. if r 0, no change 2. if 0 = r d, replace element by zero 3. if d = r, replace element by r-d I wrote a small function for this m -

Re: [R] make error: X11/Intrinsic.h: No such,,,

2005-08-08 Thread Martin Maechler
Jake == Jake Michaelson [EMAIL PROTECTED] on Fri, 05 Aug 2005 14:39:49 -0600 writes: Jake Thanks for the help -- this morning someone (on the Jake Ubuntu boards) was kind enough to point this out to Jake me. Now if there were only a decent Linux front Jake end/gui for R...

Re: [R] p-values

2005-08-08 Thread Peter Ho
Spencer, Thank you for referring me to your other email on Exact goodness-of-fit test. However, I'm not entirely sure if what you mentioned is the same for my case. I'm not a statistician and it would help me if you could explain what you meant in a little more detail. Perhaps I need to

Re: [R] using - with a changing variable name (substitute?)

2005-08-08 Thread Tamas K Papp
On Mon, Aug 08, 2005 at 04:07:10PM +0100, Prof Brian Ripley wrote: On Mon, 8 Aug 2005, Tamas K Papp wrote: m - function(b) {sapply(b, function(bb) { if (bb 0) {bb} else {if (bbd) {bb-d} else 0} })} Why use sapply? r[] - ifelse(r = d, r-d, ifelse(r = 0, 0, r)) is one more

[R] vector vs array

2005-08-08 Thread alessandro carletti
Hi! OK, I'm trying to select some useful outliers from my dataset: I defined 11 treshold values (1 for each level of a variable (sampling site) as follows: tresholds-function(x) { tapply(x,mm$NAME,FUN=mean ,simplify = T, na.rm=T)-med tapply(x,mm$NAME,FUN=sd ,simplify = T, na.rm=T)-standev

Re: [R] make error: X11/Intrinsic.h: No such,,,

2005-08-08 Thread Jake Michaelson
I use Mac OS X at home and Linux at work, so the R Aqua GUI has spoiled me. I have not seen its equal so far (on Windows or Linux). The most important thing to me is how easily accessible the help and documentation is. I like how when I begin typing a function, the form and arguments to the

[R] filled.contour help

2005-08-08 Thread m p
Hello, I plot with filled.contour and have this problem. There is an area that I want to cover with angled shading lines to represent NA in my data. Very much appreciate help. Thanks, Mark pal - palette(gray(seq(1.,0.,len=8))) filled.contour(fvec,qvec,etsarray,

[R] get the wald chi square in binary logistic regression

2005-08-08 Thread severine . erhel
hello, I work since a few time on R and i wanted to know how to obtain the Wald chi square value when you make a binary logistic regression. In fact, i have the z value and the signification but is there a script to see what is the value of Wald chi square. You can see my model below, Best

[R] Building R 2.1.0 on AIX 5.2.0.0

2005-08-08 Thread Paul Boutros
Hello, The set of messages below reports a successful build of 2.0.0 on AIX 5.2 using GCC 3.3.2 I've been trying for a while now to build 2.1.0 and 2.1.1 and have been unsuccessful. I've tried: - GCC 3.3.2 and 4.0.1 - default AIX make and GNU make - 32-bit and 64-bit builds A typical configure

[R] computationally singular

2005-08-08 Thread Weiwei Shi
Hi, I have a dataset which has around 138 variables and 30,000 cases. I am trying to calculate a mahalanobis distance matrix for them and my procedure is like this: Suppose my data is stored in mymatrix S-cov(mymatrix) # this is fine D-sapply(1:nrow(mymatrix), function(i) mahalanobis(mymatrix,

[R] Help with doing overlays plots...

2005-08-08 Thread Jamieson Cobleigh
I have a data frame with three columns, type (a factor with two values: Monolithic and Compositional), size (numeric), and states (numeric). I want to create a plot where size goes on the x-axis and states goes on the y-axis. In this plot, I want two lines, one where the type is Monolithic and

Re: [R] get the wald chi square in binary logistic regression

2005-08-08 Thread Renaud Lancelot
[EMAIL PROTECTED] a écrit : hello, I work since a few time on R and i wanted to know how to obtain the Wald chi square value when you make a binary logistic regression. In fact, i have the z value and the signification but is there a script to see what is the value of Wald chi square. You

Re: [R] computationally singular

2005-08-08 Thread Christian Hennig
Once I had a situation where the reason was that the variables were scaled to extremely different magnitudes. 1e-25 is a *very* small number but still there is some probability that it may help to look up standard deviations and to multiply the variable with the smallest st.dev. with 1e20 or

Re: [R] get the wald chi square in binary logistic regression

2005-08-08 Thread severine . erhel
th,ks for your help, i don't have this package on my R, do you know an other package that have this test...thanks Selon Renaud Lancelot [EMAIL PROTECTED]: [EMAIL PROTECTED] a écrit : hello, I work since a few time on R and i wanted to know how to obtain the Wald chi square value

[R] How to insert a certain model in SVM regarding to fixed kernels ?

2005-08-08 Thread Amir Safari
Dear R Users , Suppose that we want to regress a certain autoregressive model using SVM. We have our data and also some fixed kernels in libSVM behinde e1071 in front. The question: Where can we insert our certain autoregressive model ? During creating data frame ? Or perhaps we can make

Re: [R] Help with doing overlays plots...

2005-08-08 Thread Chuck Cleland
trellis.device() xyplot(states ~ size, groups=type, data=tmp, panel = panel.superpose, panel.groups =panel.linejoin, auto.key=TRUE) Jamieson Cobleigh wrote: I have a data frame with three columns, type (a factor with two values: Monolithic and Compositional),

Re: [R] computationally singular

2005-08-08 Thread Weiwei Shi
I think the problem might be caused two variables are very correlated. Should I check the cov matrix and try to delete some? But i am just not quite sure of your reply. Could you detail it with some steps? thanks, weiwei On 8/8/05, Christian Hennig [EMAIL PROTECTED] wrote: Once I had a

Re: [R] (more) computationally singular

2005-08-08 Thread Christian Hennig
More ideas: You can also perform an Eigenvalue decomposition of the covariance matrix and see along which directions the singularity occurs and how strong it is. Consequences could be: rescaling (or omission) of variables that are strong in these directions, taking principal components, or linear

Re: [R] (part III) computationally singular

2005-08-08 Thread Christian Hennig
Sorry, our emails crossed... On Mon, 8 Aug 2005, Weiwei Shi wrote: I think the problem might be caused two variables are very correlated. Should I check the cov matrix and try to delete some? In this case, taking principal components should do the job. Variable deletion may help as well - I

[R] modifying argument of a .C call (DUP=FALSE)

2005-08-08 Thread Tamas K Papp
I have a huge matrix on which I need to do a simple (elementwise) transformation. Two of these matrices cannot fit in the memory, so I cannot do this in R. I thought of writing some C code to do this and calling it using .C with DUP=FALSE. All I need is a simple for loop that replaces elements

[R] Square matrix plot

2005-08-08 Thread Finocchiaro Giacomo
Hi, having a matrix where rows=n and cols=m, I calculated the spearman correlation values of the matrix, this generated a square matrix m x m. Dose anyone knows how can I create a plot similar to this http://bio.ifom-firc.it/User/finoc/ask.png ( produced with hierarchical cluster explorer)

[R] GUIs (was Re: make error: X11/Intrinsic.h: No such,,,)

2005-08-08 Thread Thomas Lumley
On Mon, 8 Aug 2005, Jake Michaelson wrote: I use Mac OS X at home and Linux at work, so the R Aqua GUI has spoiled me. I have not seen its equal so far (on Windows or Linux). The most important thing to me is how easily accessible the help and documentation is. I like how when I begin

Re: [R] get the wald chi square in binary logistic regression

2005-08-08 Thread Spencer Graves
Is this a research question? If not, I'd like to know why you think the Wald test is better. Are you famililiar with Bates and Watts (1988) Nonlinear Regression Analysis and Its Applications (Wiley), and with the concepts of intrinsic and parameter effects nonlinearity?

Re: [R] vector vs array

2005-08-08 Thread Adaikalavan Ramasamy
General Notes : a) Please try to give a simple example b) Please avoid the rightwards assignment (i.e. -). Eventhough it is perfectly legal to use it, it is confusing especially when you are posting to a mailing list. 1) Here is a reproducible example set.seed(1) # for

[R] tapply huge speed difference if X has names

2005-08-08 Thread Matthew Dowle
Hi all, Apologies if this has been raised before ... R's tapply is very fast, but if X has names in this example, there seems to be a huge slow down: under 1 second compared to 151 seconds. The following timings are repeatable and are timed properly on a single user machine : X = 1:10

[R] Difference amongst spline smoothers

2005-08-08 Thread Song
Dear all, Anybody knows about the difference amongst various spline smoothers, specifically in R, 'bs' (by default a cubic spline), 'ns', smooth.spline with roughness penalty along with many other smoothers? I've consulted serveral books like 'S-plus Guide to Statistics' by Mathsoft, Ripley

[R] parametric survival plot

2005-08-08 Thread denis lalountas
Hi to all, I am new in R , and I would like to ask how to plot the survival function, and the associated baseline hazard in the case of parametric survival estimation models(SURVIVAL PACKAGE). plot.survfit works only with cox models. A lot of thanks D.Lalountas

[R] Reading large files in R

2005-08-08 Thread Jean-Pierre Gattuso
Dear R-listers: I am trying to work with a big (262 Mb) file but apparently reach a memory limit using R on a MacOSX as well as on a unix machine. This is the script: type=list(a=0,b=0,c=0) tmp - scan(file=coastal_gebco_sandS_blend.txt, what=type, sep=\t, quote=\, dec=., skip=1,

Re: [R] Square matrix plot

2005-08-08 Thread Adaikalavan Ramasamy
The URL that you sent is not working. Can you please check ? If you mean 2 dimensional hierarchical clustering as often used in microarrays, then see help(heatmap). There was a discussion last week about using red-green for heatmap. See http://tolstoy.newcastle.edu.au/R/help/05/08/9714.html Or

[R] use different symbols for frequency in a plot

2005-08-08 Thread Kerry Bush
suppose I have the following data x-c(rep(.1,5),rep(.2,6),rep(.4,10),rep(.5,20)) y-c(rep(.5,3),rep(.6,8),rep(1.2,8),rep(2.5,18),rep(3,4)) If I plot(x,y) in R, I will only get seven distinct points. What I want to do is to use different symbols to show the frequency at each point. e.g. if the

Re: [R] Reading large files in R

2005-08-08 Thread Adaikalavan Ramasamy
From Note section of help(read.delim) : 'read.table' is not the right tool for reading large matrices, especially those with many columns: it is designed to read _data frames_ which may have columns of very different classes. Use 'scan' instead. So I am not sure why you used

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Chuck Cleland
You might consider one of these approaches instead: plot(jitter(x), jitter(y)) or pdf(file=c:/AlphaExample.pdf, version = 1.4) plot(x, y, col = rgb(1, 0, 0, .2), pch = 16) dev.off() Kerry Bush wrote: suppose I have the following data x-c(rep(.1,5),rep(.2,6),rep(.4,10),rep(.5,20))

Re: [R] modifying argument of a .C call (DUP=FALSE)

2005-08-08 Thread Peter Dalgaard
Tamas K Papp [EMAIL PROTECTED] writes: I have a huge matrix on which I need to do a simple (elementwise) transformation. Two of these matrices cannot fit in the memory, so I cannot do this in R. I thought of writing some C code to do this and calling it using .C with DUP=FALSE. All I

Re: [R] Reading large files in R

2005-08-08 Thread Berton Gunter
... and it is likely that even if you did have enough memory (several times the size of the data are generally needed) it would take a very long time. If you do have enough memory and the data are all of one type -- numeric here -- you're better off treating it as a matrix rather than converting

Re: [R] modifying argument of a .C call (DUP=FALSE)

2005-08-08 Thread Prof Brian Ripley
On Mon, 8 Aug 2005, Peter Dalgaard wrote: Tamas K Papp [EMAIL PROTECTED] writes: I have a huge matrix on which I need to do a simple (elementwise) transformation. Two of these matrices cannot fit in the memory, so I cannot do this in R. I thought of writing some C code to do this and

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Adaikalavan Ramasamy
Group by which variable ? If you mean the joint distribution of 'x' and 'y' then something along the following lines x - rep( c(0.1, 0.2, 0.4, 0.5), c(5, 6, 10, 20) ) y - rep( c(0.5, 0.6, 1.2, 2.5, 3.0), c(3, 8, 8, 18, 4) ) new - factor( paste(x, y, sep=_) ) tb - table(new)

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Kerry Bush
Thank you. But I only need three classes of freqnencies (in another words, only three kinds of symbols) for 1-5, 5-10 and above 10, not to use different symbols for different frequencies. Otherwise, clearly R will run out of available symbols and the plot is also hard to view. Thank you anyway.

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Marc Schwartz (via MN)
On Mon, 2005-08-08 at 11:57 -0700, Kerry Bush wrote: suppose I have the following data x-c(rep(.1,5),rep(.2,6),rep(.4,10),rep(.5,20)) y-c(rep(.5,3),rep(.6,8),rep(1.2,8),rep(2.5,18),rep(3,4)) If I plot(x,y) in R, I will only get seven distinct points. What I want to do is to use different

Re: [R] tapply huge speed difference if X has names

2005-08-08 Thread Prof Brian Ripley
Please use a current version of R! This was fixed long ago, and you will find it in the NEWS file: split() now handles vectors with names internally and so is almost as fast as on vectors without names (and maybe 100x faster than before). On Mon, 8 Aug 2005, Matthew

[R] Help with non-integer #successes in a binomial glm

2005-08-08 Thread Haibo Huang
Hi, I had a logit regression, but don't really know how to handle the Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) problem. I had the same logit regression without weights and it worked out without the warning, but I figured it makes more sense to add

[R] reverse order of matrix rows

2005-08-08 Thread Jake
Quick question: how can I reverse the order of the rows in a matrix? i.e. make the last row first and the first row last, etc.? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!

[R] two term exponential model

2005-08-08 Thread Deming Mi
Dear R users, Does anybody know if there is an R function (package) to fit a two-terms exponential model like y = a*exp(bx) + c*exp(dx) where y is dependent variable and x is independent variable. MATLAB has a Curve Fitting Toolbox to implement this fitting, but I don't know if there is an R

[R] AIC model selection

2005-08-08 Thread Martin Kardos
Hello All; I need to run a multiple regression analysis and use Akaike's Information Criterion for model selection. I understand that this command will give the AIC value for specified models: AIC(object, ..., k = 2) with ... meaning any other optional models for which I would like AIC

Re: [R] reverse order of matrix rows

2005-08-08 Thread Jean Eid
sapply(nrow(matrix):1, function(x) matrix[x,]) On Mon, 8 Aug 2005, Jake wrote: Quick question: how can I reverse the order of the rows in a matrix? i.e. make the last row first and the first row last, etc.? __ R-help@stat.math.ethz.ch mailing

Re: [R] reverse order of matrix rows

2005-08-08 Thread Jacob Michaelson
Thanks to those who provided the one-liner answers! They worked quite well. I'm quite sure that 95% of the questions posted on this mailing list could be answered with a quick...read the manual, stupid..., but I'm very grateful to those who take the time to write one-liners. I know

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Adaikalavan Ramasamy
Remove the '6' from the code that contains 'cut'. I am not sure how it crept into my code. Then you should have the following mapping Freqpch code 1-5 1 6-102 11- 3 I am more concerned about viewers getting confused with many symbols than running

Re: [R] reverse order of matrix rows

2005-08-08 Thread Adaikalavan Ramasamy
How about simply mat - mat[ nrow(mat):1, ] Regards, Adai On Mon, 2005-08-08 at 19:44 -0400, Jean Eid wrote: sapply(nrow(matrix):1, function(x) matrix[x,]) On Mon, 8 Aug 2005, Jake wrote: Quick question: how can I reverse the order of the rows in a matrix? i.e. make the

Re: [R] AIC model selection

2005-08-08 Thread Adaikalavan Ramasamy
Are you looking for possibly stepAIC from the package MASS ? Regards, Adai On Mon, 2005-08-08 at 16:39 -0600, Martin Kardos wrote: Hello All; I need to run a multiple regression analysis and use Akaike's Information Criterion for model selection. I understand that this command will give

Re: [R] AIC model selection

2005-08-08 Thread Kerry Bush
The last time I used it, the function step() was using AIC as model selection criteria as the default. It is in the base package so you don't have to refer to other fancy functions. --- Adaikalavan Ramasamy [EMAIL PROTECTED] wrote: Are you looking for possibly stepAIC from the package MASS ?

Re: [R] use different symbols for frequency in a plot

2005-08-08 Thread Tamas K Papp
On Mon, Aug 08, 2005 at 03:17:44PM -0400, Chuck Cleland wrote: You might consider one of these approaches instead: plot(jitter(x), jitter(y)) or pdf(file=c:/AlphaExample.pdf, version = 1.4) plot(x, y, col = rgb(1, 0, 0, .2), pch = 16) dev.off() sunflowerplot() is also useful for