Re: [R] the observed log odds in logistic regression

Dieter Menne: Thank you for your reply! I know that I don't have to do any logit , but I want to understand how R fit the glm models. I will read the examples your suggested . Best regards, Bin Yue Dieter Menne wrote: Bin Yue leffgh at 163.com writes: After reading the following two

Re: [R] error trying to load biOps under 2.6.1 running XP

On Mon, 10 Dec 2007, Brian O'Gorman wrote: I'm running R 2.6.1 on a WXP machine. When I do the following I get an error message. library(biOps) Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.1/library/biOps/libs/biOps.dll': LoadLibrary failure: The

[R] Decent R code does NOT end lines in ';' !

TK == Talbot Katz [EMAIL PROTECTED] on Mon, 10 Dec 2007 14:16:52 -0500 writes: TK Hi. TK I have a procedure that reads a directory, loops through TK a set of particular .RData files, loading each one, and TK feeding its object(s) into a function, as follows: TK

Re: [R] the observed log odds in logistic regression

Bernardo Rangel Tura wrote: On Mon, 2007-12-10 at 19:42 -0800, Bin Yue wrote: (...) My problem is this : in my data set , the IVs are continuous variables, do I still have to generate such a table and compute the log odds for each level of IV according to which the log odds are

[R] Error with rgl loading in BATCH mode

Dear all, I'm trying to run a script that requires KernSmooth in BATCH mode but I get an error while loading rgl library that is needed by KernSmooth. Actually I have to run several batch files through a queue of a cluster, so I wouldn't need graphics at all. I installed the latest releases of

[R] Odp: help with fatal error message

Hi AFAIK sometimes this can happen if your .Rdata was saved when some packages had been in action. But in that case you should have your message extended with someting like: cannot load package or similar. It helped me when I started plain R session invoked necessary packages and

Re: [R] Error with rgl loading in BATCH mode

I don't think this is anything to do with BATCH mode: the machine you are running R BATCH on does not have GLU installed. rgl *will* load on a system without an X server running. KernSmooth does *not* require the rgl *package*, so you are (twice) blaming an innocent party. You have doctored

Re: [R] Alternative to For Loop?

Hi, It's not just the for loop, you are also growing objects in your code (z). Consider ?cumsum Cheers, Romain -- Mango Solutions data analysis that delivers Tel: +44(0) 1249 467 467 Mob: +44(0) 1249 467 468 Fax: +44(0) 7813 526 123 -Original Message- From: [EMAIL PROTECTED] on

Re: [R] Alternative to For Loop?

Thanks Duncan and Romain! cumsum is exactly what I was looking for! On 12/11/07, Romain Francois [EMAIL PROTECTED] wrote: Hi, It's not just the for loop, you are also growing objects in your code (z). Consider ?cumsum Cheers, Romain -- Mango Solutions data analysis that delivers

Re: [R] Sweave : change value in rnw file to generate multiple single reports ?

Thanks everybody for your help (and sorry to be silent : no network today morning), I think I will first try the solution of Greg Snow-2 or the one of Thierry (because they gave examples of script - as a newbye it is very important to me). I'm also interested in the solutions proposed by Uwe and

Re: [R] editor under MAC system

YIHSU CHEN-3 wrote: Dear R-user; I recently switched from PC to MAC. Is there a compatible editor as Win-editor with package RWinEdit for MAC? I'd recommend using Emacs with ESS (see http://ess.r-project.org/). The advantage of this (beyond the seamless integration) is that its

Re: [R] Barchart, Pareto

--- Kapoor, Bharat [EMAIL PROTECTED] wrote: 1.I could not print the data in ROF column below the bar charts, How to get full labels for each bar insted I createda new coumn ReasonCode just to fit below the bars. You could plot the barchart horizontally, and increase the margins to

[R] Odp: If Else Function

Hi [EMAIL PROTECTED] napsal dne 11.12.2007 13:06:14: Hello everyone, I would like to use the if statements and I was thinking sth like If () {} else{ if() {} else{} } Is this a possible solution and is there any syntax error? Except the first letter, nothing sooms to be wrong.

Re: [R] error trying to load biOps under 2.6.1 running XP

On Dec 11, 2007 5:11 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 10 Dec 2007, Brian O'Gorman wrote: I'm running R 2.6.1 on a WXP machine. When I do the following I get an error message. library(biOps) Error in dyn.load(file, ...) : unable to load shared library

Re: [R] editor under MAC system

Le mar. 11 déc. à 07:03, Neil Shephard a écrit : YIHSU CHEN-3 wrote: Dear R-user; I recently switched from PC to MAC. Is there a compatible editor as Win-editor with package RWinEdit for MAC? I'd recommend using Emacs with ESS (see http://ess.r-project.org/). The advantage of this

[R] creating images from console commands

Hi I have forgotten the name of the function, but I know it exists. I want to be able to export commands enterd / or output in the console to an image. Does anyone recognize the function I am looking for. Thanks Tom -- View this message in context:

[R] Hmisc compilation problem

I upgraded my system to Fedora Core 7 and got a compilation problem when installing Hmisc package. According to the error messages (shown below), I have tried to updated all of my glibc, gcc, automake rpm packages, but that did not help. Could you help me pointed out what package I have missed?

[R] R computing speed

Dear helpers, I am using R version 2.5.1 to estimate a multinomial logit model using my own maximum likelihood function (I work with share data and the default function of R cannot deal with that). However, the computer (I have an Athlon XP 3200+ with 512 GB ram) takes quite a while to estimate

Re: [R] Sweave : change value in rnw file to generate multiple single reports ?

Dear Uwe, Could you please give me the name of the function to open, to modify and to save a r script ? Just the name and I will look for the way to use them. And if you have a link explaining how to use user customized variables from an environment variable, it will be very helpful (as it is

Re: [R] R computing speed

I would suggest that you use Rprof to get a profile of the code to see where time is being spent. You did not provide commented, minimal, self-contained, reproducible code, so it is hard to tell from just looking at the code to determine what is happening. Rprof should provide an idea of where

Re: [R] Hmisc compilation problem

I think you have glibc-headers missing. On an F8 system I get eclectus% rpm -qf /usr/include/limits.h glibc-headers-2.7-2 eclectus% rpm -qf /usr/include/stdio.h glibc-headers-2.7-2 eclectus% rpm -qf /usr/include/stdlib.h glibc-headers-2.7-2 You may find that glibc-devel is also missing and

[R] book on regular expressions

Hello, Could someone recommend a good book on regular expressions with focus on applications/use as it might relate to R. I remember there was a mention of such a reference book recently, but I could not locate that message on the archive. Thanks. -Christos Christos Hatzis, Ph.D. Nuvera

Re: [R] Simulating Case Control Data

On Mon, 10 Dec 2007, R. W. wrote: Dear R-Help-List, I was wondering if anyone had experience simulating case-control data in R? I think the only simple method that allows you to specify any arbitrary population distribution of predictors and does not rely on the logistic regression model

[R] Estimated survival function in Epi package

Does anyone know if the Epi package has a function that returns/plots the survival function for interval censored survival analysis. I haven't found one in the manual that does this explicitly, but I could be missing it. I am writing a paper, and I just coded the survival function myself, but it

Re: [R] function centralm - does it exist

On Mon, 2007-12-10 at 16:41 -0500, Nuno Prista wrote: Hi, James S. Clark - Statistical computation for environmental sciences in R - mentions a function centralm (pg25) that I believe should be present in the base package but I can't find it. It is supposed to calculate means,

Re: [R] R computing speed

Dear Jim, Thanks a lot for your suggestion. Indeed substituting the function apply with rowSums made a great difference. Now the code is much faster! Cheers, Carlo -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of jim holtman Sent: 11 December 2007 15:09

Re: [R] Odp: If Else Function

Hi, I guess it is because I spread the command in different rows. Thank you very much for your help. Petr Pikal wrote: Hi [EMAIL PROTECTED] napsal dne 11.12.2007 13:06:14: Hello everyone, I would like to use the if statements and I was thinking sth like If () {} else{ if() {}

[R] Mono in postscript device

Hi, Plotting a graphic into a postscript device using family=mono returns the following error message: family 'mono' not included in PostScript device Looking at postscriptFonts() however lists the Courier font as availeable mono font. So where is the problem? Thanks guys for your help.

Re: [R] Mono in postscript device

On Tue, 11 Dec 2007, Benjamin Otto wrote: Hi, Plotting a graphic into a postscript device using family=mono returns the following error message: family 'mono' not included in PostScript device Looking at postscriptFonts() however lists the Courier font as availeable mono font. So

Re: [R] book on regular expressions

Could someone recommend a good book on regular expressions with focus on applications/use as it might relate to R. I remember there was a mention of such a reference book recently, but I could not locate that message on the archive. Mastering regular expressions by Jeffrey Friedl

Re: [R] book on regular expressions

On Tue, 11 Dec 2007, Christos Hatzis wrote: CH Hello, CH CH Could someone recommend a good book on regular expressions with focus on CH applications/use as it might relate to R. I remember there was a mention of CH such a reference book recently, but I could not locate that message on

Re: [R] book on regular expressions

Its not a book but there are some references to sites that explain regular expressions in the Links box of the gsubfn home page: http://gsubfn.googlecode.com On Dec 11, 2007 10:46 AM, Christos Hatzis [EMAIL PROTECTED] wrote: Hello, Could someone recommend a good book on regular expressions

Re: [R] Sweave : change value in rnw file to generate multiple single reports ?

I'm not Uwe, but here are some of the things to try if you want to do this fully in R. Look at the help for scan, one approach to reading in a .rnw file is to use scan, but set it to read each row of the file as a character matrix. The 'see also' section of the scan help page has some other

[R] ggplot - Setting the y-scale in a bar plot

Dear All (probably Hadley), I am now trying to customise some plots using a bar geom. I do not want to use the default binning statistic, but rather calculate the bar heigths separately. I do manage this, but for comparison purposes I would like to have a set of plots all with the same y-axis

[R] Using predict()?

I'm trying to solve a homework problem using R. The problem gives a list of cricket chirps per second and corresponding temperature, and asks to give the equation for the linear model and then predict the temperature to produce 18 chirps per second. So far, I have: # Homework 11.2.1 and 11.3.3

Re: [R] Reading through a group of .RData files

Thanks again, Benilton, I found your suggestions very helpful. But I couldn't seem to use the lapply / get combination to remove the objects that were loaded. The best I could come up with was: eval( parse( text = paste( rm(, paste( myObj, collapse = , ), ), sep = ) ) ) I'm wondering

Re: [R] Reading through a group of .RData files

actually, the lapply() was supposed to be used with your particular function... to remove, all you need is: rm(list=myObj) b On Dec 11, 2007, at 1:42 PM, Talbot Katz wrote: Thanks again, Benilton, I found your suggestions very helpful. But I couldn't seem to use the lapply / get

Re: [R] book on regular expressions

I've found the O'Reilly pocket reference Regular Expression (about USD 10.00) quite handy. It covers Perl, C, PHP, Python, Java, and .Net. David L. Reiner Rho Trading Securities, LLC -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Christos Hatzis Sent:

Re: [R] book on regular expressions

Great. Two books were consistently recommended: the pocket guide Regular Expressions and the more extensive Mastering Regular Expressions, both by O'Reilly. Thanks to all those who responded. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent:

Re: [R] Extracting clusters from Data Frame

Gustaf Rydevik wrote: On Dec 10, 2007 2:28 PM, Johannes Graumann [EMAIL PROTECTED] wrote: Hello, I have a large data frame (1006222 rows), which I subject to a crude clustering attempt that results in a vector stating whether the datapoint represented by a row belongs to a cluster or not.

[R] question regarding arima function and predicted values

Good evening! I have a question regarding forecast package and time series analysis. My syntax: x-c(253, 252, 275, 275, 272, 254, 272, 252, 249, 300, 244, 258, 255, 285, 301, 278, 279, 304, 275, 276, 313, 292, 302, 322, 281, 298, 305, 295, 286, 327, 286, 270, 289, 293, 287, 267, 267, 288,

Re: [R] Building R on Sun Solaris 10 (SPARC) using Sun Studio 12

Prof Ripley: Just curious if anyone has successfully built R on a SPARC platform running Sun Solaris 10 using the latest Sun Studio 12 set of compilers. If so, I would be interested in the compile flags that you used. Yes, the flags given in the R-admin manual. (We don't currently have

[R] matrix graph

Hi All, simple question: do you know how to graph the following object/matrix in a 'surface manner': [,1] [,2] [,3][,4] [,5][,6] [1,] -0.154 -0.065 0.129 0.637 0.780 0.221 [2,] 0.236 0.580 0.448 0.729 0.859 0.475 [3,] 0.401 0.506 0.310 0.650 0.822 0.448 [4,]

[R] postResample R² and lm() R²

Hello, I'm with a conceptual doubt regarding Rsquared of both lm() and postResample(library caret). I've got a multiple regression linear model (lets say mlr) with anR² value of 67.52%. Then I use this model pro make predictions with predict() function using the same data as input , that is, use

Re: [R] Reading through a group of .RData files

Hi, depending on what you do and how (and why) you save objects in RData files in the first place, you might be interested in knowing of the loadObject()/saveObject() methods of R.utils, as well as loadCache()/saveCache() in R.cache. The R.utils methods are basically clever wrappers around

Re: [R] matrix graph

On Tuesday 11 December 2007, threshold wrote: Hi All, simple question: do you know how to graph the following object/matrix in a 'surface manner': [,1] [,2] [,3][,4] [,5][,6] [1,] -0.154 -0.065 0.129 0.637 0.780 0.221 [2,] 0.236 0.580 0.448 0.729 0.859 0.475

Re: [R] matrix graph

Try these: x - matrix(rnorm(100), ncol=10) persp(x) contour(x) Also, look at the R graph gallery: http://addictedtor.free.fr/graphiques/ -- Tony Plate threshold wrote: Hi All, simple question: do you know how to graph the following object/matrix in a 'surface manner':

Re: [R] ggplot - Setting the y-scale in a bar plot

Hi Hadley, Well, the problem seems to be that ggplot is not recognizing the scale when set by scale_y_continuous, the maximum value stays exactly at the data range, irrespective of what I provide as range. I am not familiar yet with proto, therefore I do have some difficulty delving into the

[R] Writing a file to the disk

I am having difficulty writing the code for the following operation: I have a numeric vector pred_out of length 156. (N = 156). Under Windows XP, I need to write it to the disk in text format. Perhaps some kind soul would provide the code fragment. The file name is sheet_vec.txt. Please see [1]

[R] Using the same y-axis range for each plot in plot.ts

Hi, I would like to plot multiple time-series plots separately in the same window but I would like to have the same y-axis range for all of the plots for the sake of comparison. I am pretty sure there is a quick way to do it in plot.ts which I could not find. Any help is very much appreciated.

Re: [R] Using the same y-axis range for each plot in plot.ts

Try using plot.zoo from the zoo package. This plots them all within the range 3000 to 5000: library(zoo) plot(as.zoo(EuStockMarkets), ylim = c(3000, 5000)) On Dec 11, 2007 6:44 PM, Ugur Ozdemir [EMAIL PROTECTED] wrote: Hi, I would like to plot multiple time-series plots separately in the

[R] tm package - how to transform a TermDocMatrix to a data.frame

Hi to all, I'm using the tm package in a Windows machine. This is my sample: tts1 - TermDocMatrix(tts, weighting=tf-idf) typeof(tts1) [1] S4 How can i transform or put the tts1 TermDocMatrix in a simple data.frame or simple matrix. I need to compute some functions. For example, I need to

[R] How to plot the grid figure using R?

Now I have the forest plot data with x, y locations, and I measured the DBH for every indivicuals. The data looks like that: x=runif(100,0,100) y=runif(100,0,100) dbh=runif(100,1,100) rdata=data.frame(x,y,dbh) rdata[1:5,] x y dbh 1 99.5354145 1.412844 34.10112 2

[R] Markov Chain Monte Carlo (MCMR) in R for spatial simulation.

Dear all, I would like to know if is there some MCMR capability (functions) develped to improve spatial explicit landscape simulations in R. Kind regards, miltinho Brazil. para armazenamento! [[alternative HTML version deleted]] __

Re: [R] postResample R² and lm() R²

On Dec 11, 2007 3:35 PM, Giovane [EMAIL PROTECTED] wrote: So here comes my doubt: why do I have an value of 67.52% for R² when creating the model(that is , the model explains 67.52% of the data) and when I use this same model on the same input data, why does postResample return a very

[R] Efron's locfdr package - a component missing

Hello: Could you possibly help me. In Efron's 2004 paper Selection and Estimation ... it was mentioned that so-called effect density estimate, denoted by g1(mu) was included in the locfdr package. However, I can't find it in the description of the package. Any suggestions? Sincerely, Nik --

[R] Enc: Res: How to plot the grid figure using R?

Dear Jian, I would like help you but I need that you explain a little bit about what you really want. Sorry ask you again, but may be I don´t understood because my difficulties on english. Anyway, try this: require(akima) x=runif(100,0,100) y=runif(100,0,100) dbh=runif(100,1,100)

[R] Sys.setlocale() and text()

Dear HelpeRs, I have a question about the Sys.setlocale() command and plotting. I am running Windows XP, with R 2.6.1. My default locale is English_United States.1252. I am trying to add a lowercase sigma to a plot using the following code: Sys.setlocale(LC_CTYPE,greek) plot(1:10,1:10)

[R] Importing Large Dataset into Excel

Hello all, I seem to be having a problem importing a data set from Excel into R. I'm using the read.table command to import the data with the following line of code: newborn-read.table(newborn edit.csv, header=T, sep=,) where newborn edit.csv is the name of the file. Unfortunately, I'm

Re: [R] Importing Large Dataset into Excel

?count.fields count.fields will tell you how many items are in each line. As you said, they should all be the same, but this will confirm it. field.count - count.fields(newborn edit.csv, sep=,) table(field.count) # determine count of the fields on a line On Dec 11, 2007 7:15 PM, Wayne Aldo

[R] locfdr VS fdrtool

Hello: Could someone share the info about how these two packages compare to each other. I take it fdrtool is supposed to be better, but I'm not sure if it is so. Nik -- View this message in context: http://www.nabble.com/locfdr-VS-fdrtool-tp14288241p14288241.html Sent from the R help mailing

Re: [R] Importing Large Dataset into Excel

Sorry, the title of this should read From Excel into R. Quoting Wayne Aldo Gavioli [EMAIL PROTECTED]: Hello all, I seem to be having a problem importing a data set from Excel into R. I'm using the read.table command to import the data with the following line of code:

[R] Install from Local Zip

To install from a local zip file, install.packages option repos=NULL. Then, how can dependencies of the local zip file, which are located in the repository of contributor packages, be automatically installed? Or, is there a better way than to tell the person installing from local zip what the

Re: [R] Install from Local Zip

On Wed, 12 Dec 2007, [EMAIL PROTECTED] wrote: To install from a local zip file, install.packages option repos=NULL. Then, how can dependencies of the local zip file, which are located in the repository of contributor packages, be automatically installed? They cannot. You need a repository

Re: [R] 00LOCK error with site-library

I'm still having problems with this 00LOCK error. Tonight I recompiled R-devel from scratch, created a new site-library directory after moving the old one to scratch storage, and tried reinstalling my packages. 13 out of 290 packages successfully reinstalled and, once again, 00LOCK has

Re: [R] Sys.setlocale() and text()

Try this: plot(1:10, main = quote(sigma ^ 2)) On Dec 11, 2007 10:09 PM, Ed Merkle [EMAIL PROTECTED] wrote: Dear HelpeRs, I have a question about the Sys.setlocale() command and plotting. I am running Windows XP, with R 2.6.1. My default locale is English_United States.1252. I am trying

Re: [R] Efron's locfdr package - a component missing

I got in touch with Prof. Efron himself and he said that that part indeed was not included in the package, so there's nothing to be done. -- View this message in context: http://www.nabble.com/Efron%27s-locfdr-package---a-component-missing-tp14287868p14289411.html Sent from the R help mailing

Re: [R] Markov Chain Monte Carlo (MCMR) in R for spatial simulation.

On 12/12/07, Milton Cezar Ribeiro [EMAIL PROTECTED] wrote: Dear all, I would like to know if is there some MCMR capability (functions) develped to improve spatial explicit landscape simulations in R. Check the CRAN Spatial View [1]. Also search on this page [2] for markov. Liviu [1]

[R] Book: The New S Language

I'm struggling a bit with R with understanding functions and what's going on under the hood. For example, I was given this snippet of code via this mailing list: DF - data.frame(A =c(A, A, A, B, C), B=c(1,1,2,2,0)) g - paste(DF$A, DF$B) s - split(DF, g) split appears to be taken the string

[R] Odp: Book: The New S Language

Hi [EMAIL PROTECTED] napsal dne 12.12.2007 07:45:54: I'm struggling a bit with R with understanding functions and what's going on under the hood. For example, I was given this snippet of code via this mailing list: DF - data.frame(A =c(A, A, A, B, C), B=c(1,1,2,2,0)) g - paste(DF$A,

Re: [R] Sweave : change value in rnw file to generate multiple single reports ?

Greg wrote : Hope this helps, Sure it will ! Thanks again, Have a nice day, Ptit Bleu. -- View this message in context: http://www.nabble.com/Sweave-%3A-change-value-in-rnw-file-to-generate-multiple-%22single%22-reports---tp14256204p14290306.html Sent from the R help mailing list archive at