Re: [R] R parser for If-else

2009-02-25 Thread Martin Maechler
D == Dani danicy...@gmail.com on Tue, 24 Feb 2009 14:09:36 -0800 writes: D Hi list, D I don't know if somebody has spent a lot of time debugging strange D problems with if else positioning - the parser seems to recognize only D the syntax bellow - this is the only way of

Re: [R] biplot.princomp - changing score labels

2009-02-25 Thread Prof Brian Ripley
On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly. That's not part of the design of

[R] Using package ROCR

2009-02-25 Thread wiener30
I am trying to use package ROCR to analyze classification accuracy, unfortunately there are some problems right at the beginning. Question 1) When I try to run demo I am getting the following error message library(ROCR) demo(ROCR) if(dev.cur() = 1) [TRUNCATED] Error in

[R] Statistic community?

2009-02-25 Thread Antje
Hi there, I'm very glad to use the R-help mailing list for R-related question but more and more often I face general statistical problems. Does anyone know by chance a community (mailinglist, forum, ...) where I can ask these kind of questions? I'm glad for any link or hint :-) Antje

Re: [R] R parser for If-else

2009-02-25 Thread Wacek Kusnierczyk
Martin Maechler wrote: I think this is FAQ (or should become one): ?if [the help page you really should read before spending too much time or even post to R-help] ?if won't parse completely, you need ?'if' ;) vQ __

Re: [R] learning R

2009-02-25 Thread markleeds
David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. On Wed, Feb 25, 2009 at 3:42 AM, Wacek Kusnierczyk wrote: David Winsemius wrote: On Feb 24, 2009, at 11:36 PM, Fuchs Ira

Re: [R] learning R

2009-02-25 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 25.02.2009 06:18:04: Hi Ira: For your first question, under the hood of R, names- is actually a function so , when you do that, you need to say names(a)[2] rather than names(a[2]). why this is is tricky and I wouldn't do it justice if i tried

Re: [R] biplot.princomp - changing score labels

2009-02-25 Thread Axel Strauß
Prof Brian Ripley schrieb: On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly.

[R] R interest group at Stellenbosch University formed: r...@sun

2009-02-25 Thread Rainer M Krug
Hi I know this only affects a small number of subscribers, so I apologize to the Non Stellenbosch University subscribers for the noise. Two weeks ago, four R users met and discussed the possibility of forming an interest group of R users at SUN. The interest group (r...@sun) has the aim of: •

[R] RE : multiple regressions on columns

2009-02-25 Thread GOUACHE David
Hello and thanks for your reply, but as you said, this is not really what I'm trying to do. My purpose is not one of variable selection within a model with multiple predictors, but simply fitting a large number of models with only one predictor. I was just hoping there would be a solution as

Re: [R] learning R

2009-02-25 Thread Wacek Kusnierczyk
markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. thanks, that's good, because i made it up following the page quoted by david, and if i'm flamed for

Re: [R] An error in fitting a non linear regression

2009-02-25 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 24.02.2009 12:41:50: Hi Peter, You are totally right and it was a miscalculating and misunderstanding from me. Regarding the R-squared calculation of non linear model (question 2), is there any way to do that? I am not an expert statistician,

[R] Odp: RE : multiple regressions on columns

2009-02-25 Thread Petr PIKAL
Hi If you do not insist on matrix and use data frame instead lapply(iris4,function(x) lm(iris$Sepal.Length~x)) can do it Regards Petr r-help-boun...@r-project.org napsal dne 25.02.2009 09:56:25: Hello and thanks for your reply, but as you said, this is not really what I'm trying to do.

Re: [R] R parser for If-else

2009-02-25 Thread Martin Maechler
WK == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no on Wed, 25 Feb 2009 09:46:19 +0100 writes: WK Martin Maechler wrote: I think this is FAQ (or should become one): ?if [the help page you really should read before spending too much time or even post

[R] [R-pkgs] leaps and biglm

2009-02-25 Thread Thomas Lumley
New versions of leaps and biglm are percolating through CRAN. The new version of biglm fixes a bug in sandwich standard errors with weights, and adds predict(), deviance() and AIC() methods [based on code from Christophe Dutang]. The new version of leaps adds a regsubsets() method for biglm

Re: [R] learning R

2009-02-25 Thread Wacek Kusnierczyk
a quick follow-up: e = new.env() e$a = 1 names(e) # NULL names(e) = 'a' # error in names(e) = foo : names() applied to a non-vector this is surprising. names(e) 'works', there is no complaint, but when names- is used, the error is about the use of names, not names-.

[R] Odp: Error in var(x, na.rm = na.rm) : no complete element pairs

2009-02-25 Thread Petr PIKAL
Hi r-help-boun...@r-project.org napsal dne 22.02.2009 12:11:46: Hello all, I'm trying to calculate the standar desviation with sd(x,na.rm=TRUE) and I don't know why I have this error Error in var(x, na.rm = na.rm) : no complete element pairs when I try to calculate it, I have been

Re: [R] learning R

2009-02-25 Thread Berwin A Turlach
On Wed, 25 Feb 2009 09:57:36 +0100 Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did

Re: [R] learning R

2009-02-25 Thread Wacek Kusnierczyk
Berwin A Turlach wrote: On Wed, 25 Feb 2009 09:57:36 +0100 Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very

Re: [R] learning R

2009-02-25 Thread markleeds
Hi Wacek: Somewhere I remember reading that environments have functionality like lists EXCEPT for the names part. IIRC, I think that I read this in the R Language Reference manual also. On Wed, Feb 25, 2009 at 4:32 AM, Wacek Kusnierczyk wrote: a quick follow-up: e = new.env()

[R] RE : RE : multiple regressions on columns

2009-02-25 Thread GOUACHE David
of course ! that was so obvious I didn't see it... thanks very much and sorry for the bother David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Petr PIKAL [mailto:petr.pi...@precheza.cz]

Re: [R] learning R

2009-02-25 Thread markleeds
Thanks Berwin. You're correct in that I meant the R Language Definition. Well, it may be a draft but I read it for the first time a few months ago and it was very enlightening so, whether it's a draft or not, I highly recommend it. ( but not for total beginners. The R-intro is better for a

Re: [R] leaps question

2009-02-25 Thread Thomas Lumley
On Wed, 25 Feb 2009, Evelina Naryvska wrote: Colleagues, please help me with the simple question. How can I find R2 and p while doing best subsets regression? Also how can I see B and p for coefficients? You can't see coefficients or their p-values, because these are not computed. The subset

Re: [R] Statistic community?

2009-02-25 Thread Heather Turner
When discussions do burst out on the allstat list, people are usually pointed to one of the following alternatives: http://groups.google.com/group/MedStats http://datashaping.ning.com/forum HTH Heather Peters Gj (PSYCHOLOGY) wrote: Hey Antje list, Antje wrote: I'm very glad to use the

[R] Using very large matrix

2009-02-25 Thread Corrado
Dear friends, I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified

Re: [R] Inference for R Spam

2009-02-25 Thread Jim Lemon
Dieter Menne wrote: And, since my son asked me and I am basketball ignorant: Why are basketball scores mostly much too close to equality? The arguments (loose power when leading) Characteristic of the game. Possession of the ball changes rapidly and the probability of scoring is much higher

Re: [R] Using very large matrix

2009-02-25 Thread Philipp Pagel
I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified Any

Re: [R] Using very large matrix

2009-02-25 Thread Duncan Murdoch
Philipp Pagel wrote: I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements

Re: [R] Using very large matrix

2009-02-25 Thread Philipp Pagel
On Wed, Feb 25, 2009 at 06:37:53AM -0500, Duncan Murdoch wrote: Philipp Pagel wrote: A 8x8 matrix has 6.4 billion cells. If you assume 4 byte (32bit) for a double precision floating point number that's an impressive 25.6 Gb. Certainly does not fit into RAM on my machine. Doubles

[R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Nash
Have the counter function in R ? if we use the software SAS /*** SAS Code **/ data tmp(drop= i); retain seed x 0; do i = 1 to 5; call ranuni(seed,x); output; end; run; data new; counter=_n_; * this keyword _n_ ; set tmp; run; /* _n_ (Automatic

Re: [R] Have a function like the _n_ in R ? (Automatic count function)

2009-02-25 Thread Shubha Vishwanath Karanth
temp=data.frame(a=c(4,3,2,6),b=c(7,4,2,4)) temp a b 1 4 7 2 3 4 3 2 2 4 6 4 temp$counter=1:nrow(temp) temp a b counter 1 4 7 1 2 3 4 2 3 2 2 3 4 6 4 4 Shubha Karanth | Amba Research Ph +91 80 3980 8031 | Mob +91 94 4886 4510 Bangalore * Colombo * London * New York

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Henrique Dallazuanna
I think you can use seq function: seq(5) On Wed, Feb 25, 2009 at 9:25 AM, Nash morri...@ibms.sinica.edu.tw wrote: Have the counter function in R ? if we use the software SAS /*** SAS Code **/ data tmp(drop= i); retain seed x 0; do i = 1 to 5; call

[R] coxph: competing endpoints multiple time-dependent covariate

2009-02-25 Thread sdzhangping
Dear R users: Analysis of the impact of a time-dependent covariate (GVHD or use of steroid after bone marrow transplantation) on two competing endpoints (invasive fungal infection and death) is frequently encountered in the setting of BMT data. Coxph package can be used as the following:

Re: [R] error in dat

2009-02-25 Thread Wacek Kusnierczyk
Prof Brian Ripley wrote: On Mon, 16 Jun 2008, Wacek Kusnierczyk wrote: Paul Adams wrote: Hello everyone, I have the following code which keeps giving me an error. The code is: dat-read.table(file=C:\\Documents and Settings\\Owner\\My

Re: [R] how to NULL multiple variables of a df efficiently?

2009-02-25 Thread Peter Dalgaard
Wacek Kusnierczyk wrote: as above, this works as well: df[, vars] = list(NULL) and this, simplest of them all, works too: df[vars] = list(NULL) That's actually a curious anomaly/design-flaw/whatever... The usual rule is that you can treat data frames as lists, but aq -

Re: [R] Statistic community?

2009-02-25 Thread Keith Jewell
You might also try... http://groups.google.com/group/sci.stat.consult http://groups.google.com/group/sci.stat.edu http://groups.google.com/group/sci.stat.math Although I can't swear these don't overlap with some already mentioned. HTH Keith J Heather Turner heather.tur...@warwick.ac.uk wrote in

Re: [R] how to label the branches of a tree

2009-02-25 Thread David Winsemius
When I execute that code, I get labels both on the branching points and at the leaves of the tree. So I guess my reply is cannot reproduce or do not understand. They are however not properly positioned and the edges and bottoms of some of the labels are cut off, but that did not sound

Re: [R] Leave one out Cross validation (LOO)

2009-02-25 Thread Frank E Harrell Jr
Alex Roy wrote: Dear Frank, Thanks for your comments. But in my situation, I do not have any future data and I want to calculate Mean Square Error for prediction on future data. So, is it not it a good idea to go for LOO? thanks Alex With resampling you should be able

Re: [R] statistical significance of accuracy increase in classification

2009-02-25 Thread Max Kuhn
Monica, I have a few thoughts. - (I believe) it is usually better to put confidence in these metrics instead of relying on p-values. The intervals will allow you to make inferential statements and give you a way of characterizing the uncertainty in the estimates. You've seen how to do this with

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread David Winsemius
The _n_ construct in SAS is most analogous to that of row names in R, accessible (and modifiable) via the row.names() function: DF - structure(list(Month = structure(c(2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L), .Label = c(Aug, July, Sept), class = factor), Week = 27:39,

Re: [R] how to label the branches of a tree

2009-02-25 Thread Prof Brian Ripley
On Wed, 25 Feb 2009, David Winsemius wrote: When I execute that code, I get labels both on the branching points and at the leaves of the tree. So I guess my reply is cannot reproduce or do not understand. They are however not properly positioned and the edges and bottoms of some of the

[R] read multiplan or sylk files in R

2009-02-25 Thread GOUACHE David
Hello, This may sound crazy, but I have a large number of Multiplan data files I'm in the process of recuperating, and I'm hoping to avoid having to open them one by one to convert them into a modern, directly usable format. So I was wondering if someone somewhere had encountered this and

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread hadley wickham
And for completeness here's a function that returns the next integer on each call. n - (function(){ i - 0 function() { i - i + 1 i } })() n() [1] 1 n() [1] 2 n() [1] 3 n() [1] 4 n() [1] 5 n() [1] 6 ;) Hadley On Wed, Feb 25, 2009 at 8:27 AM, David Winsemius

Re: [R] odfWeave problem Error in xmlEventParse

2009-02-25 Thread Max Kuhn
We should make this an FAQ (or find someone who knows how to correct the bug in XML). We've been working on that. It's hard to say what the problem is without the output of sessionInfo() and a reproducible example. Fredrik - if you can send me this off-list, I'll take a look (but it may

[R] [R-pkgs] ggplot2 0.8.2

2009-02-25 Thread hadley wickham
ggplot2 ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle

Re: [R] statistical significance of accuracy increase in classification

2009-02-25 Thread Monica Pisica
Max, thanks for the reply. Yes, the models are done outside R (i will see what i can do to run some of them inside R in the future ) and the sampling is extremely skewed. But we use as truth or reference results from a field exercise where people actually went and gave detailed

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread hadley wickham
On Wed, Feb 25, 2009 at 8:41 AM, Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: hadley wickham wrote: And for completeness here's a function that returns the next integer on each call. n - (function(){   i - 0   function() {     i - i + 1     i   } })() actually, you

[R] C-index for models fitted using start, stop in Surv?

2009-02-25 Thread Eleni Rapsomaniki
Dear R-users, One can use the rcorr.cens function in Design to compute the C index when only the stop time is indicated (I think implicitely start=0 in that case). When the start and stop times are used in a Surv object, e.g. library(Design) S=with(heart, Surv(start,stop,event)) the object

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Gustaf Rydevik
On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com wrote: And for completeness here's a function that returns the next integer on each call. n - (function(){  i - 0  function() {    i - i + 1    i  } })() n() [1] 1 n() [1] 2 n() [1] 3 n() [1] 4 n() [1] 5 n()

[R] Have any way to write a funtion into a list ?

2009-02-25 Thread Nash
Have any way to write a funtion into a list ? -- Nash - morri...@ibms.sinica.edu.tw __ 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 and

Re: [R] Have any way to write a funtion into a list ?

2009-02-25 Thread Philipp Pagel
On Wed, Feb 25, 2009 at 11:11:51PM +0800, Nash wrote: Have any way to write a funtion into a list ? You can do that the same way you would use with any other object: foo - function(x){x^2} foo(12) [1] 144 a - list(foo, 12, 'as') a [[1]] function(x){x^2} [[2]] [1] 12 [[3]] [1] as cu

[R] How to make warning message colorful (or have sound)?

2009-02-25 Thread Sean Zhang
Dear R-helpers: I am new to R and wonder how to make a warning message colorful (if possible, having sound is also welcome). I did some research and failed to see options to allow this functionality. Is this a techical limitation so far, or I miss some information. Many thanks in advance. -sean

Re: [R] how to label the branches of a tree

2009-02-25 Thread Philip Twumasi-Ankrah
You may have to change/scale the sizes of the font by using cex and then to keep all labels within the plotting window, use xpd=TRUE. Like in text(fit, use.n=TRUE, cex=0.8, xpd=TRUE) Philip -- A Smile costs Nothing But Rewards Everything  

Re: [R] Have any way to write a funtion into a list ?

2009-02-25 Thread Uwe Ligges
Nash wrote: Have any way to write a funtion into a list ? Sure: A - list(mean, var) A[[1]](1:2) # 1.5 A[[2]](1:2) # 0.5 Uwe Ligges -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Charles C. Berry
On Wed, 25 Feb 2009, Gustaf Rydevik wrote: On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com wrote: And for completeness here's a function that returns the next integer on each call. n - (function(){  i - 0  function() {    i - i + 1    i  } })() n() [1] 1 n() [1] 2

[R] Data Envelopment Analysis in R

2009-02-25 Thread Arup
How do I do a data envelopment analysis in R...provide me with the step by step procedure for that..thanks in advance... Arup -- View this message in context: http://www.nabble.com/Data-Envelopment-Analysis-in-R-tp22199360p22199360.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Using very large matrix

2009-02-25 Thread Tony Breyal
looks like you've run out of memory mate, because that sure is a big matrix, you'd probably need 64 bit OS/CPU/R and loads of RAM. see thread: http://www.nabble.com/Error-in-matrix:--too-many-elements-specified-td20457910.html I know there are some packages on cran which help with large

Re: [R] All the products of common factors

2009-02-25 Thread Stavros Macrakis
On Wed, Feb 25, 2009 at 9:25 AM, Fox, Gordon g...@cas.usf.edu wrote: The tricky part isn't finding the common factors -- we knew how to do that, though not in so concise a fashion as some of these suggestions. It was finding all their products without what I (as a recovered Fortran programmer)

[R] How to get JRI to work from my NetBeans

2009-02-25 Thread Yakub Sebastian
Hi, I need your help. I have downloaded a precompiled JRI as part of rJava. I have included rJava as part of my R package libraries. Now I need to be able to work with some R functions from my Java apps. I'm using NetBeans on Windows. I have followed some instructions from

[R] Linear Discriminant Analysis

2009-02-25 Thread Arup
Kindly let me know the process to carry out a Linear discriminant analysis...thanks in advance Arup -- View this message in context: http://www.nabble.com/Linear-Discriminant-Analysis-tp22199424p22199424.html Sent from the R help mailing list archive at Nabble.com.

[R] read and reshape time series table with empty items

2009-02-25 Thread Bastian Pöschl
Dear useR's, I have a problem to read data (daily precipitation). The data are formated in months by columns wich leads to empty items in months with less then 31 days. What i did was reading the file and try to reshape the object a- read.table(nds.txt, header=TRUE, sep=;, dec = ., na.string=NA)

[R] survival::predict.coxph

2009-02-25 Thread Bernhard Reinhardt
Hi, if I got it right then the survival-time we expect for a subject is the integral over the specific survival-function of the subject from 0 to t_max. If I have a trained cox-model and want to make a prediction of the survival-time for a new subject I could use survfit(coxmodel,

Re: [R] read multiplan or sylk files in R

2009-02-25 Thread Philip Twumasi-Ankrah
According to the microsoft site http://support.microsoft.com/kb/323626;, SYLK files are ordinary text or csv files with a peculiar character in that the first two characters of the file are the uppercase letters. For example for a csv file, the first column may contain the

Re: [R] how to label the branches of a tree

2009-02-25 Thread Utkarsh Singhal
Hi David, May be I was not clear, but I want to label the branches itself and not the branching points or the leaves. Regards Utkarsh From: Philip Twumasi-Ankrah [mailto:nana_kwadwo_der...@yahoo.com] Sent: Wednesday, February 25, 2009 9:07 PM To:

Re: [R] Linear Discriminant Analysis

2009-02-25 Thread Jorge Ivan Velez
Dear Arup, See the lda function in the MASS package. In general, require(MASS) Loading required package: MASS ?lda HTH, Jorge On Wed, Feb 25, 2009 at 4:44 AM, Arup arup.pramani...@gmail.com wrote: Kindly let me know the process to carry out a Linear discriminant analysis...thanks in

[R] Similarity between clusters generated by hclust + cutree

2009-02-25 Thread Corrado
Dear friends I have clustered some objects using the hclust algorithm, with method ward. I then cutree with 48 classes. distPredTurn-as.dist(resultMatrix) hctr-hclust(distPredTurn,ward) cutree(hctr,k=NC) I would like to estimate the similarity between each pair of the 48 clusters, for

Re: [R] Linear Discriminant Analysis

2009-02-25 Thread Christos Hatzis
Maybe as a starter RSiteSearch(linear discriminant analysis) R has tools to help you help yourself with this types of questions. -Christos -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Arup Sent: Wednesday, February 25,

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Wacek Kusnierczyk
hadley wickham wrote: On Wed, Feb 25, 2009 at 8:41 AM, Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: hadley wickham wrote: And for completeness here's a function that returns the next integer on each call. n - (function(){ i - 0 function() { i - i + 1

Re: [R] Help with Latex (Hmisc)

2009-02-25 Thread Marc Schwartz
on 02/25/2009 07:52 AM Frank E Harrell Jr wrote: Dieter Menne wrote: Frank E Harrell Jr f.harrell at vanderbilt.edu writes: ... Word and pdf It depends on how you copy. By all means use Insert ... Picture ... from file and directly insert pdf. Please, tell me how you got this to work.

Re: [R] How to get JRI to work from my NetBeans

2009-02-25 Thread Rowe, Brian Lee Yung (Portfolio Analytics)
Did you set a system property for java.libary.path that points to the native library as the error message instructs? I'm not familiar with NetBeans, but in Eclipse you can set the JVM properties in a dialog. Otherwise you can always pass it in via the command line: -Djava.library.path=path to the

Re: [R] Have a function like the _n_ in R ? (Automatic count function )

2009-02-25 Thread Gustaf Rydevik
On Wed, Feb 25, 2009 at 4:43 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Wed, 25 Feb 2009, Gustaf Rydevik wrote: On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com wrote: And for completeness here's a function that returns the next integer on each call. n -

[R] : record which entry in one file doesn't appear in a different file

2009-02-25 Thread Laura Rodriguez Murillo
Hi dear list, If anybody could help me, it would be great! I have two files: File 1 is a list (one column and around 10 rows) File 2 is a list with all the names from file one and a few more (one column and more than 10 rows) What I want is to add a column in file 2 that says which name

Re: [R] : record which entry in one file doesn't appear in a different file

2009-02-25 Thread Tal Galili
Hi Laura. Let's assume file 1 and 2 are vectors loaded in R named: vec1 and vec2, here is a short code (with dummy numbers) for a solution: vec1 - c(1,2,34,4,3,6,76) vec2 - c(1,2,34,76,24,62,1,4234,435,4333,4422,304,776) which.vec2.where.in.vec1 - vec2 %in% vec1

[R] Computing sd across an array with missing values

2009-02-25 Thread Matt Oliver
Dear help, suppose I have this array and want to compute sd aross rows and columns. p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3)) apply(p, 1:2, sd) fails because sd requires at least 2 numbers to compute sd apply(p, 1:2, sd, na.rm = TRUE) fails for the same reason I crafted my own

[R] Anova Help?

2009-02-25 Thread Dar
I am conducting an experiment where students are put into 5 total groups (one is the control group). They are given a task and then I'm measuring if there are differences (A 5 X 1 between-subject design will be used for the experiment). I'm a little confused on the data explanation (or should I

Re: [R] Anova Help?

2009-02-25 Thread Tal Galili
Hi Dar. I am not sure I got your question - Are you asking what analysis to perform ? Or how to perform it ? Could you please give more details ? On Wed, Feb 25, 2009 at 5:52 PM, Dar darre...@aol.com wrote: I am conducting an experiment where students are put into 5 total groups (one is

Re: [R] : record which entry in one file doesn't appear in a different file

2009-02-25 Thread Patrizio Frederic
hey Laura, I hope this help f1 = c(a,b,c) f2 = c(b,a,c,d) match(f2,f1) f3 = match(f2,f1,0) ?match cbind(f2,f3) cbind(f2,f30) f4 = ifelse(f30,yes,no) cbind(f2,f4) data.frame(f2,f4) Patrizio 2009/2/25 Laura Rodriguez Murillo laura.lmuri...@gmail.com: Hi dear list, If anybody could help me, it

Re: [R] Computing sd across an array with missing values

2009-02-25 Thread Jorge Ivan Velez
Dear Matt, Here are two ways: # Data p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3)) # First res-apply(p,3,function(X) c(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,2,sd,na.rm=TRUE)) ) res # Second res2-apply(p,3,function(X)

[R] Using gregexpr with multiple search elements

2009-02-25 Thread Corey Sparks
Dear list, I am trying to use gregexpr to see if entries in a dataframe have either of two possible values for a string. here's an example text-c(fat, rat, cat, dog, log, fish) If I just wanted to find if any one of the elements in text match the pattern at I would do gregexpr(\\at, text)

[R] survival::survfit,plot.survfit

2009-02-25 Thread Jeff Xu
I am confused when trying the function survfit. my question is: what does the survival curve given by plot.survfit mean? is it the survival curve with different covariates at different points? or just the baseline survival curve? for example, I run the following code and get the survival curve

Re: [R] Using gregexpr with multiple search elements

2009-02-25 Thread Christos Hatzis
gregexpr(\\at|\\og, text) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Corey Sparks Sent: Wednesday, February 25, 2009 11:50 AM To: R Help Subject: [R] Using gregexpr with multiple search elements Dear list, I am

Re: [R] All the products of common factors

2009-02-25 Thread Gordon Fox
Sorry - I didn't express myself very clearly. Yes, we're looking for common factors of A and B. One way to get there is by my initial approach: find the prime factors of each, select those that are in common, and then take pairwise products. My initial question was about the last step only.

Re: [R] Computing sd across an array with missing values

2009-02-25 Thread Jorge Ivan Velez
Hi Mark, There is a typo in the first way. My apologies. It should be: # First res-apply(p,3,function(X) c(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,1,sd,na.rm=TRUE)) ) res HTH, Jorge On Wed, Feb 25, 2009 at 11:42 AM, Jorge Ivan Velez jorgeivanve...@gmail.com wrote: Dear

[R] vertically aligned X axis labels disappear off R Graphics window

2009-02-25 Thread R User R User
Hi guys, I'm evaluating R for basic data exploration. I produce a bar plot of the data, with the x axis labels aligned vertically. However, the start of labels longer than about 10 characters are cut off by the bottom of the graphics window. I'd appreciate your help in properly spacing the space

Re: [R] C-index for models fitted using start, stop in Surv?

2009-02-25 Thread Frank E Harrell Jr
Eleni Rapsomaniki wrote: Dear R-users, One can use the rcorr.cens function in Design to compute the C index when only the stop time is indicated (I think implicitely start=0 in that case). When the start and stop times are used in a Surv object, e.g. library(Design) S=with(heart,

Re: [R] how to label the branches of a tree

2009-02-25 Thread David Winsemius
How do you want the labels to appear? Each branch will be the logical conjunction of the criteria for *all* of the upstream splits. Perhaps you can get direction by looking at the code of text.rpart: getAnywhere(text.rpart) Any split would need to add an Split-N yes or an Split-N No to

Re: [R] multiple regressions on columns

2009-02-25 Thread Greg Snow
Well add1 (and others) does fit the regressions you asked about if you give it the base model only including the intercept and the scope including the x variables of interest. Unfortunately it only returns certain statistics on those models, not the whole object, but if you were interested in

Re: [R] C-index for models fitted using start, stop in Surv?

2009-02-25 Thread Eleni Rapsomaniki
rcorr.cens is not meant for that. Thank you for the clarification. On a second thought, I think (hope) a time-dependent AUC index should be more appropriate in this case, such as survivalROC. Many many thanks for all your help! Eleni Rapsomaniki Research Associate Tel: +44 (0) 1223

Re: [R] how to label the branches of a tree

2009-02-25 Thread David Winsemius
Following Dr Ripley's advice I looked at the text.rpart documentation a bit more thoroughly and after seeing The edges connecting the nodes are labeled by left and right splits. I find that the fancy=TRUE invocation does cause a labeling of what you appear to be calling branches. See if

[R] monotonic GAM with more than one term

2009-02-25 Thread Benjamin Tyner
Hi, Does anyone know how to fit a GAM where one or more smooth terms are constrained to be monotonic, in the presence of by variables or other terms? I looked at the example in ?pcls but so far have not been able to adapt it to the case where there is more than one predictor. For example,

Re: [R] vertically aligned X axis labels disappear off R Graphics window

2009-02-25 Thread Uwe Ligges
R User R User wrote: Hi guys, I'm evaluating R for basic data exploration. I produce a bar plot of the data, with the x axis labels aligned vertically. However, the start of labels longer than about 10 characters are cut off by the bottom of the graphics window. I'd appreciate your help in

Re: [R] Anova Help?

2009-02-25 Thread Dar
I’m just setting up the experiment and need help explaining what the data analysis would be. Let me know of any questions….. what would be compared and how it would be measured. Is it a multi-way or 1-way anova? Thanks! A 5 X 1 between-subject design will be used for the experiment. Four tool

[R] make check reg-tests-1.R error on solaris

2009-02-25 Thread Karen Noel
R 2.5.1 compiled, passed the make check and has been successfully running for a couple years on a Sun Fire V490 running Solaris 9. I need a newer version of R, but can't get a newer version of R to pass the make check. I've tried 2.8.1, 2.7.2, 2.6.2 and 2.6.0. (2.5.1 still passes on this

[R] Gradient function for optim.

2009-02-25 Thread rkevinburton
I have read that when the gradient function is not supplied (is null) then first order differencing is used to find the differential. I was trying to track down this for my own information but I run into .Internal(optim.). I was not sure where to look next to see the function that is

Re: [R] run latent class analysis with R

2009-02-25 Thread Drew Linzer
poLCA is designed to work this way. There's a complete user's guide and manual on the project website at http://userwww.service.emory.edu/~dlinzer/poLCA/ http://userwww.service.emory.edu/~dlinzer/poLCA/ Thanks, Drew == Drew Linzer Assistant Professor Department of Political Science Emory

Re: [R] biplot.princomp - changing score labels

2009-02-25 Thread Héctor Villalobos
Perhaps this may help you. Regards data(iris3) ir - rbind(iris3[ , , 1], iris3[ , , 2], iris3[ , , 3]) ir.pca - princomp(ir) biplot(ir.pca) # Rehacer Biplot # Calcular Factor para re-escalar scores y eigenvectores lambda - ir.pca$sdev[1:2] * sqrt(ir.pca$n.obs) scores - t(

Re: [R] biplot.princomp - changing score labels

2009-02-25 Thread stephen sefick
have you thought about extracting the data and using this in ggplot? On Wed, Feb 25, 2009 at 3:52 AM, Axel Strauß a.stra...@tu-bs.de wrote: Prof Brian Ripley schrieb: On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1),

Re: [R] read and reshape time series table with empty items

2009-02-25 Thread Gabor Grothendieck
Try this: Lines - 'Jahr;Tag;Jan;Febr;März;April;Mai;Juni;Juli;Aug;Sept;Okt;Nov;Dez 1978;1;NA;NA;NA;0.0;5.5;0.0;11.8;0.0;2.4;6.4;0.0;0.0 1978;2;NA;NA;NA;0.0;0.5;0.0;2.0;2.0;0.0;9.0;0.0;0.0 1978;3;NA;NA;NA;0.3;0.0;3.0;3.2;0.4;0.0;24.7;0.0;0.0 1978;4;NA;NA;NA;0.7;0.0;0.0;24.4;1.1;0.0;8.6;0.0;0.0

[R] make check reg-tests-1.R error on solaris

2009-02-25 Thread Karen Noel
R 2.5.1 compiled, passed the make check and has been successfully running for a couple years on a Sun Fire V490 running Solaris 9. I need a newer version of R, but can't get a newer version of R to pass the make check. I've tried 2.8.1, 2.7.2, 2.6.2 and 2.6.0. (2.5.1 still passes on this server)

[R] R, joint scaling test, quantitative genetic analysis sensitivity to model violations

2009-02-25 Thread Maureen Ryan
Hi all,This is really a stats question as much as an R question. I'm trying to do a joint scaling test (JST - see below) on some very oddly-distributed data and was wondering if anyone can suggest a good way of dealing with model violations and/or using R to evaluate how sensitive the model

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