[R] [R-pkgs] Version 0.7 of package tsDyn, nonlinear time series

Hi Version 0.7 of package tsDyn presented at useR! 2009 is now on CRAN, extended with several new features. The package tsDyn is aimed at estimating nonlinear time series models which exhibit regime specific properties. The regime switching dynamics can either be described by smooth transit

[R] ROC curve using epicalc (after logistic regression) (re-sent)

Dear R-help, I am resending as I believe I screwed up the e-mail address to R-help earlier. Sorry for my lack of attention to detail, and for any inconvenience. I have also sent the question to the package maintainer, as suggested in the posting guide. Regards, Cliff -- Forwarded me

[R] smoothScatter problems

Hello, I'm having some trouble getting a good result for a smoothScatter plot. I have some data that I want to log-plot, but when I use smoothScatter the result is not correct. The problem seems to be that with the log="x" argument smoothScatter calculates the bins linearly, so the plot will be s

Re: [R] running a .r script and saving the output to a file

Check out: http://akastrin.wordpress.com/category/r/ David Riebel wrote: Hello, I am running R under Ubuntu 8.04. I am trying to do numerous linear fits to various subsets of my data set. I am having trouble convincing R to send the output from these fits to text files from within a script. W

Re: [R] Superstring in text()

Sorry, there should be a caret symbol (^) between "R" and "2". Murray Pung wrote: I'd like to paste a superstring with a number in an object. Thanks for any help. Murray mycor <- cor(1:10,1:10) plot(1:10,1:10) text(8,2,paste(expression(R^2)," = ",mycor)) [[alternative HTML version d

Re: [R] Superstring in text()

mycor <- cor(1:10,1:10) plot(1:10,1:10) text(8,2,bquote(R^2 == .(mycor))) HTH, Andrej Murray Pung wrote: I'd like to paste a superstring with a number in an object. Thanks for any help. Murray mycor <- cor(1:10,1:10) plot(1:10,1:10) text(8,2,paste(expression(R^2)," = ",mycor)) [[alt

[R] Writing to a UDP server from R?

Hello, I have used socketConnection to connect to a TCP server. I havent figured out a way to do the same with a UDP server. i.e I have a server listening on 9000, communicating via UDP. I would like to , from R, send packets to this server, This does not work u <- socketConnection('localhost',9

Re: [R] how to use do.call together with cbind and get inside a function

Use lapply(ColNameVec, get, environment()) so that it gets the objects from the current environment. See: ?get ?environment On Sun, Jul 26, 2009 at 11:16 PM, Sean Zhang wrote: > Dear R-helpers: > I have a question related to using do.call to call cbind and get. > > #the following works > vec1 <- c

[R] Superstring in text()

I'd like to paste a superstring with a number in an object. Thanks for any help. Murray mycor <- cor(1:10,1:10) plot(1:10,1:10) text(8,2,paste(expression(R^2)," = ",mycor)) [[alternative HTML version deleted]] __ R-help@r-project.org mailing

[R] Disable summary statistics in LaTeX tables using MEMISC package

Dear All, The "mtable" function in "memisc" package is very useful in producing publication quality tables directly from estimated models. There are cases where only the estimated coefficients and standard errors are needed in the table but not the summary staitstics such as N, value of the likeli

Re: [R] Specify CRAN repository from command line

On 27 July 2009 at 14:55, Aaron Hicks wrote: | It feels like I should be able to do something like: | | R CMD INSTALL lib='/usr/lib64/R/library' repos='http://proxy.url/cran' package Here's what I do using littler, you can substitute Rscript as well: #!/usr/bin/env r # # a simple ex

[R] how to use do.call together with cbind and get inside a function

Dear R-helpers: I have a question related to using do.call to call cbind and get. #the following works vec1 <- c(1,2) vec2 <- c(3,4) ColNameVec <- c('vec1','vec2') mat <- do.call("cbind",lapply(ColNameVec,get)) mat #put code above into a function then it does not work #before doing so, first remo

[R] Specify CRAN repository from command line

Hi, It feels like I should be able to do something like: R CMD INSTALL lib='/usr/lib64/R/library' repos='http://proxy.url/cran' package We have a bunch of servers (compute nodes in a Rocks cluster) in an isolated subnet, there is a basic pass-through proxy set up on the firewall (the head node

Re: [R] normal mixture model

Hi, Christian, Thank you for the reply. I just tried. Does the function mclustBIC only give the best model, or does it also do EM to get the cluster means and variances according to the best model it picks? I didn't find it. Is there a way to automatically select the best number of components and

Re: [R] running a .r script and saving the output to a file

You have to explicitly 'print' the output. At the command line there is an implicit 'print'. Try: sink(file="x_seq2_fit.dat") print(summary(x_seq2_fit)) sink() sink(file="x_seq1_fit.dat") print(summary(x_seq1_fit)) sink() On Sun, Jul 26, 2009 at 4:47 PM, David Riebel wrote: > Hello, > > I am ru

Re: [R] normal mixture model

You can use mclustBIC in package mclust (uses the BIC for deciding about the number of components and hierarchical clustering for initialisation). Christian On Sun, 26 Jul 2009, cindy Guo wrote: Hi, All, I want to fit a normal mixture model. Which package in R is best for this? I was using

[R] normal mixture model

Hi, All, I want to fit a normal mixture model. Which package in R is best for this? I was using the package 'mixdist', but I need to group the data into groups before fitting model, and different groupings seem to lead to different results. What other package can I use which is stable? And are the

Re: [R] running a .r script and saving the output to a file

Hi Dave, I don't know about using sink(), but if you run your script in batch mode all the output will be saved to a text file foryou. R CMD BATCH infile outfile (at the linux prompt, not from within R). Sarah On Sun, Jul 26, 2009 at 4:47 PM, David Riebel wrote: > Hello, > > I am running R und

Re: [R] splitting multiple data in one column into multiple rows with one entry per column

Try this: > x <- read.table(textConnection("snp ensembl_gene_id + rs8032583 + rs1071600 ENSG0101605 + rs13406898 ENSG0167165 + rs7030479 ENSG0107249 + rs1244414

[R] ROC curve using epicalc (after logistic regression)

Dear R-help list, I'm attempting to use the ROC routine from the epicalc package after performing a logistic regression analysis. My code is included after the sessionInfo() result. The datafile (GasketMelt1.csv) is attached. I updated both R and the epicalc packages and tried again before send

Re: [R] running a .r script and saving the output to a file

Hello, I am running R under Ubuntu 8.04. I am trying to do numerous linear fits to various subsets of my data set. I am having trouble convincing R to send the output from these fits to text files from within a script. When I run my script, all the plots are created as postscript files in the co

[R] Question about rpart decision trees (being used to predict customer churn)

Hi, I am using rpart decision trees to analyze customer churn. I am finding that the decision trees created are not effective because they are not able to recognize factors that influence churn. I have created an example situation below. What do I need to do to for rpart to build a tree with the v

Re: [R] labelling points plotted in a 2D plan

Hello Tal! Nothing showed up when I used those commands! The plot still shows dots with no labels! Thanks On Sun, Jul 26, 2009 at 7:28 AM, Tal Galili wrote: > Hi Khaled, > Did my answer help ? > > > > > On Sun, Jul 26, 2009 at 12:15 AM, Khaled OUANES wrote: > >> Thanks for the answer Tal! >>

Re: [R] moving text labels in plot

Luis Iván Ortiz Valencia wrote: > > Hi R users > > I need to specify some parameter input in plot code to move Y text label > to > left. > > plot(temp, develo_rate, xlab = expression(paste("Temperature (C"^o,")")), > ylab = expression(paste("Development rate (d"^-1,")")),las=1,pch=19, >

[R] mixdist package in R

Hi, All, I fitted a 3-component normal mixture model with the mixdist package in R. How can I get the density of a new data after I fit the model? Is there any function to do it? Thanks, Cindy [[alternative HTML version deleted]] __ R-help@r-

[R] splitting multiple data in one column into multiple rows with one entry per column

Dear R colleagues, I annotated a list of single nuclotide polymorphiosms (SNP) with the corresponding genes using biomaRt. The result is the following data.frame (pasted from R): snp ensembl_gene_id 1 rs8032583 2 rs1071600

Re: [R] obtain names of variables and data from glm object

Try this: g <- glm(demand ~ Time, BOD, family = gaussian) all.vars(formula(g)) The result will be a character vector whose 1st component is the name of the response and whose subsequent components are the names of the predictor variables. On Sun, Jul 26, 2009 at 3:14 PM, Jacob Wegelin wrote: > S

[R] obtain names of variables and data from glm object

Suppose we have some glm object such as: myglm <- glm( y ~ x, data=DAT) Is there an elegant way--or the "right way" within the R way of thinking--to obtain the names of the response variable, the predictor variables, and the dataset, as character strings? For instance, suppose the "right way" wa

Re: [R] Determine the dimension-names of an element in an array in R

Sauvik De schrieb: > Hi: > Lots of thanks for your valuable time! > > But I am not sure how you would like to use the function in this > situation. > > As I had mentioned that the first element of my output array should be > like: > > cor(DataArray_1[dimnames(Correl)[[1]][1],dimnames(Correl)[[2]][1

Re: [R] moving text labels in plot

Try this: par(mar=c(4,6,2,1)) plot(0, xlab = expression(paste("Temperature (C"^o,")")), ylab = "" ,las=1,pch=19, xlim=c(0,32),ylim=c(0,0.03),xaxs = "i", yaxs = "i") mtext(expression(paste("Development rate (d"^-1,")")), 2, line=4) 2009/7/26 Luis Iván Ortiz Valencia : > Hi R users > > I need

Re: [R] problems hist() and density

"sums to one" I should have said. On Sun, Jul 26, 2009 at 7:43 AM, Jan Teichmann wrote: > Hello, > > I have a problem with the hist() function and showing densities. The > densities sum to 50 and not to 1! I use R version 2.9.1 (2009-06-26) and > I load the seqinR library. > > My data is the foll

Re: [R] problems hist() and density

It is the 'area' under the curve that sums to zero. Look at what the difference is between the 'breaks' (0.02). multiply this by 50 and you get 1. On Sun, Jul 26, 2009 at 7:43 AM, Jan Teichmann wrote: > Hello, > > I have a problem with the hist() function and showing densities. The > densities s

[R] smoothScatter problems

Hello, I'm having some trouble getting a good result for a smoothScatter plot. I have some data that I want to log-plot, but when I use smoothScatter the result is not correct. The problem seems to be that with the log="x" argument smoothScatter calculates the bins linearly, so the plot will be sk

[R] problems hist() and density

Hello, I have a problem with the hist() function and showing densities. The densities sum to 50 and not to 1! I use R version 2.9.1 (2009-06-26) and I load the seqinR library. My data is the following vector: [1] 0.140 0.200 0.220 0.2828283 0.160 0.160 0.360 [8] 0.160

[R] Non-Linear Regression with two Predictors

Hello there, I am using nls the first time for a non-linear regression with a logistic growth function: startparam <- c(alpha=3e+07,beta=4000,gamma=2) fit <- nls(dataset$V2~(( alpha / ( 1 + exp( beta - gamma * dataset$V1 ) ) ) ),data=dataset,start=startparam) Everything works fine and i get

[R] moving text labels in plot

Hi R users I need to specify some parameter input in plot code to move Y text label to left. plot(temp, develo_rate, xlab = expression(paste("Temperature (C"^o,")")), ylab = expression(paste("Development rate (d"^-1,")")),las=1,pch=19, xlim=c(0,32),ylim=c(0,0.03),xaxs = "i", yaxs = "i")

Re: [R] suggestion for paired t-tests

jacktanner wrote: > > There's a funny inconsistency in how t.test handles paired=T or paired=F. > If x > and y parameters are lists, paired=F works, but paired=T doesn't. > >> lg=read.csv("my.csv") >> a = subset(lg, condition=="a")["score"] >> b = subset(lg, condition=="b")["score"] >> t.test(

Re: [R] Collinearity in Linear Multiple Regression

Stephan Kolassa wrote: Hi Alex, I personally have had more success with the (more complicated) collinearity diagnostics proposed by Belsley, Kuh & Welsch in their book "Regression Diagnostics" than with Variance Inflation Factors. See also: Belsley, D. A. A Guide to using the collinearity di

Re: [R] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?

I will send you offline an enhancement for read.xls that accepts ftp connections. On Sun, Jul 26, 2009 at 11:32 AM, wrote: > It works if the web file adress is of the type:  "http://";. > It does not work if the web file adress is of the type:  "'ftp://";. >> outFile <- >> read.xls("ftp://ftp.sa

[R] R: R: Is there a way to extract some fields data fromHTML pages through any R function ?

It works if the web file adress is of the type: "http://";. It does not work if the web file adress is of the type: "'ftp://";. > outFile <- > read.xls("ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/miRNA.xls";) Error in xls2csv(xls, sheet, verbose = verbose, ..., perl = perl) : Unable

Re: [R] How to add 95% confidence intervals in the calibration plot?

zhu yao wrote: Thanks for your reply. Actually, I'm confused about the results in the article "Postoperative nomogram for survival of patients with retroperitoneal sarcoma treated with curative intent" http://annonc.oxfordjournals.org/cgi/content/abstract/mdp298v1 It stated as: nomogram mod

Re: [R] How to add 95% confidence intervals in the calibration plot?

Thanks for your reply. Actually, I'm confused about the results in the article "Postoperative nomogram for survival of patients with retroperitoneal sarcoma treated with curative intent" http://annonc.oxfordjournals.org/cgi/content/abstract/mdp298v1 It stated as: nomogram model The Cox model was

Re: [R] How to add 95% confidence intervals in the calibration plot?

zhu yao wrote: Dear experts: I am a newbie to R. Recently, I try to make prediction models with R and the Design library. I have read Prof. Harrell's excellent book. But I did not quite understand. I have two problems about the validation and calibration of prediction models: 1. Can someone expl

Re: [R] Determine the dimension-names of an element in an array in R

Hi: Lots of thanks for your valuable time! But I am not sure how you would like to use the function in this situation. As I had mentioned that the first element of my output array should be like: cor(DataArray_1[dimnames(Correl)[[1]][1],dimnames(Correl)[[2]][1],dimnames(Correl)[[4]][1],],DataArr

[R] Is there an R implementation for the "Barnard's exact test" (a substitute for fisher.test) ?

Hello R help members. I came across today with an article on Barnard's exact test (http://www.cytel.com/Papers/twobinomials.pdf), that is supposed to give a more powerful fisher.test - Because it doesn't assume that we know the row and column totals are in advance. Any pointers to such a function ?

Re: [R] zoo plot: yearly marks on X-Axis

stvienna wiener schrieb: > Hi all, > > I am plotting a financial time series, but I need a more detailed X-Axis. > > Example: > x <- zoo(rnorm(1:6000), as.Date("1992-11-11")+c(1:6000)) > plot(x) > > The X-Axis is labeled "1995", "2000" and "2005". > I would need either "1995", "1997", etc. or maybe

Re: [R] Determine the dimension-names of an element in an array in R

Sauvik De schrieb: > Hi Gabor: > Many thanks for your prompt reply! > The code is fine. But I need it in more general form as I had mentioned that > I need to input any 0 to find its dimension-names. > > Actually, I was using "sapply" to calculate correlation and this idea was > required in the mid

Re: [R] Sweave, cacheSweave, and data frame

Shige Song wrote: Dear All, I have been using Sweave (mainly via the Sweave.sh script) and really like it. I am working a paper (using Sweave, of course) which includes several time-consuming computations, and it gets tedious to re-compile the whoel thing every time I made changes. Then I discov

Re: [R] Sweave, cacheSweave, and data frame

Shige Song wrote: > > I have been using Sweave (mainly via the Sweave.sh script) and really like > it. I am working a paper (using Sweave, of course) which includes several > > To check what's wrong, please post a reproducible minimal example. It is difficult to guess if this has to do w

Re: [R] Determine the dimension-names of an element in an array in R

Hi Gabor: Many thanks for your prompt reply! The code is fine. But I need it in more general form as I had mentioned that I need to input any 0 to find its dimension-names. Actually, I was using "sapply" to calculate correlation and this idea was required in the middle of correlation calculation.

Re: [R] Sweave, cacheSweave, and data frame

Right. Its to avoid making the vignettes when you are mainly interested in testing out a package. On Sun, Jul 26, 2009 at 3:07 AM, Shige Song wrote: > Dear Gabor, > > Thanks for the suggestion. I am writing a research paper using Sweave, not > building a R package. If i understand correctly, the -

Re: [R] Sweave, cacheSweave, and data frame

Dear Gabor, Thanks for the suggestion. I am writing a research paper using Sweave, not building a R package. If i understand correctly, the --no-vignettes option does not really help in my case. Shige On Sun, Jul 26, 2009 at 11:56 AM, Gabor Grothendieck < ggrothendi...@gmail.com> wrote: > Anoth