[R] spline for implicit functions

Hello list, is there any R function for generating spline for implicit functions, for example a spline for an two-column data frame where for one value for one variable there maybe several correspondent values for another? Many thanks. Currently I'm using this home-made one: > spline2d <- function

Re: [R] tcltk freezes R

hi, problem solved. it was a problem of the x-server. after installing the xquartz 2.6.3 for snow leopard (i have lion, but there is no such version), logging in and out to make it the default x-server, it worked. cheers, t -- View this message in context: http://r.789695.n4.nabble.com/tcltk-f

Re: [R] Plot map by region using kasc and adehabitat

On 09/21/2011 01:39 AM, Alex Olssen wrote: > Dear R-help, > > I have a raster map which has a measure of profitability of land by > parcel over several regions of geographic aggregation (think of > counties). This data is stored in an ASCII file. If I type > > plot(profit) > > I get a raster map

[R] R crash

Dear users, I have already sent this email last week, but haven't received an answer. So here is my second try. By running the script below, R crashes systematically at the last command, namely dev.off(), on Windows 7, but not on Windows XP. I therefore don't provide a reproducible example an

Re: [R] tcltk freezes R

On Tue, 20 Sep 2011, tm wrote: Hi there, I have the following problem on my macbook air with mac os x lion on it. when any program tries to load the tcltk library the R GUI or R command line freezes. also happens if I just use library(tcltk) changing versions of tcltk and/or R doesn't help. cu

Re: [R] ARIMA - Skipping intermediate lags

On Tue, 20 Sep 2011, leighton155 wrote: Hello, I am a new R user. I am trying to use the arima command, but I have a question on intermediate lags. I want to run in R the equivalent Stata command of ARIMA d.yyy, AR(5) MA(5 7). This would tell the program I am interested in AR lag 5, MA lag 5

[R] Problem with predict and lines in plotting binomial glm

Problems with predict and lines in plotting binomial glm Dear R-helpers I have found quite a lot of tips on how to work with glm through this mailing list, but still have a problem that I can't solve. I have got a data set of which the x-variable is count data and the y-variable is proportional

Re: [R] R crash

On Wed, Sep 21, 2011 at 8:57 AM, Ivan Calandra wrote: > Dear users, > I therefore don't provide a reproducible example and do not really extract > the relevant parts of the script because it has most likely nothing to do > with the script itself. I can do it though if you think it might be > rele

[R] R CMD build and vignettes

Dear R-helpers, www.statistik.lmu.de/~*leisch*/*Sweave*/*Sweave*-Rnews-2003-2.pdf says that R CMD build creates the pdf from a .Rnw file. But when I do R CMD build followed by R CMD check it gives me a warning that there is a vignette without a PDF. My query is : when R CMD build works it create

Re: [R] R crash

Dear Barry, Thanks for your input, that is indeed a very good idea (shame on me not to have thought about it...). As expected, it works fine on Windows XP, but crashes on Windows 7 at dev.off (which means that the svg file is correctly created, but R crashes every time, a bit annoying). This

Re: [R] Problem with predict and lines in plotting binomial glm

Hi Anina, predict.glm returns predicted probabilities, when used with type="response", so you have to either scale the probs to the number of trials for any x or you plot probs from start: par(mfcol=c(1,2)) plot(x, successes) lines(x, (successes+failures)*predict(glm1, type= "response"), lwd=2) pl

[R] Poisson-Gamma computation (parameters and likelihood)

Good afternoon/morning readers. This is the first time I am trying to run some Bayesian computation in R, and am experiencing a few problems. I am working on a Poisson model for cancer rates which has a conjugate Gamma prior. 1) The first question is precisely how I work out the parameters. #Sup

[R] problem with function "Truncate" in package "distr"

Hello all, Can someone tell me why the following mixture of two log-normal distributions does not get truncated? What puzzles me is that the function works almost always, but for certain combinations (like the one below), it does not. # R code example library(distr) mix<-UnivarMixingDistribution(

[R] Cannot allocate vector of size x

Dear all, I am running a simulation in which I randomly generate a series of vectors to test whether they fulfill a certain condition. In most cases, there is no problem. But from time to time, the (randomly) generated vectors are too large for my system and I get the error message: "Cannot alloca

Re: [R] Cannot allocate vector of size x

Check one of the examples in ?try It has this heading: ## run a simulation, keep only the results that worked. If your system is Windows, you can also try to increase the memory available for one application, in order to avoid the problem. Do a search for "3GB switch" HTH Dr. Ruben H. Roa-Ur

Re: [R] Cannot allocate vector of size x

how much memory do you have on your system? How large are the vectors you are creating? How many other large vectors do you have in memory? Remove all unused objects and do gc() to reclaim some of the memory. Remember all objects are in memory and you have to understand how large they are and h

[R] Statmath-R-Forge: Request denied

Dear All, I want to subscribe for Statmath-R-Forge mailing list. But I am getting the following reply and I am unable to subscribe. Any insight on this would be appreciated. Regards Vikram Bahure __ Your request to the Statmath-R-Forge mailing list Subscription request has been re

[R] Strucchange gbreakpoints

Hi, I am a new user to R. I am using strucchange to generate breakpoints: -- > res <- gbreakpoints(GDP.new ~ 1,data=a,h=2,breaks=5) > print(res) Optimal 6-segment partition for `lm' fit: Call: gbreakpoints

Re: [R] R CMD build and vignettes

Hi Ashim, after 'R CMD build' the vignettes are in the *.tar.gz file, not in your package directory. So if you run 'R CMD build ' and then 'R CMD check *.tar.gz', you should not get that warning. For such questions you may get better answers on R-devel; see, eg, this thread here https://

Re: [R] Cannot allocate vector of size x

Yes, on a recent heavy-duty job -profile likelihood of Tweedie power parameter for a relatively complex glm with hundreds of thousands rows dataframe- I had the "cannot allocate vector ..." error, then I just closed-saved the main workspace, full of large objects, then I did the profiling on a f

Re: [R] R CMD build and vignettes

Dear Enrico, Many thanks for your reply.I was doing R CMD check pkg ( where pkg is the directory name and NOT the tar ball ). May I ask another query or should this goto R-devel ? Once I do a R CMD build the vignette PDF's are inside the tar ball ,how will I put the PDF for the vignette in the pk

Re: [R] Strucchange gbreakpoints

On Wed, 21 Sep 2011, Vikram Bahure wrote: Hi, I am a new user to R. I am using strucchange to generate breakpoints: The answer is still the same as last week: https://stat.ethz.ch/pipermail/r-help/2011-September/289944.html -

Re: [R] R crash

On Wed, Sep 21, 2011 at 10:12 AM, Ivan Calandra wrote: > Dear Barry, > > Thanks for your input, that is indeed a very good idea (shame on me not to > have thought about it...). > > As expected, it works fine on Windows XP, but crashes on Windows 7 at > dev.off (which means that the svg file is cor

Re: [R] R CMD build and vignettes

There are various options, and it depends on your work flow and the people that you expect to use the code. If they get a working copy of the directory (with only the Rnw-files*) and then build/install the package, they get the pdfs; so you do not need to add the pdfs. (If they don't build th

Re: [R] R crash

On 11-09-21 5:12 AM, Ivan Calandra wrote: Dear Barry, Thanks for your input, that is indeed a very good idea (shame on me not to have thought about it...). As expected, it works fine on Windows XP, but crashes on Windows 7 at dev.off (which means that the svg file is correctly created, but R cr

Re: [R] R CMD build and vignettes

On Wed, Sep 21, 2011 at 5:15 PM, Enrico Schumann wrote: > > There are various options, and it depends on your work flow and the people > that you expect to use the code. If they get a working copy of the directory > (with only the Rnw-files*) and then build/install the package, they get the > pdfs

Re: [R] R crash

I think Duncan answered it: because there is no svg() in R2.13.1 for Windows. Thank you for your help Ivan Le 9/21/2011 13:40, Barry Rowlingson a écrit : On Wed, Sep 21, 2011 at 10:12 AM, Ivan Calandra wrote: Dear Barry, Thanks for your input, that is indeed a very good idea (shame on me no

Re: [R] R crash

Dear Duncan, Thanks for the info. I'll be waiting for it then. I once tried to contact the maintainer of this package, but never got an answer; so I haven't tried this time. I'll try again. Ivan Le 9/21/2011 13:45, Duncan Murdoch a écrit : On 11-09-21 5:12 AM, Ivan Calandra wrote: Dear Barr

Re: [R] help in interpreting paired t-test

Ted Harding wrote on 09/20/2011 05:26:58 PM: > > Further to the plot suggested below, the plot > > plot(log(A),log(B/A),pch="+",col="blue") > > reveals an interesting structure to the data. Distinct curved > sequences are clearly visible. While their curved form is a > consequence of the fact

Re: [R] Statmath-R-Forge: Request denied

On 09/21/2011 10:11 AM, Vikram Bahure wrote: > Dear All, > > I want to subscribe for Statmath-R-Forge mailing list. But I am getting the > following reply and I am unable to subscribe. > > Any insight on this would be appreciated. > > Regards > Vikram Bahure > > __ > > Your request to the

Re: [R] R-help Digest, Vol 103, Issue 20

Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el. Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu). Üdvözlettel, Mihalicza Péter I will be out of the office from 12 till 26 September with no access to my emails. In urgent cases please contact

[R] Problem with caret + foreach + M5 combination

Hello, I often use the caret package to develop regression models and compare their performance. The foreach package is integrated in caret and can be used to speed up the process through parallel computations. Since caret version 5.01-001, one just need to register the cores with one of the "do"

[R] Reading data in lisp format

Hi, I am trying to read the "credit.lisp" file of the Japanese credit database in UCI repository, but it is in lisp format which I do not know how to read. I have not found how to do that in the foreign library http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening

[R] R help on write.csv

Hi, I wanted to write the data created using R on existing csv file. However everytime I use write.csv, it overwrites the values already there in the existing csv file. Any workaround on this. Thanks for your help Ashish Kumar Estee Advisors Pvt. Ltd. Email: ashish.ku...@esteeadv

Re: [R] Data

On 09/20/2011 10:28 PM, barb wrote: > Hey everybody, > > i am using the rugarch-package and its great! > I have a pretty easy problem, but i just dont get it, so thanks if you can > help me. > > Normally i use: > / > data(DATANAME) > spec = ugarchspec() > fit = ugarchfit(data = x[,1], spec = sp

Re: [R] R help on write.csv

The append argument of write.csv()? Michael On Sep 21, 2011, at 8:01 AM, "Ashish Kumar" wrote: > Hi, > > > > I wanted to write the data created using R on existing csv file. However > everytime I use write.csv, it overwrites the values already there in the > existing csv file. Any workarou

Re: [R] R help on write.csv

I don't think there is an append argument to write.csv() (well, actually there is one, but set to FALSE). There is however one to write.table() Ivan Le 9/21/2011 14:54, R. Michael Weylandt a écrit : The append argument of write.csv()? Michael On Sep 21, 2011, at 8:01 AM, "Ashish Kumar" wr

[R] Making ?source act as if it is run through the terminal

Hello dear R help, The motivation for my question is wanting to run HTMLStart {R2HTML package} from "source". *Background:* I was happy to discover the [ HTMLStart/HTMLStop, HTMLplot] functions in the R2HTML package. They allow my R code to run almost as is, but while writing most of the output

Re: [R] R help on write.csv

You haven't followed the rules of the posting guide. No reproducible code. No OS or R version. I'm guessing you are a newer R user and didn't know this. So please read that guide. It'll help others to help you more quickly. If you're new you may not know about using ?object. So if you ty

Re: [R] Binary optimization problem in R

Michael Haenlein escpeurope.eu> writes: > Dear all, > > I would like to solve a problem similar to a multiple knapsack problem and > am looking for a function in R that can help me. > > Specifically, my situation is as follows: I have a list of n items which I > would like to allocate to m grou

[R] heatmap.2 with colsep and sepwidth

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is th

Re: [R] glmnet for Binary trait analysis

The man page tells you that y must be a factor. Is it? -- Bert On Tue, Sep 20, 2011 at 5:25 PM, Noah wrote: > Hello, > > I got an error message saying > > Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, : > NA/NaN/Inf in foreign function call (arg 5) > > when I try to an

Re: [R] R help on write.csv

Touche -- perhaps we could make one though? write.csv.append <- function(..., append = TRUE) { Call <- match.call(expand.dots = TRUE) for (argname in c("col.names", "sep", "dec", "qmethod")) if (!is.null(Call[[argname]])) warning(gettextf("attempt to set '%s' ignored", argname),

Re: [R] Poisson-Gamma computation (parameters and likelihood)

Hi Sebatiano, Take a look at > require(MCMCpack) > ?MCpoissongamma HTH, Jorge On Wed, Sep 21, 2011 at 5:25 AM, Sebastiano Putoto <> wrote: > Good afternoon/morning readers. This is the first time I am trying to run > some Bayesian computation in R, and am experiencing a few problems. > > I am

[R] Row percentage labels within mosaic graph

Hi, I have the following sample data x <- c(1,2,1,1,2,3,1,2,3,2,3,1,2,2,1,3,2,3,1,3) y <- c(1,2,1,2,2,2,1,2,1,1,1,1,2,2,1,2,2,1,2,1) w <- c(1, 1, 1.5, 1, 1.2, 0.8, 0.9, 1.7, 1, 1.3, 1, 1, 0.7, 0.8, 1.4, 1.3, 1, 1, 0.9, 0.7) d1 <- data.frame(x,y,w) and I wish to build a x,y mosaic graphs that

Re: [R] adding labels to x,y points

A sample data would help. But you could modify as text(x,y, label = row.names(colon[1:20,])) HTH Weidong Gu On Tue, Sep 20, 2011 at 7:43 PM, baumeist wrote: > Hi, > I am new to R. > > I have a matrix that I have assigned to the object “colon”. > >> colon<-read.table("c:\\alon.txt",header=T,ro

Re: [R] Reading data in lisp format

Em 21/9/2011 07:39, ESTEBAN ALFARO CORTES escreveu: Hi, I am trying to read the "credit.lisp" file of the Japanese credit database in UCI repository, but it is in lisp format which I do not know how to read. I have not found how to do that in the foreign library http://archive.ics.uci.edu

Re: [R] glmnet for Binary trait analysis

... another possibiity, probably more likely since you read your files in from disk, is that there is a stray character of some sort (e.g. extra comma, quotation mark, period) in your data that is causing what should be numeric data to be read in as character. Check your data after you've read them

Re: [R] Package dependency

On 21.09.2011 06:20, Tyler Rinker wrote: Greetings R community, I am making my first package and have run into the need to use other packages. I pass all the checks in the command prompt running Rcmd check package.name. In the Description file I have included: Depends: R (>= 2.13), plot

Re: [R] problem with function "Truncate" in package "distr"

On 21.09.2011 11:53, Duarte Viana wrote: Hello all, Can someone tell me why the following mixture of two log-normal distributions does not get truncated? What puzzles me is that the function works almost always, but for certain combinations (like the one below), it does not. # R code example

[R] chippeakanno package: "getAllPeakSequence" problem

Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: > peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100, > downstream = 100, genome = Hsapiens)

Re: [R] Reading data in lisp format

If you think that R is loosely typed, then examining LiSP code will change your mind, or at least give you a new data point further out on the "Loose-Tight" axis. I think you will need to do the processing "by hand". The organization of the data is fairly clear. There are logical colum

Re: [R] R help on write.csv

Michael, You example doesn't seem to work. Append isn't passed on to the write.table call. You will need to add a Call$append<- append to the function. And even then there will be a problem with the headers that are repeated when appending. An easier solution is to use write.table dir

Re: [R] chippeakanno package: "getAllPeakSequence" problem

On 21.09.2011 17:08, Nico902 wrote: Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: peaksWithSequences<- getAllPeakSequence(peakList, upstream = 100,

Re: [R] adding labels to x,y points

#This should work (again, without your data ??) colon<-read.table("c:\\alon.txt",header=T,row.names=1) row.names(colon) <-paste("g",c(1:nrow(colon)),sep="") with(colon[1:20,], plot(norm1, norm2, type='n',xlab='x norm1 sample',ylab='y norm2 sample',main='Norm1 vs Norm2 - 20 genes')) with(co

Re: [R] chippeakanno package: "getAllPeakSequence" problem

On 09/21/2011 08:08 AM, Nico902 wrote: Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: peaksWithSequences<- getAllPeakSequence(peakList, upstream = 100,

Re: [R] chippeakanno package: "getAllPeakSequence" problem

On Sep 21, 2011, at 11:08 AM, Nico902 wrote: Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: peaksWithSequences <- getAllPeakSequence(peakList, u

Re: [R] R help on write.csv

Michael, You example doesn't seem to work. Append isn't passed on to the write.table call. You will need to add a Call$append<- append to the function. And even then there will be a problem with the headers that are repeated when appending. An easier solution is to use write.table dire

Re: [R] R help on write.csv

Michael, You example doesn't seem to work. Append isn't passed on to the write.table call. You will need to add a Call$append<- append to the function. And even then there will be a problem with the headers that are repeated when appending. An easier solution is to use write.table dire

[R] Power calculation for survival analysis

useR's, I am trying to do a power calculation for a survival analysis using a logrank test and I need some help properly doing this in R. Here is the information that I know: - I have 2 groups, namely HG and LG - Retrospective analysis with subjects gathered from archival data over 20 years. No ne

[R] logistic regression: default computed probability

Hello all, Suppose in a logistic regression model, the binary outcome is coded as 0 or 1. In SAS, the default probability computed is for Y = 0 (smaller of the two values) . However, in SPSS the probability computed is for Y = 1 (greater of the two values). Which one does R compute, the probabili

Re: [R] logistic regression: default computed probability

On Sep 21, 2011, at 10:25 AM, n wrote: > Hello all, > > Suppose in a logistic regression model, the binary outcome is coded as > 0 or 1. > In SAS, the default probability computed is for Y = 0 (smaller of the > two values) . However, in SPSS the probability computed is for Y = 1 > (greater of the

Re: [R] help in interpreting paired t-test

It looks like Bland-Altman procedures would be appropriate for this project (http://en.wikipedia.org/wiki/Bland-Altman_plot). -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Pedro Mardones Sent: Tuesday, September 20, 2011 11:47

Re: [R] help in interpreting paired t-test

> cor(A, B) [1] 0.9986861 The data are very, very highly correlated. The higher the correlation, the greater the power of the t-test to detect the same difference between the means. Jeremy On 20 September 2011 10:46, Pedro Mardones wrote: > Dear all; > > A very basic question. I have the follow

Re: [R] Specifying Start/End Dates for X-axis Range in plot()/xyplot()

On Tue, 20 Sep 2011, David Winsemius wrote: It seems likely even if you got past that error, you would encounter problems from the hashed up syntax in this portion of that plot call: z[, $'Burns Mg'] David, Yes, that's not close to correct. If I specify plot(z[, "Burns Mg"]) #

Re: [R] tcltk freezes R

was all prebuilt. -- View this message in context: http://r.789695.n4.nabble.com/tcltk-freezes-R-tp3828263p3830663.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/

Re: [R] help in interpreting paired t-test

Jeremy, Correlation alone is irrelevant when comparing two separate sets of measurements on the same specimen. Correlation does not mean good agreement, but good agreement tends to infer high correlation. T1 <- rnorm(50, mean = 100) > mean(T1) [1] 99.80257 T2 <- T1 * 1.5 > mean(T2) [1] 149.7

Re: [R] Power calculation for survival analysis

On Sep 21, 2011, at 8:54 AM, Duke wrote: > useR's, > I am trying to do a power calculation for a survival analysis using a > logrank test and I need some help properly doing this in R. Here is the > information that I know: > - I have 2 groups, namely HG and LG > - Retrospective analysis with sub

Re: [R] Power calculation for survival analysis

Thanks for your response, Marc. HG and LG are high-grade/low-grade tumors. The data has not been collected yet, but will be soon. It's all archived data that will be pulled from computer records. The IRB wants some mention of power or sample size, but doing it for this scenario has been a bit o

Re: [R] Making ?source act as if it is run through the terminal

Maybe some of the source() options will work. Suppose you have the following in an R file: junk.R 1:5 x = 1:10 library(ggplot2) data(VADeaths) pl <- ggplot(melt(VADeaths),aes(value, X1))+ geom_point() + facet_wrap(~X2)+ylab("") pl Then from the command line: > source("junk.R") ## No o

Re: [R] glmnet for Binary trait analysis

Hi Bert, You are correct. I checked the data and did find some empty values in the X matrix. Thanks for your kindly help! Noah -- View this message in context: http://r.789695.n4.nabble.com/glmnet-for-Binary-trait-analysis-tp3828547p3830581.html Sent from the R help mailing list archive at Na

Re: [R] help in interpreting paired t-test

Thanks for all the replies and comments. I've followed Marc's suggestion of using the Bland-Altman's approach which I found pretty clarifying for comparing data collected on the same subjects. BR, PM On Wed, Sep 21, 2011 at 1:39 PM, Marc Schwartz wrote: > Jeremy, > > Correlation alone is irrelev

Re: [R] help with installing tar.gz package

Yay! Thanks! I installed it too! Now the question would be how to use it -- View this message in context: http://r.789695.n4.nabble.com/help-with-installing-tar-gz-package-tp3791086p3830836.html Sent from the R help mailing list archive at Nabble.com.

[R] Weighted Average on More than One Variable in Data Frame

Dear R Users, I have looked for a solution to the following problem and I have not been able to find it on the archive, through Google or in the R documentation. I have a data frame, say df, which has 4 variables, one of which I would like to use as a grouping variable (g), another one that I woul

Re: [R] package / function for monitoring processes?

Here is the function I use: my.stats <- function (text = "stats", reset = FALSE, oper = "") { procTime <- proc.time()[1:3] if (reset) { Level <<- 1 Stack[Level, ] <<- c(procTime[3], procTime[1] + procTime[2]) } if (oper == "push") { if (Level < MaxLevel)

Re: [R] R help on write.csv

Oh darn, I had that line and then when I copied it to gmail I thought I'd be all slick and clean up my code: oh well...just not my day/thread... It's possible to work around the repeated headers business (change to something like "Call$col.names <- !append") but yeah, at this point I'm thinking it

[R] Quelplot

Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307–320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Hadley -- Assistant Professor / Dobelman Family Junior Chai

Re: [R] Power calculation for survival analysis

On Sep 21, 2011, at 12:37 PM, Duke wrote: > Thanks for your response, Marc. HG and LG are high-grade/low-grade tumors. > The data has not been collected yet, but will be soon. It's all archived > data that will be pulled from computer records. The IRB wants some mention > of power or sample s

Re: [R] Weighted Average on More than One Variable in Data Frame

Try this sapply(split(df, df$g), function(x) apply(x[, 1:2], 2, weighted.mean, x$w)) Jean StellathePug wrote on 09/21/2011 01:15:33 PM: > > Dear R Users, > I have looked for a solution to the following problem and I have not been > able to find it on the archive, through Google or in the R

[R] Limitations of audio processing in R

Hello everybody I am trying to process audio files in R and had some problems with files size. I´m using R packages 'audio' and 'sound'. I´m trying a really simple thing and it is working well with small sized .wav files. When I try to open huge audio files I received this error message: "cannot a

Re: [R] Limitations of audio processing in R

If you are running Windows it may be as simple as using memory.limit() to allow R more memory -- if you are on another OS, it may be possible to get the needed memory by deleting various things in your workspace and running gc() Of course, if your computer's memory is <3GB, you are probably going

[R] Problem indexing a factor variable

Hi, I have a dataframe "gexp_1" with 115 rows of samples and 27000 columns of gene expression measurements with each column corresponding to one gene. I now have a smaller vector of genes "tp" for which I need to pull out the data form the data frame. # first gene from the list with 16 genes

Re: [R] Problem indexing a factor variable

Your problem is a fairly common one and it has to do with how factors are stored internally in R. They look like "geneA","geneB", etc to you, but to R (for many things) they are kept as integers 1,2,3. It should suffice to set x <- as.character(tp[1,]) which forces x to be the string "geneA" and

Re: [R] Specifying Start/End Dates for X-axis Range in plot()/xyplot() [RESOLVED]

On Wed, 21 Sep 2011, Rich Shepard wrote: Is there documentation I can read that will teach me the proper syntax? Or, can you show me how to specify those dates when plotting z elements? Got it: extract the window for the times of interest, then plot that window. Rich _

Re: [R] Limitations of audio processing in R

Hi Ulisses! Yes, "get more creative" -- or "get more memory"! On the "creative" side, it may be worth thinking about using an independent (non-R) audio file editor. I'm writing from the standpoint of a Linux/Unixoid user here -- I wouldn;t know how to set ebout this in WIndows. You could use R to

Re: [R] Limitations of audio processing in R

Also with Linux you can add more swap memory(which I'm pretty sure R spills into if it hasn't reached it's internal limits on 32 bit installations). Windows pagefile is kind of obnoxious. Ken Hutchison On Sep 21, 2554 BE, at 5:05 PM, (Ted Harding) wrote: > Hi Ulisses! > Yes, "get more cre

[R] raster plot is empty

Dear R-help, I have a problem plotting maps using the raster package when I use R on my workplace server, but not when I use my own desktop. I suspect the server version must be missing something and was wondering if anyone would have any ideas. The problem occurs after library(raster) f <- sys

Re: [R] raster plot is empty

Alex, We definitely need the output of sessionInfo(), the version of raster, and a reproducible example. Without knowing the versions & OS, it's impossible to say. But my first guess (and it IS a guess) is that the server needs to be updated. Sarah On Wed, Sep 21, 2011 at 5:45 PM, Alex Olssen

Re: [R] Limitations of audio processing in R

A more general question: What tools are available in R for reading parts of binary files? 'scan' allows you to 'skip' a certain number of records and read the next 'nlines'. Unfortunately, scan only seems to work for text files not binary, and I cannot find a comparable function that would w

Re: [R] Limitations of audio processing in R

Once again, I would myself be inclined to farm this out (in Linux) to the tools which come with the system. In this case the command "dd" is useful (though one may need to be careful about setting the options. For instance, dd -bs=1 skip=54321 count=31415 if=infile of=outfile would (having set

Re: [R] raster plot is empty

Dear Sarah, I am not sure how to make a reproducible example. The 3 lines of code are exactly what I type in either system. The code can be reproduced, but the result is unlikely to be reproduced - for example on my desktop this all works fine. Is there something more I can do to make this repr

Re: [R] Limitations of audio processing in R

Dear Ted, Thank you very much about your answer, it really helped. Now I am working on the function that will do all the job with sox help. All the best, Ulisses 2011/9/21 Ted Harding > Hi Ulisses! > Yes, "get more creative" -- or "get more memory"! > > On the "creative" side, it may be worth th

Re: [R] Weighted Average on More than One Variable in Data Frame

Thanks Jean, that worked perfectly! Try this sapply(split(df, df$g), function(x) apply(x[, 1:2], 2, weighted.mean, x$w)) Jean StellathePug wrote on 09/21/2011 01:15:33 PM: > > I have a data frame, say df, which has 4 variables, one of which I would > like to use as a grouping variable (g), an

Re: [R] raster plot is empty

Hi, On Wed, Sep 21, 2011 at 6:31 PM, Alex Olssen wrote: > Dear Sarah, > > I am not sure how to make a reproducible example.  The 3 lines of code > are exactly what I type in either system.  The code can be reproduced, > but the result is unlikely to be reproduced - for example on my > desktop thi

Re: [R] raster plot is empty

Please ensure that it is really the exact same code, I'm sure you did not mean to plot "f", but "r" (for example). Also, sessionInfo results are helpful always - see the posting guide for ways to post better questions. > library(raster) Loading required package: sp raster version 1.9-5 (28-July-2

Re: [R] Limitations of audio processing in R

On Thu, Sep 22, 2011 at 8:08 AM, Spencer Graves wrote: > A more general question:  What tools are available in R for reading parts of > binary files?  'scan' allows you to 'skip' a certain number of records and > read the next 'nlines'.  Unfortunately, scan only seems to work for text > files not

Re: [R] raster plot is empty

Yes, Mike you are correct. In fact I did use plot(r) The code is exactly the same in both cases - the axis labels have the same numbers, same with the legend - there is just no picture. sessionInfo() for my desktop - where the code works R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/

Re: [R] raster plot is empty

Adding $0.01 to this: Maybe comparing outputs of capabilities() gives some clues. /Henrik On Wed, Sep 21, 2011 at 6:00 PM, Alex Olssen wrote: > Yes, Mike you are correct. > > In fact I did use > > plot(r) > > The code is exactly the same in both cases - the axis labels have the > same numbers,

Re: [R] raster plot is empty

Unfortunately the capabilities are identical too. For both systems I get jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUEFALSE

[R] Numbering entries for each subject

Hi R Users I am hoping someone might be able to give some pointers on alternative code to the for loop described below. I have a dataset which is ordered by subject ID and date, what I would like to do is create a new variable that numbers the entries for each person (e.g. 1,2,3,) As an e

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