[R] Hierarchical clustering with centroid method

Dear everybody! In the function hclust, at each stage distances between clusters are recomputed by the Lance-Williams dissimilarity update formula according to the particular clustering method being used. Using centroid method, Lance-Williams recurrence formula works properly only for euclidean

[R] Plot zooming i.e. changing ylim according to xlim

Dear R-gurus, I would like to zoom in a plot, e.g. I select a region on the x-axis and then I would like the ranges on the y-axis to change accordingly. Is it possible to do this with existing functions, or do I have to invent some data selection before plotting? See below a short example,

Re: [R] Plot zooming i.e. changing ylim according to xlim

Search the archives for zoom and you will find plenty of answers on this question. RSiteSearch(zoom) Tom -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Henrik Andersson Sent: Tuesday, 26 July 2005 4:16 PM To: r-help@stat.math.ethz.ch Subject: [R]

Re: [R] Plot zooming i.e. changing ylim according to xlim

Dear R-gurus, I would like to zoom in a plot, e.g. I select a region on the x-axis and then I would like the ranges on the y-axis to change accordingly. Is it possible to do this with existing functions, or do I have to invent some data selection before plotting? See below a short example,

Re: [R] Plot zooming i.e. changing ylim according to xlim

Hi Not avoiding trial and error but you can do it interactively by point clicking on a plot. replot function (x, y, type = l) { body - locator(2) plot(x, y, xlim = range(body$x), ylim = range(body$y), type = type) } HTH Best regards Petr Pikal On 26 Jul 2005 at 10:16, Henrik

Re: [R] passing formula arguments cv.glm

Adai, using traceback() helps, as does giving a reproducible example when reporting a problem. However, the problem is I think the line d.glm - update(glmfit, data = data[j.in, , drop = FALSE]) in cv.glm. I think that should be d.glm - eval.parent(update(glmfit,

Re: [R] Plot zooming i.e. changing ylim according to xlim

Well here is the better shot x - seq(0,20) y - exp(-x) plot(x,y, type=l) intervalx-c(19,20) intervaly-y[x%in%intervalx] plot(x,y, xlim=range(intervalx), ylim=range(intervaly), type=l) HTH Petr On 26 Jul 2005 at 11:13, Henrik Andersson wrote: Dear R-gurus, I would like to zoom in a

[R] sort a table

hi all, I need to sort a table like this one: n tmp s 1 215 0 2 654 1 3 213 0 4 569 1 5 954 1 6 562 1 7 252 0 8 555 0 9 988 1 I want to organize it with tmp increasing to produce the same tab but ordered by tmp I think it is simple but just show me how good you are in R ... thks guillaume.

Re: [R] sort a table

[EMAIL PROTECTED] wrote: hi all, I need to sort a table like this one: n tmp s 1 215 0 2 654 1 3 213 0 4 569 1 5 954 1 6 562 1 7 252 0 8 555 0 9 988 1 test - read.table(clipboard,header=T) test[order(test$tmp),] n tmp s 3 3 213 0 1 1 215 0 7 7 252 0 8 8 555 0 6 6 562 1 4 4 569

[R] problem with Hershey fonts

This was reported to me by a colleague in China, so I may not be reproducing exactly what they are seeing (which I suspect is rw2011), but this is what I see: version _ platform i386--netbsdelf arch i386 os netbsdelf system i386, netbsdelf status major2 minor1.1 year

Re: [R] passing formula arguments cv.glm

Dear Prof. Ripley, Thank you for your response. See below for my comments. On Tue, 2005-07-26 at 10:57 +0100, Prof Brian Ripley wrote: Adai, using traceback() helps, as does giving a reproducible example when reporting a problem. You are right. The traceback below indicates that your

[R] any package to fit such model?

I have search the internet but none are found.The lme function is like the proc mixed the SAS.But I know no package to fit the model described in http://gsbwww.uchicago.edu/computing/research/SASManual/ets/chap20/sect17.htm ,which fit with the proc tscs in SAS. Thank you.

[R] OpenBSD and large R vectors

Is anyone running R on OpenBSD? I've got R-2.1.1 installed on OpenBSD -current and have some microarray datasets that took ~1.4 GB RAM on FreeBSD (computer has 4 GB total, Pentium 4 system). With FreeBSD, setting maxdsiz in /boot/loader.conf worked very well. With OpenBSD, even after setting

Re: [R] passing formula arguments cv.glm

On Tue, 26 Jul 2005, Adaikalavan Ramasamy wrote: Dear Prof. Ripley, Thank you for your response. See below for my comments. On Tue, 2005-07-26 at 10:57 +0100, Prof Brian Ripley wrote: Adai, using traceback() helps, as does giving a reproducible example when reporting a problem. You

Re: [R] grep help needed

Dear Denis, I don't believe that anyone fielded your question -- my apologies if I missed a response. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Denis Chabot Sent: Monday, July 25, 2005 9:46 PM To: R list Subject: [R] grep help needed Hi,

[R] text on some lines

Hi, I would like to write text on 2 lines for example. For example, if you have a long sentence and you want to cut it at the 45 caracter and put the continuation underneath! Is it possible? Thanks Sabine - [[alternative HTML

Re: [R] text on some lines

Navarre Sabine wrote: Hi, I would like to write text on 2 lines for example. For example, if you have a long sentence and you want to cut it at the 45 caracter and put the continuation underneath! Is it possible? Do you mean for output to console / in plots? Simply insert a \n

Re: [R] text on some lines

plot(1:10,type=n) title(main=cut in the 45 char \n new line) pay attention to the \n,which means new line. is it what you want? === 2005-07-26 21:59:04 您在来信中写道：=== Hi, I would like to write text on 2 lines for example. For example, if you have a long sentence and you want to

[R] Association rules

Hello ! I just start in using R, and I have already questions... I want to use the arules package : I have installed the package, and have the arules package 's reference manual, but I haven't yet understood how to use it. I have my data (from Excel, .txt), that I have read on R : I think (hope

Re: [R] text on some lines

On Tue, 26 Jul 2005, Uwe Ligges wrote: Navarre Sabine wrote: I would like to write text on 2 lines for example. For example, if you have a long sentence and you want to cut it at the 45 caracter and put the continuation underneath! Is it possible? Do you mean for output to console / in

Re: [R] Association rules

library(foreign) in the foreign package,you can use read.csv command to read the csv file.you can use excel to open the file and save as cvs file.you should read the manuals first,which tells in details how to import your data into R. before you use the command frome the arules package,you

Re: [R] passing formula arguments cv.glm

It works ! Thank you very much. Can I request this fix in the next version of boot package please if it is likely not to break compatibility with other functions. The modified cv.glm function can be found at www.cbrg.ox.ac.uk/~ramasamy/cv.glm2.R Thank you again. Regards, Adai On Tue,

Re: [R] passing formula arguments cv.glm

On Tue, 26 Jul 2005, Adaikalavan Ramasamy wrote: It works ! Thank you very much. Can I request this fix in the next version of boot package please if it is likely not to break compatibility with other functions. The modified cv.glm function can be found at

[R] SETAR Estimation

Dear R-helpers, I was wondering if anyone has or knows someone who might have an implementation of algorithm for estimating SETAR models including the lag-order. For some reason my code gives me a bit wrong results. I am fighting with it for a week and cannot bring it down. Thanks a million in

[R] farimaSim

Hello! I installed the fSeries package to get some farima time-series which i tried with farimaSim, but unfortunately i got always an error. I tried it this way: farimaSim(n = 1000, model = list(ar = 0.5, d = 0.3, ma = 0.1), method=freq) Error in farimaSim(n = 1000, model = list(ar = 0.5, d =

[R] Assign new observations to Clara clusters

Dear all, I need to assign new observations to cluster groups previously identified for a different dataset. The original clustering was performed using Clara. I gess one way is to assign each new observation to the nearest medioid of the original cluster. Is there a way of doing this in R? Is

Re: [R] Assign new observations to Clara clusters

On Tue, 26 Jul 2005, Nestor Fernandez wrote: Dear all, I need to assign new observations to cluster groups previously identified for a different dataset. The original clustering was performed using Clara. I gess one way is to assign each new observation to the nearest medioid of the

[R] Compute dissimilarity matrix for ordinal data

Dear All, I have been trying to use the daisy routine to compute the dissimilarity matrix but I have not been successful in defining the data as ordinal. Might you kindly help me please? Thanks in advance and best regards, Tom __

Re: [R] farimaSim

Hansi == Hansi Weissensteiner [EMAIL PROTECTED] on Tue, 26 Jul 2005 17:40:45 +0200 writes: Hansi Hello! I installed the fSeries package to get some Hansi farima time-series which i tried with farimaSim, but Hansi unfortunately i got always an error. I tried it this Hansi

[R] plotting horizontally

Hello, Is there any way to use plot() horizontally similar to boxplot(., horiz=TRUE)? I want to use to illustrate the distribution of y-values on an adjacent plot using layout(). Thanks in advance for any help. Regards, --Dan __

Re: [R] any package to fit such model?

Have you looked at ?lm, including the examples? The link in your email described a standard one-way, fixed effects ANOVA, and the lm help page includes a worked example for that. spencer graves ronggui wrote: I have search the internet but none are found.The lme function

[R] draw ellipse of equal concentration

Dear all, do you know some routines to draw ellipses and its axes given the algebraic equation? The application is to draw ellipses of equal concentration for bivariate normal distribution given the vector mean and the covariance matrix. Thank you. Sincerely, Salvatore Ingrassia

Re: [R] draw ellipse of equal concentration

On 7/26/2005 1:49 PM, Salvatore Ingrassia wrote: Dear all, do you know some routines to draw ellipses and its axes given the algebraic equation? The application is to draw ellipses of equal concentration for bivariate normal distribution given the vector mean and the covariance matrix. The

[R] tapply t.test

I cannot find in the literature a way to conduct the following t.test on 2 objects, A and B A B col1 col2 col3 col1 col2 col3 Where col(i)'s name is identical in both A and B (they are names of tissues). How do I test (t.test) if each

[R] FFT post-processing

List, Can anyone point me at a user guide for doing signals processing after applying the FFT? I'm looking for some info on postprocessing steps, trying to see if there are any packages already written, etc. TIA, Pete __

Re: [R] cluster

Dear Weiwei, your question sounds a bit too general and complicated for the R-list. Perhaps you should look for personal statistical advice. The quality of methods (and especially distance choice) for down-sampling ceratinly depends on the structure of the data set. I do not see at the moment

Re: [R] alaska map?

Look at: http://www.census.gov/geo/www/cob/bdy_files.html There are shapefiles of the 50 states there, outlines, counties, and others. Greg Snow, Ph.D. Statistical Data Center, LDS Hospital Intermountain Health Care [EMAIL PROTECTED] (801) 408-8111 Caitlin Burgess [EMAIL PROTECTED]

[R] error with scan

Hi: I am trying to read a large (50+ lines) with scan() as read.table is unable to read it. I get a strange error (below) which says that 'a real' was expected and '5' was read. Can someone help? Thanks, jp type=list(a=0,b=0,c=0,d=0,e=0,f=,g=0,h=0,i=0) tmp2 - scan(file=tmp2.txt,

[R] T test across tissues

I cannot find in the literature a way to conduct the following t.test on 2 objects, A and B A B col1 col2 col3 col1 col2 col3 Where col(i)'s name is identical in both A and B (they are names of tissues). How do I test (t.test) if each

Re: [R] Plot zooming i.e. changing ylim according to xlim

On 7/26/05, Henrik Andersson [EMAIL PROTECTED] wrote: Dear R-gurus, I would like to zoom in a plot, e.g. I select a region on the x-axis and then I would like the ranges on the y-axis to change accordingly. Is it possible to do this with existing functions, or do I have to invent some

[R] a question about fft ( fast fourier transform)

Dear listers In R, if I have a sequence x(t), t=1,...N, fft(x) is actually giving us sum(x(t)exp(-i*omega*t)) at fourier frequency omega= 2*pi*i/N, i=0,1,...(N-1). The question is if I want to calculate sum(x(t)exp(-i*2*omega*t)), how can I do it? thanks a lot!

[R] Help on T test

ok I created a matrix C with A B CA1 B1C1 .. . the columns contain the gene expression values.. I ran the following t.test: apply(C, 1, function(x) t.test( x[1:3], x[4,6] )$p.value ) which outputs out 16063 pvalues

Re: [R] grep help needed

Thanks for your help, the proposed solutions were much more elegant than what I was attempting. I adopted a slight modification of Tom Mulholland's solution with a piece from John Fox's solution, but many of you had very similar solutions. require(maptools) nc -

Re: [R] cluster

Dear Chris: You are right and It IS too general. I think I should ask like what kind of cluster algorithms or functions are available in R , which might be easier. But for that, I probably can google or use help() in R to find out. I want to know more about the performance of clustering on this

Re: [R] error with scan

Can you show us the first line of the file? The error means that in one of the values you specified as numeric (first, second, third, fourth, fifth, seventh, eighth, ninth), it found the character value it displayed. Otherwise, this looks like a good use of scan. Kevin -Original

Re: [R] plotting horizontally

On Tue, 2005-07-26 at 08:58 +0700, [EMAIL PROTECTED] wrote: Hello, Is there any way to use plot() horizontally similar to boxplot(., horiz=TRUE)? I want to use to illustrate the distribution of y-values on an adjacent plot using layout(). Thanks in advance for any help. Regards,

[R] elegant solution to transform vector into percentages?

Hi, I am looking for an elegant way to transform a vector into percentages of values that meet certain criteria. store-c(1,1.4,3,1.1,0.3,0.6,4,5) # now I want to get the precentages of values # that fall into the categories =M , M =N , N # let M -.8 N - 1.2 # In my real example I have many

[R] choose between dates and times

Dear R-helpers, I have the following data: yhappenat x 5185 (07/22/05 00:05:14) 14 5186 (07/22/05 00:15:14) 14 5187 (07/22/05 00:25:14) 14 5188 (07/22/05 00:35:14) 14 .. I want to choose between 07/25/05 15:30:00 and 07/26/05 12:30:00. Anybody

Re: [R] elegant solution to transform vector into percentages?

hist() or cut() followed by tabulate() would probably be the ingredients you'd want. Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, July 26, 2005 3:49 PM To: r-help@stat.math.ethz.ch Subject: [R] elegant

Re: [R] elegant solution to transform vector into percentages?

use 'cut': store-c(1,1.4,3,1.1,0.3,0.6,4,5) x.1 - cut(store, breaks=c(-Inf,.8,1.2,Inf)) table(x.1)/length(x.1)*100 x.1 (-Inf,0.8] (0.8,1.2] (1.2,Inf] 25 25 50 On 7/26/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I am looking for an elegant way to

[R] / Right division.

Dear R gurus. Is there an R function equivalent to octaves / (Right division) withouth forming the inverse of Y' using solve ? [snip - from octave docu] Right division. This is conceptually equivalent to the expression (inverse (y') * x')' but it is computed without forming

Re: [R] / Right division.

On 7/26/2005 4:02 PM, nwew wrote: Dear R gurus. Is there an R function equivalent to octaves / (Right division) withouth forming the inverse of Y' using solve ? [snip - from octave docu] Right division. This is conceptually equivalent to the expression (inverse (y') *

Re: [R] choose between dates and times

If happenat is not a datetime value, convert it with strptime(). Then, one solution is to transform it in the following way: num.time - as.numeric(format(happenat,%Y%m%d%H%M%S)) This way, 07/22/05 00:05:14 becomes 20050722000514, and you can subset your data frame with dfr[which(num.time =

Re: [R] elegant solution to transform vector into percentages?

On Tue, 2005-07-26 at 15:48 -0400, [EMAIL PROTECTED] wrote: Hi, I am looking for an elegant way to transform a vector into percentages of values that meet certain criteria. store-c(1,1.4,3,1.1,0.3,0.6,4,5) # now I want to get the precentages of values # that fall into the categories

Re: [R] choose between dates and times

Kerry Bush [EMAIL PROTECTED] writes: Dear R-helpers, I have the following data: yhappenat x 5185 (07/22/05 00:05:14) 14 5186 (07/22/05 00:15:14) 14 5187 (07/22/05 00:25:14) 14 5188 (07/22/05 00:35:14) 14 .. I want to choose between

[R] Wishart Density

Dear R users, I am doing MCMC using Metropolis-Hastings. My model is bivariate-log-normal and the prior for variance-covariance is wishart distribution. I am wondering if there are some simple codes about how to get the density of Wishart distribution in my case ? Thanks in advance.

Re: [R] Help on T test

Mark, Please do not post the same question to both R-help and BioC-help mailing lists because 1) there are many people who are on both lists and 2) people's replies will be archived in two different places making it harder to others to search in future. Please see the responses on BioC-help

Re: [R] elegant solution to transform vector into percentages?

Why not write a function ? Here is one. mytable - function(x, br){ n - length(br) tb - table( cut( x, breaks=c(-Inf, br, Inf) ) ) tb - 100 * tb / sum(tb) tb.n - paste( c(, br), c(br, ), sep= x = ) tb.n[1] - paste(x = , br[1], sep=) tb.n[n+1] - paste(x , br[n],

[R] Durbin test for Incomplete block

Hi R-users, Does anyone know of a package that contains a function to conduct Durbin's test and it's extension for incomplete block designs, as described in Rayner and Best 2001 A contingency Table Approach to Nonparametric Testing? Peter -- ISR-Porto

[R] Difficulty getting standard deviation of ALL odds ratios with glm function, logistic regression, need cov of parameters

I am trying to do logistic regression with a categorical predictor variable with the glm() function, family=binomial. Using glm() I would like to be able to calculate the confidence intervals of all three possible odds ratios for a factor (the factor has three categories). Three categories imply

[R] Anybody have a binary version of SJava for rw2001 (Windows)?

I am not a techie and have been struggling 2 days solid to try and install SJava (the source from http://www.omegahat.org/RSJava/). Does anybody have a binary file for me (I am Windows XP and rw2001)? I have tried installing Perl, mingwin and the cygwin tools but still no luck. When I try “R CMD

Re: [R] Difficulty getting standard deviation of ALL odds ratios with glm function, logistic regression, need cov of parameters

On Tue, 26 Jul 2005, Garrett Fox wrote: I am trying to do logistic regression with a categorical predictor variable with the glm() function, family=binomial. Using glm() I would like to be able to calculate the confidence intervals of all three possible odds ratios for a factor (the factor

Re: [R] problem with Hershey fonts

Hi Ray Brownrigg wrote: This was reported to me by a colleague in China, so I may not be reproducing exactly what they are seeing (which I suspect is rw2011), but this is what I see: version _ platform i386--netbsdelf arch i386 os netbsdelf system i386, netbsdelf

[R] spss.read factor reversal

Hi, I'm having a problem with spss.read reversing my factor input. Here is the input copied from the spss data editor: color cost 1 2.30 2 2.40 3 3.00 1 2.10 1 1.00 1 2.00 2 4.00 2 3.20 2 2.33 3 2.44 3 2.55 For color, red=1, blue=2, and green = 3. It's type is 'String' and out=read.spss(file)

[R] CART analysis

Is there an R package that can be used for CART analysis? Thank you, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC and University of Maryland School of Medicine Claude Pepper OAIC University of Maryland School of Medicine Division of

Re: [R] spss.read factor reversal

I think it is doing what is supposed to do but I never used read.spss, so take this with a pinch of salt. In R when you use as.integer on a factor, the one with the lowest level gets a value of 1 and so on. The lowest level of the factor can determined from levels() function. f - factor(

Re: [R] CART analysis

RSiteSearch(CART) should bring up a few hits including http://finzi.psych.upenn.edu/R/Rhelp02a/archive/25850.html Regards, Adai On Tue, 2005-07-26 at 20:25 -0400, John Sorkin wrote: Is there an R package that can be used for CART analysis? Thank you, John John Sorkin M.D., Ph.D.

Re: [R] CART analysis

--- Adaikalavan Ramasamy [EMAIL PROTECTED] wrote: RSiteSearch(CART) should bring up a few hits including http://finzi.psych.upenn.edu/R/Rhelp02a/archive/25850.html CART is a trademarked statistical procedure owned by Salford Systems of San Diego, CA. If you're looking for an

[R] trellis graphics/ trellis.par.set()

Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 - Colleagues I want to increase the size of the axis markings and labels on some trellis graphs, and I am having some trouble with trellis.par.set()

[R] Error in FUN(newX[, i], ...) : `x' must be atomic

Hello Group, What is the meaning of the error. is there any place to look for this. I guess 'atomic' seems to be OOP related concept. thank you srini __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] Error in FUN(newX[, i], ...) : `x' must be atomic

Perhaps a reproducible example and short explanation of what you want to do might help. I suspect that you fed a null value into a function that expects a non-null value or something. On Tue, 2005-07-26 at 19:22 -0700, Srinivas Iyyer wrote: Hello Group, What is the meaning of the error. is

Re: [R] Error in FUN(newX[, i], ...) : `x' must be atomic

Actually, atoms are originally a Lisp concept. Objects are either atoms or not. Atoms are data types that cannot be taken apart, such as numbers or symbols. Lists and vectors (of length 1) are examples of non-atomic data types. Did you pass a vector to FUN? Cheers, Simon. At 12:22 PM

[R] Problem specifying function for mle operation

Hello fellow R users, Below are two cases using the mle operation from the stats4 package. In CASE 1 the code runs fine, in CASE 2 errors occur: CASE 1 x, alpha_current, s, and n are vectors of the same length. ll_beta-function(b0=0,b1=0)

[R] gamma distribution

Hi R Users This is a code I wrote and just want to confirm if the first 1000 values are raw gamma (z) and the next 1000 values are transformed gamma (k) or not. As I get 2000 rows once I import into excel, the p - values beyond 1000 dont look that good, they are very high. -- sink(a1.txt);

[R] A question about par.plot in gamlss

Hello I am using the following code to plot a data matrix into a form that seems suitable for the use of par.plot. library(gamlss) a-matrix(c(1,2,3,4,5,6,7,8,9,8,7,6),nrow=3) rownames(a)-c(trt1,trt2,trt3) colnames(a)-c(col1,col2,col3,col4) hpar.plot-function(ZZ){ ZZvar-c(t(ZZ))