[R] problem in installing R packages on linux

I am facing problem in installing the R package on linux . When i put the command install.packages(BART) Then it asks for selecting the mirror , i have selected the mirrror , but it is showing no package in repository .I have selected different different repository still i am getting the same

[R] problem in installing R packages on linux

I am facing problem in installing the R package on linux . When i put the command install.packages(BART) Then it asks for selecting the mirror , i have selected the mirrror , but it is showing no package in repository .I have selected different different repository still i am getting the same

Re: [R] glm(quasipoisson) with non-integer response

On Thu, 17 Apr 2008, Mark wrote: Hi, I have count data that have been meddled with enough to make them non integers. Using glm(poisson) returns a non integer error but glm(quasipoisson) does not. Just wondering if anyone knows if I am violating the assumptions of a quasipoisson error

Re: [R] problem in installing R packages on linux

man4ish wrote: I am facing problem in installing the R package on linux . When i put the command install.packages(BART) The screenshot is not there, but I suspect you want to install package BARD rather than BART. Uwe Ligges Then it asks for selecting the mirror , i have selected the

Re: [R] multivariate time series

Hello Erin, have you considered the package bundle dse on CRAN? Best, Bernhard Dear R People: I was looking to see if there are any functions for Vector ARMA modeling. I found Vector AR(p) but no Vector ARMAs. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and

Re: [R] spatialpixelsdataframe

Dave Depew wrote: I have a spatialpixelsdataframe containing bathymetry data. Is it possible to save this as something similar to the meuse.grid so it can be loaded without having to run the spatial interpolation each time the script is called? I don't see a straightforward method in the

Re: [R] vector in filename

Hi, Simon Blomberg wrote: How about this: x - 1 y - 1 mmax - 10 my.files - paste(foo, x:mmax, .png, sep=) for (i in my.files) { png(filename=i, pointsize=20, width=600, height=600, units=px, bg=#eaedd5) plot(x, y) dev.off() x - x+1 y - y+1 }

[R] Overall p-value from a factor in a coxph fit

Hi all. If I run the simple regression when x is a categorical variable ( x - factor(x) ): MyFit -coxph( Surv(start, stop, event) ~ x ) How can I get the overall p-value on x other than for each dummy variable? anova(MyFit) does NOT provide that information as previously suggested on the

[R] validation of logistic regression model with weighted presences and absences

Hello everyone! I want to validate logistic regression models of species distrubution data where presences and absences are weighted differently. I used lrm from Design package but unfortunately, validate.lrm ignores weights in the validation process. Has anyone an idea (package, code) how I can

Re: [R] EM algorithm for multiple-locus haplotypes frequencies

From: Marcin Kozak [EMAIL PROTECTED] Subject: [R] EM algorithm for multiple-locus haplotypes frequencies Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Look at all

[R] how to find the multiregression on the

I am trying to calculate the multi regression for the follwing data 0 1 2 3 7 5 0 4 4 3 0 3 4 5 4 0 5 4 5 4 0 1 1 0 1 0 1 1 1 0 1 0 4 5 6 1 2 3 2 1 keeping Ist column as dependent variable and other as independent varialbles,how can i do this using lm funciotn in stats please send me the code

[R] space between plots

I've set layout(matrix(c(1,3,2,4),ncol=2)) and par(mar=c(0, 4, 4, 0) + 0.0) and par(mar=c(0, 0, 4, 3) + 0.0) for the upper-left and upper-right plots, but still get an space between both plots, is there any way to completely eliminate that space? Thanks Agus -- Dr. Agustin Lobo Institut de

[R] Permanent change to the working directory

Dear helpers, I've looked in the help files (maybe not very thoroughly but I looked) and I couldn't find a straightforward way to permanently set the working directory (where I save and read files). Each time I startup R the working dir is automatically C:/R/bin [using:getwd()], and I know I can

Re: [R] Permanent change to the working directory

On windows machines you could change the `Start in' field of the desktop shortcut for R to the desired working directory - you will find this in the properties of the shortcut. You could easily create several shortcuts for different projects this way. You may also consider changing your

Re: [R] problem in installing R packages on linux

Uwe Ligges-3 wrote: man4ish wrote: I am facing problem in installing the R package on linux . When i put the command install.packages(BART) The screenshot is not there, but I suspect you want to install package BARD rather than BART. Uwe Ligges Then it asks for selecting

Re: [R] Permanent change to the working directory

On 4/18/2008 3:15 AM, francogrex wrote: Dear helpers, I've looked in the help files (maybe not very thoroughly but I looked) and I couldn't find a straightforward way to permanently set the working directory (where I save and read files). Each time I startup R the working dir is automatically

Re: [R] Is there any function to skip a loop in a for loop ?

next break Another 'Introduction to R', or even ?for question G. On Fri, Apr 18, 2008 at 04:55:01PM +0800, Ng Stanley wrote: Hi, Is there any function to skip a loop in a for loop ? Thanks Stanley [[alternative HTML version deleted]]

Re: [R] space between plots

When I try this: layout(matrix(c(1,3,2,4),ncol=2)) par(mar=c(0, 4, 4, 0) + 0.0) plot(1) par(mar=c(0, 0, 4, 3) + 0.0) plot(2) plot(3) plot(4) the upper left and right are butted together. Exactly what 'space' are you talking about? On Fri, Apr 18, 2008 at 4:19 AM, Agustin Lobo [EMAIL

[R] spdep question - Moran's I

Dear all, I would like to calculate a Moran's I statistic using the moran function in the spdep package. The problem I'm having deals with how to create the listw object. My data stems from the area of social network analysis. I have list of poeple and for each pair of them I have a measure of

[R] Vertical bars with barchart

Hallo, What is the right way to get vertical bars in a barchart? For instance barchart(VADeaths, key=simpleKey(colnames(VADeaths),points=F,rectangles=T)) gives what I need, only I would like the bars to be vertical. But barchart(VADeaths,horizontal=F,

Re: [R] problem in installing R packages on linux

man4ish wrote: No i am trying to install BART which is valid name , i have 30-40 times for other packages still facing the same pblm .How can i rectify this.Please help me out. Rather than sending a screenshot of a terminal (and note the posting guidelines with regards to

Re: [R] problem in installing R packages on linux

On Fri, 18 Apr 2008 01:47:43 -0700 (PDT) man4ish wrote: M The screenshot is not there, but I suspect you want to install M package BARD rather than BART. M M Uwe Ligges M No i am trying to install BART which is valid name , i have 30-40 M times for other packages still facing the same pblm

Re: [R] Matched pairs with two data frames

On Wed, 16-Apr-2008 at 11:58AM +0200, Udo wrote: | I only need line 1, 6 and 9. To show this, | I added needed by hand. | |age school out1 out2 needed | 11 10 9.5 1.1 yes | 21 10 9.5 2.0 no | 31 10 9.5 3.5 no | 41 10

Re: [R] Vertical bars with barchart

On Fri, 18 Apr 2008 12:00:13 +0200 G. Draisma wrote: GDbarchart(VADeaths,horizontal=F, GDkey=simpleKey(colnames(VADeaths),points=F,rectangles=T)) GD does not give what I need, Works for me. Do you have the current R (2.6.2) and lattice? btw. it also works with barchart(VADeaths,

[R] Working with graphs.

Hi, Im created some pie charts using R. I have two segments, I am just wondering how can I add a number to each segment that represents each each segment? Also is there a way to change the colors of each segment? Sorry if this frustrates anyone because of its simplicity, but I am new to R.

Re: [R] Working with graphs.

?pie Look at the example which I think addresses most of your questions On Fri, Apr 18, 2008 at 6:31 AM, hoogeebear [EMAIL PROTECTED] wrote: Hi, Im created some pie charts using R. I have two segments, I am just wondering how can I add a number to each segment that represents each each

Re: [R] Help with using 'get' function and variable scope

If you define your functions in the loop you can it directly since then the scoping rules work in your favor: for(i in 1:4) { f - function() i*i print(f()) } or via lapply: F - function(i) { f - function() i*i; print(f()) } lapply(1:4, F) Often the sort of situation you discuss is really

[R] problem in installing R packages on linux

install.packages(BayesTree) Is my guess for using function BART /Niels Niels Steen Krogh Konsulent ZiteLab ApS Mail: -- [EMAIL PROTECTED] Telefon: --- +45 38 88 86 13 Mobil: - +45 22 67 37 38 Adresse: --- ZiteLab ApS Solsortvej 44 dk

[R] [R-pkgs] RExcelInstaller

RExcelInstaller_2.0-15 installs RExcel, an add-in for Excel, which connects R and Excel. RExcel allows to transfer data between R and Excel, writing VBA macros using R as a library for Excel, and calling R functions as worksheet function in Excel. RExcel integrates nicely with R Commander

Re: [R] Problem with links in R website

On Thu, 17 Apr 2008 11:36:30 +0100, Robin Taylor (RT) wrote: Not sure who to send this to... On the books page http://www.r-project.org/doc/bib/R-books.html the entries from [54] down have three forward slashes in the hyperlinks to publisher info and so they don't work Thanks a lot

Re: [R] Help with using 'get' function and variable scope

On 18/04/2008 7:27 AM, Gabor Grothendieck wrote: If you define your functions in the loop you can it directly since then the scoping rules work in your favor: for(i in 1:4) { f - function() i*i print(f()) } f doesn't need to be in the loop, it just needs to be defined in the same

[R] ts.plot() labeling x-axis

Hello, I have tried a few variants of a solution from the previous posts, but perhaps my syntax is wrong. I am using ts.plot(data_as_columns) and would like the label the x axis using some labels (in my case minutes after 9am). Any ideas how to use the plot params and the Axis function to

[R] Function redefinition - not urgent, but I am curious

This is just my curiousity working. Suppose I write: f1 - function(x) x + 1 f2 - function(x) 2 * f1(x) f2(10) # 22 f1 - function(x) x - 1 f2(10) # 18 This is quite obvious. But is there any way to define f2 in such a way that we freeze the definition of f1? f1 - function(x) x + 1 f2 -

Re: [R] validation of logistic regression model with weighted presences and absences

Eva Mosner wrote: Hello everyone! I want to validate logistic regression models of species distrubution data where presences and absences are weighted differently. I used lrm from Design package but unfortunately, validate.lrm ignores weights in the validation process. Has anyone an idea

Re: [R] Function redefinition - not urgent, but I am curious

Try f2 - local({f1 - f1; function(x) 2 * f1(x) }) On Fri, Apr 18, 2008 at 8:22 AM, Alberto Monteiro [EMAIL PROTECTED] wrote: This is just my curiousity working. Suppose I write: f1 - function(x) x + 1 f2 - function(x) 2 * f1(x) f2(10) # 22 f1 - function(x) x - 1 f2(10) # 18 This is

Re: [R] Constrained Nelder-Mead

jangarita at ipc.com.co writes: Dear Mr, I saw by the web your request about the code in Language C of the method Nelder-Mead with constraints, I would like if you got the program, it's posible you can help us to get the code in C, This doesn't make much sense. I can imagine that

[R] Labels in cluster nodes

Hello all, I am novice in R, I've started to work with cluster, and in the cluster i obtain: $merge [,1] [,2] [1,] -1 -2 [2,] -3 1 $height [1] 2.291288 3.834058 $order [1] 1 2 3 When i use plot, obtain (in 'chargraphics'): | --- | | |

Re: [R] Function redefinition - not urgent, but I am curious

you could define 'f1' inside 'f2' or assign 'f1' to a new environemnt (or use local()): # 1st f2 - function(x){ f1 - function(x) x + 1 2 * f1(x) } f2(10) f1 - function(x) x - 1 f2(10) # 2nd myenv - new.env() assign(f1, function(x) x + 1, myenv) f2 - function(x){ f1 - get(f1, envir

Re: [R] 3-D-Plot

Edwin Sendjaja wrote: Hi Uwe, I decided to use scatterplot3d, because it looks better. I have some questions: Is it possible to get 1 axis( for example: z-axis) not as numeric, but as character. Because I have date set like this: x=relative Time: 0,3 ms; 0,5ms, etc y=Delay:10

Re: [R] space between plots

ok, I see: I was confused because the box goes a bit beyond the axes: layout(matrix(c(1,3,2,4),ncol=2)) par(mar=c(0, 4, 4, 0) + 0.0) plot(1,yaxt=n) par(mar=c(0, 0, 4, 3) + 0.0) plot(2,bty=n,yaxt=n) ...and I'm not plotting the box in my graphic. Thanks Agus jim holtman escribió: When I try

Re: [R] spatialpixelsdataframe

Thanks Paul, Will keep that in mind for my next query :-) Paul Hiemstra wrote: Dave Depew wrote: I have a spatialpixelsdataframe containing bathymetry data. Is it possible to save this as something similar to the meuse.grid so it can be loaded without having to run the spatial

Re: [R] survreg with frailty

The combination of survreg + gamma frailty = invalid model, i.e., the example that you quote. I did not realize that this had been added to the survreg help file until very recently. I will try to fix the oversight. Other, more detailed documentation states that Gaussian frailty + AIC

Re: [R] Help with using 'get' function and variable scope

On Fri, Apr 18, 2008 at 7:49 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 18/04/2008 7:27 AM, Gabor Grothendieck wrote: If you define your functions in the loop you can it directly since then the scoping rules work in your favor: for(i in 1:4) { f - function() i*i print(f()) }

Re: [R] vector in filename

On Thu, Apr 17, 2008 at 8:05 PM, [Ricardo Rodriguez] Your XEN ICT Team [EMAIL PROTECTED] wrote: Hi, I am trying to generate a group of graphics with an iteration. Some thing like this... x=1 y=1 max=10 myfiles - paste(foo, x:max, .png, sep=) while (x = max) {

Re: [R] Help with using 'get' function and variable scope

On 4/18/2008 9:19 AM, Gabor Grothendieck wrote: On Fri, Apr 18, 2008 at 7:49 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 18/04/2008 7:27 AM, Gabor Grothendieck wrote: If you define your functions in the loop you can it directly since then the scoping rules work in your favor: for(i in

Re: [R] Matched pairs with two data frames

Udo [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Daniel, thank you! I want to perfrom the simplest way of matching: a one-to-one exact match (by age and school): for every case in treat find ONE case (if there is one) in control . The cases in control that could be matched, should

[R] R CMD check PACKAGE Error

Hi, Can anyone give me a hint on what's wrong if R CMD check PACKAGE gives me this error: Rd files with unknown encoding: FILENAME.Rd I have checked that file over and over and can't find any weired characters or some such. How can I fix this? Thanks for your time, Joh

[R] [R-pkgs] new candisc package on CRAN

I'm happy to announce the candisc package, v 0.5-9, now on CRAN. Generalized Canonical Discriminant Analysis Description This package includes functions for computing and visualizing generalized canonical discriminant analyses for a multivariate linear model. They are designed to provide

Re: [R] vector in filename

Thanks Hadley, hadley wickham wrote: Have you looked at ?png : filename: the name of the output file. The page number is substituted if a C integer format is included in the character string, as in the default. (The result must be less than 'PATH_MAX'

[R] rzinb (VGAM) and dnbinom in optim

Dear R-help gurus (and T.Yee, the VGAM maintainer) - I've been banging my head against the keyboard for too long now, hopefully someone can pick up on the errors of my ways... I am trying to use optim to fit a zero-inflated negative binomial distribution. No matter what I try I can't get

[R] help me to debug this part of code?

I am trying to solve the integration equation, for different values of K from 4 to 25, the integration is with respect to u, Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) * integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper= sqrt(a^2*k/(k+1-a^2)) ) = the similar expression as

Re: [R] Problems with R2WinBUGS

Hello, Further to my previous e-mail, I think I know why I am having problems with the initialization of model parameters in R2WinBUGS. My model.bug file contains a portion of code which defines some pairwise odds ratios (e.g., or[1,2], or[1,3], or[1,4], or[2,3], or[2,4],

Re: [R] rzinb (VGAM) and dnbinom in optim

I'm not going to look into what's happening in-depth but it looks like the bounds for your parameters need to be set with care; the below (with slight re-def. of your residual function) gives results that seem to match vglm approximately, with 1e-10 standing in for a bound of 0 and 1-e-10 standing

Re: [R] Overall p-value from a factor in a coxph fit

Paul Johnson wrote: On Fri, Apr 18, 2008 at 3:06 AM, Kåre Edvardsen [EMAIL PROTECTED] wrote: Hi all. If I run the simple regression when x is a categorical variable ( x - factor(x) ): MyFit -coxph( Surv(start, stop, event) ~ x ) How can I get the overall p-value on x other than for

Re: [R] help me to debug this part of code?

On Fri, 18 Apr 2008, jinjin wrote: I am trying to solve the integration equation, for different values of K from 4 to 25, the integration is with respect to u, Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) * integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper=

Re: [R] problem in installing R packages on linux

On Fri, Apr 18, 2008 at 1:28 PM, Niels Steen Krogh [EMAIL PROTECTED] wrote: install.packages(BayesTree) What is the error message? Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] efficiently replacing values in a matrix

Still it is pretty slow when entering values into a large matrix. Case in point: a - matrix(nrow=1,ncol=1) system.time(a[1,1] - 1903908.80385) user system elapsed 30.840 6.226 41.416 is.matrix(a) [1] TRUE Is there a better way to enter values into large matrices? If I have to

Re: [R] Legend Clipping

Here is a better example. I am also trying to put gaps between the bars on the graphs, and this work-around is the only way I can make it work satisfactorily. Any suggestions about that? windows(); nf - layout(matrix(c(1,2,5,0,3,4),3,2,byrow=TRUE), c(2.2,2.2), c(2.2,1,2.2), TRUE) layout.show(nf);

[R] Fw: efficiently replacing values in a matrix

- Forwarded Message From: Nnamdi [EMAIL PROTECTED] To: roger koenker [EMAIL PROTECTED] Sent: Friday, April 18, 2008 1:08:58 PM Subject: Re: [R] efficiently replacing values in a matrix I tried the sparse matrix implementation, still there are issues: a - matrix(nrow=1,ncol=1)

Re: [R] efficiently replacing values in a matrix

Nanmdi, I think this is simply because a lot of time is taken transforming the matrix from logical (default when you create it) to numeric (when you add the number to [1,1]. If you do the same thing again to [1,2], it is done instantaneously: a - matrix(nrow=1,ncol=1) system.time(a[1,1]

[R] RPy

I'm curious if there are users of RPy on this list. I've recently created a gui front end using Tkinter for some python scripts I've written for some of our internal operations and I am quite pleased with how this program works. I wonder if it is possible to also get this gui to run R functions

[R] Correspondence and detrended correspondence analysis

Hi, I hope someone knows the answer to this or has a real good reference about it (I am using Legendre Legendre, Numerical Ecology, 1998) My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using

[R] Embedding fonts in pdfs

Hi all, I'm having problems embedding fonts in my graphics - and I've tried embedFonts to no avail. I have a pdf file and pdffonts tells me: name type emb sub uni object ID - --- --- --- -

Re: [R] Embedding fonts in pdfs

hadley wickham wrote on 04/18/2008 02:40 PM: Hi all, I'm having problems embedding fonts in my graphics - and I've tried embedFonts to no avail. I have a pdf file and pdffonts tells me: name type emb sub uni object ID

Re: [R] using rbind() on multiple objects at once

do.call(rbind, list.foo) On Fri, 18 Apr 2008, Andrew Yee wrote: Is there an efficient way to use rbind() with the five dataframes described in the following example: a - c(1:5) list.foo - lapply(a, function(x) data.frame(beta=a*rnorm(10), deta=a*rnorm(10))) big.data.frame -

Re: [R] Response to R across the university

On 18 Apr 2008, at 6:42 pm, Peter Dalgaard wrote: Antony Unwin wrote: ... The course itself went very well. We encouraged people to bring their laptops and work in groups. Using JGR as the interface to R helped a lot, as it was easier for people to load their own data and use

[R] Line-wrap problem

I'm wondering if someone can tell me how R determines where to wrap lines in its output. I'd like to understand this because occasionally often after running a script the output of R no longer wraps at the correct location. For example, the statement, '1:40' would ordinarily return

[R] 2.2e-16 a magic number? ks.test help

Hello, I'm trying to test my data for normality. I enter the data (95ish species counts) run ks.test (data,pnorm) and get a p- value 2.2e-16 But this seems to be the p-value no matter what the data I enter. (I have multiple datasets and am testing them all for normality). [Actually, I just

Re: [R] Response to R across the university

Antony Unwin wrote: A couple other maybe not all that trivial things to do is to improve the data import (it is losing out on most of the things that I tried) Now what would Brian say to a comment like that? Please insert your favourite put-down here:

Re: [R] help me to debug this part of code?

There are a lot of syntax errors such as unclosed parentheses, missing commas etc; Example: exp@(@lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k), where the parenthesis between the @s is not closed. I suggest you get an editor such as Tinn that can highlight those for you. In addition I notice that you use

Re: [R] Bug in Merge?

Edwin Sendjaja wrote: Hello, I find strange number in my merge data set. My first coloumn consist row numbers. --- my.data: AbsTime RelTime PE_IDEvent Delay 4238 1208514343.812086

[R] Distribution Graph Idea/Help

For pedagogical reasons (i.e., moving a way from tables of distributions) I want to plot a probability density or distribution function with a shaded area corresponding to the calculated value or user input. For example, I want a plot to visually demonstrate the result of pnorm(1.3) I have

[R] Problem with JGR_1.5-18

R version 2.7.0 Under development (unstable) (2008-03-04 r44677) i386-apple-darwin8.10.1 locale: C attached base packages: [1] grid grDevices datasets graphics stats utils methods base other attached packages: [1] lattice_0.17-6 MASS_7.2-41JGR_1.5-18 iplots_1.1-2

[R] How to insert a vector or matrix into an existing matrix

Hi, Is there any functions to insert a vector or matrix into an existing matrix say between row 5 and 6 or column 8 and 9, without creating a temporary matrix ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org

Re: [R] eval and parent.frame [was: Error in Design package: dataset not found for options(datadist)]

Charles C. Berry wrote: On Fri, 18 Apr 2008, Gad Abraham wrote: Frank E Harrell Jr wrote: Gad Abraham wrote: Hi, Design isn't strictly an R base package, but maybe someone can explain the following. When lrm is called within a function, it can't find the dataset dd: library(Design)