[R] more question

Hello, thank you very much for your help in last email. it is very helpful. right now, i have more questions about my project, 1. solve can i remove the NA from a vectors: for exmample, if my vector is: v <- (NA, 1, 2, 3, 4, 5) how can I remove the NA from vector v 2. how I can get input from

RE: [R] lme and varFunc()

> I am currently analyzing a dataset using lme(). The model I > use has the following structure: > > model<-lme(response~Covariate+TreatmentA+TreatmentB, >random=~1|Block/Plot,method="ML") > > When I plot the residuals against the fitted values, I see a clear > positive trend (meani

Re: [R] several boxplots or bwplots into one graphic

On 24 Jan 2005 at 14:44, Christoph Lehmann wrote: > Hi > I have 10 variables and 2 groups. I know how to plot a bwplot for ONE > var. e.g. > > var.a var.b var.c .. GROUP > 0.2 0.5 0.2 .. 0 > 0.3 0.2 0.2 .. 0 > .. > 0.1 0.8 0.7 .. 1 > 0.5 0.5 0.1 .. 1 > .. > > > bwplot(

RE: [R] error preparing a package for lazy loading with R CMD

That's the way John Fox advised to turn the problem. Indeed it works but doe snot explain this bug in lazy loading. I don't think that it may come for a syntax error somewhere. All the functions have been checked and the problem does not occur if any of the 35 functions is removed. Something ha

[R] Zipf random number generation

Hi, Is there a Zipf-like distribution RNG in R? Thanks, Weiguang __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

[R] agglomerative coefficient in agnes (cluster)

I haven't read the book, but could anyone explain more about this parameter? help(agnes) says that ac measures the amount of clustering structure found. From the definition given in help(agnes.object), however, it seems that as long as the dissimilarity of the merger in the final step of the al

[R] Recursive default argument reference

"Recursive default argument reference" keeps appearing when I try to run a haplo.score function in R for Windows. I'm new to using this program. Does anyone know what this means? - [[alternative HTML version deleted]] ___

[R] Estimating error rate for a classification tree

Hi, I created an rpart object and pruned the tree using 1-SE rule. I used 10-fold cross validation while creating the tree. Then, I extracted the cross-validated predictions for my data points using xpred.rpart and obtained some statistics like precision, recall, overall error rate, etc. However,

RE: [R] Related with "kmeans"

> From: [EMAIL PROTECTED] > > Hi, > I am new here. > I used y<-kmeans(x, 2)(x is a vector) to do the cluster > analysis. I get > y has $cluster, $center etc. I need to pull out the data belong to > cluster 1 and cluster 2. How can I do that? Here's an example: > cl <- round(runif(20)) >

[R] Related with "kmeans"

Hi, I am new here. I used y<-kmeans(x, 2)(x is a vector) to do the cluster analysis. I get y has $cluster, $center etc. I need to pull out the data belong to cluster 1 and cluster 2. How can I do that? Thanks, Ming __ R-help@stat.math.ethz.ch

RE: [R] Weighted.mean(x,wt) vs. t(x) %*% wt

Just look at the code: > weighted.mean function (x, w, na.rm = FALSE) { if (missing(w)) w <- rep.int(1, length(x)) if (is.integer(w)) w <- as.numeric(w) if (na.rm) { w <- w[i <- !is.na(x)] x <- x[i] } sum(x * w)/sum(w) } So the differences a

Re: [R] survreg: fitting different location parameters

I am still trying to find a common intercept but a different slopes for each group within my lifetime data. By stratifying the variable stress (the groups) I get different scale parameters which is not my goal. So I did this: survreg(Surv(lfailure)~as.factor(stress),data=steel,dist="extreme") a

Re: [R] some questions about font

Hi Bobai Li wrote: Hi, I have been using R to create some mathematical and statistical graphs for a book manuscript, but I got some problems: 1) Some web positngs said that default typeface for math expressions is italic, but in my system (R 2.01 on WinXP), the default is regular font. How can

Re: [R] animation without intermediate files?

Hi Cari G Kaufman wrote: Hello, Does anyone know how to make "movies" in R by making a sequence of plots? I'd like to animate a long trajectory for exploratory purposes only, without creating a bunch of image files and then using another program to string them together. In Splus I would do thi

[R] Weighted.mean(x,wt) vs. t(x) %*% wt

What is the difference between the above two operations ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posti

RE: [R] lookups and joins

All together now: ?merge :-) -Original Message- From: [EMAIL PROTECTED] on behalf of Paul Sorenson Sent: Mon 1/24/2005 10:34 PM To: r-help@stat.math.ethz.ch Cc: Subject:[R] lookups and joins I have some data coming from SQL sources that I wish to relate in various w

[R] lookups and joins

I have some data coming from SQL sources that I wish to relate in various ways. For reasons only known to our IT people, this can't be done in SQL at present. I am looking for an R'ish technique for looking up new columns on a data frame. As a simple, hardwired example I have tried the followi

[R] Job Opportunity: Senior Statistician CC 083

Greetings, Thanks for your time in reviewing the following role located in the RTP, NC area. Our client is a drug development platform technology company whose patent-pending intellectual property is poised to dramatically impact both drug discovery and development processes by accurately mea

[R] Re:[ R] Wilcoxon test for mixed deisgn

Marco Chirandini writes: "is there any extension of the pairwise Wilcoxon test to a dependent samples layout with replicates (or, in other terms, a one-way layout with blocking and replicates)? The Wilcoxon method with matched pairs works for the case of dependent samples with one observation per

RE: [R] Deleted objects keep coming back

> From: Ken Termiso > > Having a very strange and frustrating problem with v2.0.1 > under Mac OSX > 10.3. I have several closely related workspaces in the same > directory that I > need to keep separate from one another (there are a few > objects common to > all workspaces, and then there ar

[R] Deleted objects keep coming back

Having a very strange and frustrating problem with v2.0.1 under Mac OSX 10.3. I have several closely related workspaces in the same directory that I need to keep separate from one another (there are a few objects common to all workspaces, and then there are other objects that store the results o

Re: [R] an R script editor for Mac

Hi, There is also SubEthaEdit, quite an elegant editor with R/S syntax highlighting as 1 of the many available modes. With AppleScript its easy to sent the edit window, a file, a selection etc. to R for execution. http://www.codingmonkeys.de/subethaedit/ Rob On Jan 24, 2005, at 8:41 AM, Paul Ro

[R] R 2.0.1 and Rggobi install issues on windows XP

Has anyone else ran into problems installing Rggobi with R 2.0.1 on a windows platform? I've followed all the instructions available and I still can not get R to recognize Rggobi as a library (package). I I've already emailed Duncan Temple Lange at ggobi.org and bell labs and both emails have boun

Re: [R] hist() and database

jcb wrote: Hello, I'm a new R user and I'm having a little trouble getting started. I'm hoping someone can help me out. I read numbers (integer) from a SQL database. Some calculations as mean()are possible but hist() give an error. Here are the commands: library(RMySQL) Loading required package

[R] hist() and database

Hello, I'm a new R user and I'm having a little trouble getting started. I'm hoping someone can help me out. I read numbers (integer) from a SQL database. Some calculations as mean()are possible but hist() give an error. Here are the commands: library(RMySQL) Loading required package: DBI > con

[R] Follow-up on nls convergence failure with SSfol

A couple of weeks ago there was a question regarding apparent convergence in nls when using the SSfol selfStart model for fitting a first-order pharmacokinetic model. I can't manage to find the original message either in my archive or in the list archives but the data were time conc dose

Re: [R] lme and varFunc()

Dear Christoph, what command are you using to plot the residuals? If you use the default residuals it will not reflect the variance model. If you use the argument type="p" then you get the Pearson residuals, which will reflect the weights model. Try something like this: plot(model, resid(.,

Re: [R] converting R objects to C types in .Call

Hi Barry, Thanks for your reply. On Mon, 24 Jan 2005, Barry Rowlingson wrote: Firstly, R is expecting an SEXP as a return value! Ouch... I haven't found anything that says this explicitly, but it looks like .Call expects a SEXP to be returned to R. At any rate, trying to use void instead gives a

RE: [R] which.pmin?

That's what "ifelse" is for: ifelse(fpr(b, k.floor) < fpr(b, k.ceiling), k.floor, k.ceiling) Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Seung Jun Sent: Friday, January 21, 2005 5:27 PM To: R-help@stat.math.ethz.ch Subject: [R] whic

Re: [R] converting R objects to C types in .Call

On Mon, 24 Jan 2005, Faheem Mitha wrote: I'm trying to write an R wrapper for a C++ library, using .Call. I've never used .Call before. I'm currently having some difficulties converting a R character string to a C one. Here is a little test program. #include #include #include SEXP testfn(SEXP

Re: [R] converting R objects to C types in .Call

Faheem Mitha wrote: SEXP testfn(SEXP chstr) { char * charptr = CHAR(chstr); printf("%s", charptr); } I am sure I am making an obvious mistake, but can someone help me to sort it out? Thanks in advance. Please cc me, I'm not subscribed. Firstly, R is expecting an SEXP as a return value! And s

[R] converting R objects to C types in .Call

Dear People, I'm trying to write an R wrapper for a C++ library, using .Call. I've never used .Call before. I'm currently having some difficulties converting a R character string to a C one. Here is a little test program. #include #include #include SEXP testfn(SEXP chstr) { char * charptr =

RE: [R] proj() function for lm objects

Dear Piet, You'll find more of an explanation in Sec. 5.3.3 of Chambers and Hastie, eds., Statistical Models in S. Briefly, proj() computes the orthogonal projections of the response (y) sequentially onto the subspaces spanned by columns of the model matrix (X) corresponding to terms in the model

Re: [R] using eval() with pre-built expression inside function

If you look at the beginning of lm(), you'll see that match.call() is used and name of the function (in this case "f1") is replaced with "model.frame". Does something like this work? f1 <- function(formula, data) { mf <- match.call(expand.dots = FALSE) mf[[1]] <- as.name("model.

Re: [R] an R script editor for Mac

Jacques VESLOT wrote: > Could someone please make me know if there is a nice script editor available > under Mac, similar to Crimson, that offers R syntax highlighting (and pairs > of parentheses underlining) ? Did you look into BareBone's TextWrangler, 'BBEdit Lite' replacement? It's now availab

[R] using eval() with pre-built expression inside function

I'm trying to evaluate a pre-built expression using eval(), e.g. dataset <- data.frame(y = runif(30, 50,100), x = gl(5, 6)) # one like this mf <- expression(model.frame(y~x)) eval(mf, dataset, parent.frame()) # rather than this eval(expression(model.frame(y~x)), dataset, parent.frame()) In the

[R] proj() function for lm objects

Dear all, I'm trying to find a clear explanation of what the 'proj(lm)' function produces after having fit a linear model using 'lm'. I find the help page on the proj() function highly unclear (surely part to my limited knowledge of statistics). Can anybody provide a pointer to a clearer ex

[R] R: text miner:

See: http://wwwpeople.unil.ch/jean-pierre.mueller/ ttda - tools for textual data analysis Regards Vito you wrote: Hi, Does a text miner exist in R-language similar to Splus miner or SAS text miner? I would appreciate any information. TIA, Aldi = Diventare costruttori di soluzioni Became

Re: [R] How to use "identify" --- Summary

I asked why my call to identify wasn’t working. Thanks to Petr Pikal, Tom Mulholland, Gavin Simpson, and Duncan Murdoch for explaining that I had misinterpreted the ?identify help page, and that I needed to feed both the x and y vectors in the plot to identify(). It’s working fine for me now.

[R] parameter couldn't be set in high-level plot() function

Dear R users, I am using function bandplot from the gplots package. To my understanding (viewing the source of bandplot) it calls function plot (add = FALSE) with the same parameters (except for a few removed). I would like to give extra parameters 'xlab' and 'ylab' to function bandplot, but, a

Re: [R] several boxplots or bwplots into one graphic

Your variables (var.*) seem to be on the same scale. How about reshaping the data into a univariate layout and then using bwplot as follows: mydata <- data.frame(ID = 1:20, A = runif(20), B = runif(20), C = runif(20), GROUP = rep(c(0,1), c(10,10))) mydata.uni <- reshape(m

Re: [R] an R script editor for Mac

> "TomH" == Thomas Schönhoff <[EMAIL PROTECTED]> > on Fri, 21 Jan 2005 23:21:30 +0100 writes: TomH> Hello, TomH> Am Freitag, den 21.01.2005, 06:39 -0500 schrieb Sean Davis: >> Consider using ESS and xemacs or emacs. You get syntax highlighting, >> auto-indent, command

Re: [R] functions not found after installing DBI/RDBI packages

RE: [R] functions not found after installing DBI/RDBI packagesColin, There is an ODBC driver for postgres and there is a binary installer for postgres, just in case you want to use postgres. I think both are available at http://www.postgresql.org. If all you are doing is storing and retrieving

RE: [R] error preparing a package for lazy loading with R CMD

Not sure if this will help, but have you tried loading the package after install with no lazyload? I've found that if there are syntax errors in the R source, that can give the problem you described. Just a guess. Andy > From: Patrick Giraudoux H > > Dear Lister, > > I work with R 2.0.1 and

[R] several boxplots or bwplots into one graphic

Hi I have 10 variables and 2 groups. I know how to plot a bwplot for ONE var. e.g. var.a var.b var.c .. GROUP 0.2 0.5 0.2 .. 0 0.3 0.2 0.2 .. 0 .. 0.1 0.8 0.7 .. 1 0.5 0.5 0.1 .. 1 .. bwplot(var.a ~ GROUP, data = my.data) How can I plot 10 bwplots (or boxplots) automatical

[R] lme and varFunc()

Dear R users, I am currently analyzing a dataset using lme(). The model I use has the following structure: model<-lme(response~Covariate+TreatmentA+TreatmentB,random=~1|Block/Plot,method="ML") When I plot the residuals against the fitted values, I see a clear positive trend (meaning that the var

[R] CIS inquiries

Does anyone have an automated way to make Current Index to Statistics inquiries from R, or from the Unix command line? I thought it might be convenient to have something like this for occasions in which I'm in a foreign domain and would like to make inquires on my office machine without firing up

Re: [R] printing PCA scores

On Mon, 24 Jan 2005, Jari Oksanen wrote: On Sat, 2005-01-22 at 17:31 -0500, Jérôme Lemaître wrote: Hey folks, I have an environmental dataset on which I conducted a PCA (prcomp) and I need the scores of this PCA for each site (=each row) to conduct further analyses. Can you please help me with that

[R] limma "ref"

Hi, I have a question about limma. I have data from spotted arrays. I have class A and Class B on the same slide. In Limma if I put class A as the reference (ref), are the list of genes I get in the output for class A or class B? #design <- modelMatrix(targets, ref="classA") design Josephin

Re: [R] survreg: fitting different location parameters

On Sun, Jan 23, 2005 at 03:10:18PM -0500, [EMAIL PROTECTED] wrote: > Hi R-Help! > > My question: I have lifetime/failure data of machines with different > stress levels and i think an weibull/extreme value distribution would > fit this data. So I did: > > model1 <- survreg(Surv(lfailure)

Re: [R] mcnemar.test odds ratios, CI, etc.

"Bliese, Paul D LTC USAMH" <[EMAIL PROTECTED]> writes: > Does anyone know of another version of the Mcnemar test that provides: > > > > 1. Odds Ratios > > 2. 95% Confidence intervals of the Odds Ratios > > 3. Sample probability > > 4. 95% Confidence intervals of the sample probability

Re: [R] How to use "identify"

On Sun, 23 Jan 2005 18:35:00 -0500, David Parkhurst <[EMAIL PROTECTED]> wrote : >I can't get identify to work, using R 2.0.1 under windows xp pro, >service pack 2. Here's what I enter, and the result: > > > plot((our.frame2$c1),(our.frame2$c9)) # Produces desired plot > > identify(our.frame2$c1

Re: [R] Wilcoxon test for mixed design (between-within subjects)

Hallo Christoph, > There is always the possibility to summarize the replicates and > then calculate a common pairwise Wilcoxon test. mmmh, in this case I prefer the Friedman test, I would like not to loose any data. > The Friedman test calculates the ranks inside of the blocks, for > each blo

RE: [R] functions not found after installing DBI/RDBI packages

hi - thanks for the response, I've changed to using the ODBC driver and MySQL as i didn't want to be tied to using linux, and it seems there is no easily installable version of the postgres driver for windows. cheers, colin -Original Message- From: Sean Davis [mailto:[EMAIL PROTECTED] S

Re: [R] Wilcoxon test for mixed design (between-within subjects)

Hallo Marco Marco Chiarandini writes: > Hallo, > > is there any extension of the pairwise Wilcoxon test to a dependent > samples layout with replicates (or, in other terms, a one-way layout > with blocking and replicates)? > There is always the possibility to summarize the replicates and

Re: [R] package dependency error on loading lme4

[EMAIL PROTECTED] wrote: Hi all, I recently (today) updated the Matrix package and installed the latticeExtra package, but then when I tried to load the lme4 package, I got the following error message:- library(lme4) Loading required package: Matrix Loading required package: latticeExtra Error i

Re: [R] How to use "identify"

David Parkhurst wrote: I can't get identify to work, using R 2.0.1 under windows xp pro, service pack 2. Here's what I enter, and the result: > plot((our.frame2$c1),(our.frame2$c9)) # Produces desired plot > identify(our.frame2$c1) # Plot comes to forefront, so I select a point warning: no po

Re: [R] How to use "identify"

Does this work for you? x <- runif(30) y <- runif(30) z <- 1:30 plot(x,y) identify(x,y,z) That is you need to tell it everything it is looking for. Sometimes x is boy x and y because they use xy.coords Tom David Parkhurst wrote: I can't get identify to work, using R 2.0.1 under windows xp pro, s

Re: [R] How to use "identify"

__ 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] read data from a file and vector expansion

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

[R] mcnemar.test odds ratios, CI, etc.

Does anyone know of another version of the Mcnemar test that provides: 1. Odds Ratios 2. 95% Confidence intervals of the Odds Ratios 3. Sample probability 4. 95% Confidence intervals of the sample probability Obviously the Odds Ratios and Sample probabilities are easy to calculate f

Re: [R] scan command

Hi Olivia On 22 Jan 2005 at 20:55, Olivia Fant wrote: > I am using the scan command to read a file I called data1. The > program returns > >Error in file(file,"r") : unable to open connection In >addition: Warning message: cannot open file 'data1' > I am not e

Re: [R] printing PCA scores

On Sat, 2005-01-22 at 17:31 -0500, Jérôme Lemaître wrote: > Hey folks, > > I have an environmental dataset on which I conducted a PCA (prcomp) and I > need the scores of this PCA for each site (=each row) to conduct further > analyses. > > Can you please help me with that? > Did you try help(prc

[R] package dependency error on loading lme4

Hi all, I recently (today) updated the Matrix package and installed the latticeExtra package, but then when I tried to load the lme4 package, I got the following error message:- > library(lme4) Loading required package: Matrix Loading required package: latticeExtra Error in importIntoEnv(impen

[R] How to use "identify"

I can't get identify to work, using R 2.0.1 under windows xp pro, service pack 2. Here's what I enter, and the result: > plot((our.frame2$c1),(our.frame2$c9)) # Produces desired plot > identify(our.frame2$c1) # Plot comes to forefront, so I select a point warning: no point with 0.25 inches nume

[R] read data from a file and vector expansion

hello, if i need to read data from a file one line and one how can do? I am using lines <- ("input.txt") so that now the variable lines holds all the data in my file and i am using for loop to loop each lines[i] to get each line. for exmaple, right now my lines[i] = "1 2 3 44 54 23 24" I am wo

[R] survreg: fitting different location parameters

Hi R-Help! My question: I have lifetime/failure data of machines with different stress levels and i think an weibull/extreme value distribution would fit this data. So I did: model1 <- survreg(Surv(lfailure)~stress,data=steel,dist="extreme") (where lfailure=log(failure)) Now I would

[R] error preparing a package for lazy loading with R CMD

Dear Lister, I work with R 2.0.1 and Windows XP, and meet a strange trouble trying to make a R package with a make-package.bat file John Fox has kindly provided (see detailed script below). I am working with it since some months with excellent results (I do'nt use compiled C code so far). Just

Re: [R] Hardware Suggestions

We've been running servers with AMD Opterons (both duals and 4-ways) using SuSE SLES 8 and Fedora Core 2 and 3 (64 bit). All work well and R can access up to ~15GB of RAM on our 4-way machine (which has 16GB installed). One of the Red Hat Enterprise Linux versions comes with a buggy compiler but

[R] survreg: fitting different location parameters

Hi R-Help! My question: I have lifetime/failure data of machines with different stress levels and i think an weibull/extreme value distribution would fit this data. So I did: model1 <- survreg(Surv(lfailure)~stress,data=steel,dist="extreme") (where lfailure=log(failure)) Now I would like t

[R] comparing glmmPQL models

Dear R users, Is there a way to compare glmmPQL models differing in their fixed-effects structure (similar to the ANOVA approach in lme) ? Thank you very much for your help! Chris. This mail was sent through http://webmail.uni-jen

[R] scan command

I am using the scan command to read a file I called data1. The program returns Error in file(file,"r") : unable to open connection In addition: Warning message: cannot open file 'data1' I already checked to see if the starting directory in R was correct and it is.

[R] survreg: fitting different location parameters

Hi R-Help! My question: I have lifetime/failure data of machines with different stress levels and i think an weibull/extreme value distribution would fit this data. So I did: model1 <- survreg(Surv(lfailure)~stress,data=steel,dist="extreme") (where lfailure=log(failure)) Now I would like t

[R] printing PCA scores

Hey folks, I have an environmental dataset on which I conducted a PCA (prcomp) and I need the scores of this PCA for each site (=each row) to conduct further analyses. Can you please help me with that? Thanks a lot Jérôme Lemaître __ R-help@stat.mat

Re: [R] Plotting with Statistics::R, Perl/R

Peter Dalgaard wrote: d) Use bitmap(). It requires a working Ghostscript install, but is otherwise much more convenient. Newer versions of Ghostscript have some quite decent antialiasing built into some of the png devices. Currently you need a small hack to pass the extra options to Ghostscript --

[R] statistical test improvement of readability (was average disjunction)

Dear all ReadeRs I was finding a quick method to improve test readability adding or constructing (with your help) one or more function that allow what follow. Please consider Trt<-c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5) Block<-c(1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4,1,2,3,4) AD2DAT<-c(1.44,2.32,

[R] Wilcoxon test for mixed design (between-within subjects)

Hallo, is there any extension of the pairwise Wilcoxon test to a dependent samples layout with replicates (or, in other terms, a one-way layout with blocking and replicates)? The Wilcoxon method with matched pairs works for the case of dependent samples with one observation per block, while the M