[R] batch job GLM calculations

Hello I want to batch job the calculation of many GLM-models, extract some values and store them in a file. Almost everything in the script below works (read file, extract values and write them to file) except I fail in indexing the GLM with the modelstructure it should run. Running GLM's

Re: [R] a question of substitute

Dear Prof. Ripley, Thank you for this extensive explanation. It looks like my first solution is similar to (b): creating new variables inside the wrapper (and new data if not missing). This course is only introductory, with simple models, and I do point students to each test separately if they

Re: [R] batch job GLM calculations

as.formula(modelstructure[i]) in the glm function Indermaur Lukas [EMAIL PROTECTED] 01/11/07 7:34 PM Hello I want to batch job the calculation of many GLM-models, extract some values and store them in a file. Almost everything in the script below works (read file, extract values and write

Re: [R] batch job GLM calculations

From ?glm: formula: a symbolic description of the model to be fit. The details of model specification are given below. which could be clearer. It needs to be a object of type 'formula'. I believe as.formula(modelstructure[i]) will do what you want (but your posting has come out

[R] Error in plot.new() : Figure margins too large

Hello, was could be the reason for such an error message??? I'd like to create a window with 10x6 barplot and save it as pdf. I tried: pdf(histogram.pdf,width=7, height=7) windows(cols, rows) par(mfcol = c(rows,cols)) sapply(mat, calcHist) dev.off() Within the method of sapply, I call

Re: [R] Error in plot.new() : Figure margins too large

Antje wrote: Hello, was could be the reason for such an error message??? Generically, that the (per-subplot) figure region is so small that subtracting margins leaves nowhere to plot. Reasons include: Plotting area too small, too many subplots, too many lines of text in margins, too large

Re: [R] Error in plot.new() : Figure margins too large

Hmm, but what can be the solution? Any idea? Or any documentation on that which I could read to find a solution by myself? with the windows statement, I wanted to achive a format which fits for my plots, so that each plot will have a quadratic area. I guess, I did not unstand that much of

Re: [R] Error in plot.new() : Figure margins too large

Antje wrote: Hmm, but what can be the solution? Any idea? Or any documentation on that which I could read to find a solution by myself? with the windows statement, I wanted to achive a format which fits for my plots, so that each plot will have a quadratic area. OK, so what was the

[R] warning in GAM

Hello, I have a problem when doing gam (from gam library; I am using R 2.4.0, windows xp platform) When doing: example(gam) There is this error message (which also happens when using my data) Warning: a final empty element has been omitted the part of the args list of 'list' being

[R] Three horizontal axes OR Two axes on same side?

Dear list: I need to reproduce a plot with three different horizontal axes. I know how to make plot with two different horizontal axes (one above, one below) using axis(): axis(1, ) axis(3, ) However, I don't know how to produce two axes on the same side of the plot. Any pointers

Re: [R] Three horizontal axes OR Two axes on same side?

Rafael Jimenez wrote: Dear list: I need to reproduce a plot with three different horizontal axes. I know how to make plot with two different horizontal axes (one above, one below) using axis(): axis(1, ) axis(3, ) However, I don't know how to produce two axes on the same

[R] [R-pkgs] tm 0.1 uploaded to CRAN

Dear useRs, a first version of tm has just been released on CRAN. tm provides a sophisticated framework for text mining applications within R. It offers functionality for managing text documents, abstracts the process of document manipulation and eases the usage of heterogeneous text formats in

[R] levelplot not adjusting colors

Hi all, I try to make a levelplot from the Trellis graphics package of count data given a certain x and y variable. The problem is that I can adjust the colorkey colors, but the colors of the actual values in the plot will be unchanged if I change the colorkey. e.g. my_lvl_plot -

Re: [R] Three horizontal axes OR Two axes on same side?

However, I don't know how to produce two axes on the same side of the plot. Any pointers or examples? Try manually drawing the axis using lines() or segments() or arrows() and text() or mtext() __ R-help@stat.math.ethz.ch mailing list

[R] gbm with jumps

Hi everybody I'd like to simulate a Generalized Wiener Process with jumps. Any suggestion? Thanks Marcella -- View this message in context: http://www.nabble.com/gbm-with-jumps-tf2959052.html#a8278026 Sent from the R help mailing list archive at Nabble.com.

[R] simpler solution (untested)

?axis says that this function has the logical parameter outer indicating whether the axis should be drawn in the outer plot margin, rather than the standard plot margin. You could try two calls to it with different outer values. __

[R] gbn with jumps

Hi everybody I'd like to simulate a Generalized Wiener Process with jumps. Any suggestion? Thanks Marcella -- View this message in context: http://www.nabble.com/gbn-with-jumps-tf2959051.html#a8278025 Sent from the R help mailing list archive at Nabble.com.

Re: [R] Three horizontal axes OR Two axes on same side?

axis(1, line=-3) I have just come to this solution. However, it seems, I don't understand the meaning of the outer parameter. What is it for? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] warning in GAM

Please update your gam package: this was fixed in 0.98. And the _warning_ (not 'error') message is explained in the NEWS file for R 2.4.0. (It will be an error in R 2.5.0.) On Thu, 11 Jan 2007, Marta Rufino wrote: Hello, I have a problem when doing gam (from gam library; I am using R

Re: [R] zero margin / marginless plots (in lattice?)

Thanks. The xaxs|yaxs='i' works well for the base graphics. Is there an additional parameter in play for lattice graphics? The closest I could gotten is the below which still leaves a bit of a margin: xy-data.frame(x=c(0,1,1,0,0),y=c(0,1,0,0,1))

[R] overdispersion

How can I eliminate the overdispersion for binary data apart the use of the quasibinomial? help me Eva Iannario -- Passa a Infostrada. ADSL e Telefono senza limiti e senza canone Telecom http://click.libero.it/infostrada11gen07

[R] maximum likelihood, 1st and 2nd derivative

Hi guys again, it seems I haven't been doing the maximum likelihood estimation correctly. I quote below, can someone explain to me please what does it mean that the 2nd and 3rd derivatives of the function equals zero and how to compute that in R. We have our initial estimated, subjective

[R] How to use RBF nueral network to predict

Hi all: I'm trying to use RBF neural network for predicting. The package I'm using now is neural. The type of network that I have to use is RBF. But I didn't find predict function in this package. Does anyone have such an experience? Any advice is appreciated! Thank you!

[R] Treatment for Unequal Column Lengths?

Fellow R Users: I have a .csv dataset that I have brought into R via read.table (and also via read.csv). The dataset has columns that are not equal in length. Essentially, this data file has vectors/columns in which I plan to use different analyses on, hence they are unequal in length. Also, the

[R] February Courses: (1) Prof Frank Harrell *** Regression Modeling Strategies in R/Splus, (2) R/Splus Advanced Programming, (3) R/Splus Fundamentals and Programming Techniques

XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce February courses: (1) Regression Modeling Strategies in R/Splus --- by Prof Frank Harrell http://www.xlsolutions-corp.com/Rstats2.htm *** New York,

[R] R graphics with Linux (libpng)

Hello, I'm trying to adapt some R code that works on Windows so that it will work on a Linux machine. The command : png(myFile.png, width=600, height=600) fails claiming that it is impossible to establish a connection with X11. (Error messages are in French, so I'm not pasting them here!)

Re: [R] overdispersion

evaiannario wrote: How can I eliminate the overdispersion for binary data apart the use of the quasibinomial? There is no such thing as overdispersion for binary data. (The variance of a two-point distribution is a known function of the mean.) If what you want to do is include random effects

Re: [R] R graphics with Linux (libpng)

I forgot to mention that bitmap() will do what you want without an X11 connection. b On Jan 11, 2007, at 1:09 PM, Rebecca Tagett wrote: Hello, I'm trying to adapt some R code that works on Windows so that it will work on a Linux machine. The command : png(myFile.png, width=600,

Re: [R] R graphics with Linux (libpng)

Hi Rebecca, png (and also jpeg, for example) require an X11 connection. So, assuming you're working from the command line and that your X11 server is up, you would need to do something like: linux$ export DISPLAY=:0.0 before loading R... and if your linux machine is remote (and you're

Re: [R] R graphics with Linux (libpng)

On Thu, 11 Jan 2007, Rebecca Tagett wrote: Hello, I'm trying to adapt some R code that works on Windows so that it will work on a Linux machine. The command : png(myFile.png, width=600, height=600) fails claiming that it is impossible to establish a connection with X11. (Error messages

Re: [R] Treatment for Unequal Column Lengths?

One of the ways that R (and S-plus) is different from most other stats packages (all that I can think of) is that it forces you to think about your data up front. This is a good thing. It sounds like you really have multiple datasets in one file, it is best to read them into R as separate

[R] Exploratory multivariate analysis of categorical data

This is my first post to R-help. I am doing some research into the text of the New Testament, specifically places where textual variation occurs across manuscripts. (See http://purl.org/tfinney/NTText/book/index.html for details.) New Testament textual critics call places where the text varies

[R] Matching on multiple columns

Am I correct in believing that one cannot match on multiple columns? One can indeed subset on multiple criteria from different variables (or columns) but not from unique combinations thereof. I need to exclude about 1 rows from 108000 rows of data based on several unique combinations of

Re: [R] maximum likelihood, 1st and 2nd derivative

francogrex francogrex at mail.com writes: [SNIP] This maximisation involves a search in five-dimensional parameter space {θ: α1,α2, β1, β2, P} for the vector that maximises the likelihood as evidenced by the first and second derivatives of the function being zero. The likelihood is L(θ) =

Re: [R] Matching on multiple columns

On Thu, 11 Jan 2007, Farrel Buchinsky wrote: Am I correct in believing that one cannot match on multiple columns? One can indeed subset on multiple criteria from different variables (or columns) but not from unique combinations thereof. I need to exclude about 1 rows from 108000 rows of

[R] rank function and NA in 2.3.1

Hi. I am using R 2.3.1 on WIndows XP, and I am having trouble with the rank function in the presence of numerical NA data. I want the NA's all to get the same rank, but they don't. Here is an example from my session: ct_align_rets_f2$liq[6851:6859] [1] 115396 NA 362595 NA 242986

[R] mean on a table

Please suggest areas that I should troubleshoot. This command used to give me an answer and now it gives me an error. mean(no.genot,na.rm=T) Error in tapply(x, by, sum, na.rm = TRUE) : arguments must have same length I tried removing the na.rm=T) mean(no.genot) Error in

Re: [R] mean on a table

Farrel Buchinsky wrote: Please suggest areas that I should troubleshoot. This command used to give me an answer and now it gives me an error. mean(no.genot,na.rm=T) Error in tapply(x, by, sum, na.rm = TRUE) : arguments must have same length I tried removing the na.rm=T)

[R] Making TIFF images with rtiff

Many medical journals and publishers require that images, whether photographs or line art, be submitted as high resolution .TIFF images. One option for R users is to produce an image in one format and to convert it to a .TIFF file using a second software program. My experience has been that this

Re: [R] Making TIFF images with rtiff

From: Inman, Brant A. M.D. [mailto:[EMAIL PROTECTED] Many medical journals and publishers require that images, whether photographs or line art, be submitted as high resolution .TIFF images. One option for R users is to produce an image in one format and to convert it to a .TIFF file using a

Re: [R] mean on a table

Not that I know of. When I get back to the office I will check it out. I certainly do not recall having created one. I wonder if a library I am working with maybe created a mean function. How do I figure out if I have a loose cannon mean function on the run in my system? On 1/11/07, Peter

Re: [R] Making TIFF images with rtiff

Brant, On Jan 11, 2007, at 9:33 PM, Inman, Brant A. M.D. wrote: Many medical journals and publishers require that images, whether photographs or line art, be submitted as high resolution .TIFF images. One option for R users is to produce an image in one format and to convert it to a .TIFF

[R] Linear Optimization

Hi, I am using constrOptim for a linear optimization problem. But it is giving an error that initial value is not feasible, even though the initial value provided is feasible. I am using the following code. --Code fr-function(x){ x1=x[1] x2=x[2] x3=x[3] x4=x[4]

Re: [R] Making TIFF images with rtiff

Kort, Eric wrote: From: Inman, Brant A. M.D. [mailto:[EMAIL PROTECTED] Many medical journals and publishers require that images, whether photographs or line art, be submitted as high resolution .TIFF images. One option for R users is to produce an image in one format and to convert it to

Re: [R] mean on a table

Hi On 11 Jan 2007 at 23:11, Farrel Buchinsky wrote: Date sent: Thu, 11 Jan 2007 23:11:00 -0500 From: Farrel Buchinsky [EMAIL PROTECTED] To: Peter Dalgaard [EMAIL PROTECTED] Copies to: r-help@stat.math.ethz.ch Subject:

Re: [R] rank function and NA in 2.3.1

Hi one workaround could be to change your NA values to some number and do the rank with average, min or max option. x-1:12 x[c(5,10)]-NA rank(x) [1] 1 2 3 4 11 5 6 7 8 12 9 10 rank(x, ties=average) [1] 1 2 3 4 11 5 6 7 8 12 9 10 x[which(is.na(x))]-999 rank(x,