Re: [R] loading igraph package on Solaris

On Tue, 8 Jan 2008, Peter McMahan wrote: Hello, I'm having trouble getting the igraph package to load on Solaris. I can get igraph to compile and install from a local directory without issues using simply R CMD INSTALL igraph, however library(igraph) from within R gives the following errors:

Re: [R] Polynomial fitting

Dear Mr. Rowlingson, Rizopoulos, Jaworski, and Ripley Thank you for your help with the polynomial. Regards, Jonas On Jan 7, 2008 5:18 PM, Barry Rowlingson [EMAIL PROTECTED] wrote: Dimitris Rizopoulos wrote: try this: y - c(15.51, 12.44, 31.5, 21.5, 17.89, 27.09, 15.02, 13.43, 18.18,

Re: [R] choose the intercept from glm and lm

Chuck Cleland schrieb: Regards Knut Here is one way: outcome - relevel(outcome, ref=2) ?relevel Thank you very much. Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] memory problems (not me. my pc!)

Dear R users, I have got an error message related with memory size, but I could not understand if and how to solve it. Could you please help me? I was using the source quickPCNM-761.R, for a space matrix with 12572 rows (with X and Y (UTM) coordinates), and an Y matrix containing response

Re: [R] Constrained minimization solver for nonlinear programming

On Jan 9, 2008 4:01 AM, tom soyer [EMAIL PROTECTED] wrote: I noticed that R has a few bound-constrained nonlinear min and max solvers, such as optim, nlm, etc. But I could not find a constrained min and max solver that is not LP. Does this mean R do not have this capability? It is hard to

[R] WG: subsetting

-Ursprüngliche Nachricht- Von: Matthias Wendel [mailto:[EMAIL PROTECTED] Gesendet: Mittwoch, 9. Januar 2008 13:06 An: '[EMAIL PROTECTED]' Cc: 'Gabor Grothendieck' Betreff: AW: [R] subsetting Thank you, Gabor, for this clarificaton. This is very helpful für me. Matthias

[R] labels to values

I couldn't find out how the following to solve: There is a column in a data.frame: d[, 'Y6'] [1] 6 3 8 11 8 9 6 8 3 5 10 15 NA 9 8 3 8 16 6 6 NA 10 5 2 7 7 6 16 7 15 7 10 12 8 7 12 12 16 7 6 8 8 15 6 [45] NA 8 99 7 12 8 9 16 7 16 8 7 7 1 15 12 8 7 10

[R] Rscript on OSX

Hi, I directed somebody to install R (2.6.1) on his OSX computer, following instructions from http://cran.r-project.org/bin/macosx. She can run R from the console. But plot(1:10) doesn't produce any output or open a window (as I am used to from linux). More importantly: Rscript is not in the

Re: [R] Constrained minimization solver for nonlinear programming

Thanks Paul. yes, with equality constraints. What are friends? I read the document for optim, but still could not figure out how to do this. Do you just set the lower bound equal to the upper bound? Also, is it possible to ask R to search for a solution based on a target value instead of min and

Re: [R] Constrained minimization solver for nonlinear programming

On Jan 9, 2008 1:14 PM, tom soyer [EMAIL PROTECTED] wrote: Thanks Paul. yes, with equality constraints. What are friends? I read the document for optim, but still could not figure out how to do this. Do you just set the lower bound equal to the upper bound? constrOptim is a friend of optim.

Re: [R] Plotting labeled impulses: label collision

Jim, I finally got back to this implementation of mine and dude, this function is amazing! Thank you so much! Joh On Saturday 05 January 2008 11:42:30 Jim Lemon wrote: Johannes Graumann wrote: Dear all, As you can see from the attachment I'm using R to automatically annotate peptide

Re: [R] Can R solve this optimization problem?

If its too large the the primary portion of the objective basically just looks like roundoff error. By the way there is also rdonlp2 which can handle constraints. Not on CRAN -- try google. On Jan 9, 2008 6:45 AM, Paul Smith [EMAIL PROTECTED] wrote: On Jan 8, 2008 2:58 AM, Gabor Grothendieck

Re: [R] Rscript on OSX

Ido - R for OSX generally runs via an application, called R.app, which your colleague could find in their applications directory. It can run scripts and has a rather nice script editor associated with it. You can run R as you would in linux using X11.app, found in Applications-Utilities

Re: [R] Constrained minimization solver for nonlinear programming

Thanks Paul. I thought constrOptim does not do equality. I will check again. A concrete example for finding a solution based on a target value instead of min or max would be something like this: let's say I am trying exponential smoothing on a time series and would like to find a solution for the

Re: [R] Two dependent variables in formula

On Wednesday 09 January 2008 1:57 pm, Carla Rebelo wrote: Hello, I' m trying to change the formula in the rpart function. The format of a general formula is Answer ~ expression, where Answer is the dependent variable and expression is set of terms containing the independent variables

Re: [R] Rscript on OSX

On 2008-January-09 , at 15:01 , Andrew Beckerman wrote: R is not designed to run from Terminal.app (actually, terminal does not do graphics well for R). Actually it can, provided that you: - install the package CarbonEL which allows you to plot to quartz windows from outside R.app (with

Re: [R] I need arguments pro-S-PLUS and against SAS...

You might find this article useful Kellie B. Keeling and Robert J. Pavur, A comparative study of the reliability of nine statistical software packages, Computational Statistics Data Analysis, Volume 51, Issue 8, 1 May 2007, Pages 3811-3831.

Re: [R] as.date - german date format

Konga wrote: Hi, I have a data.frame with the following variable: $ xx :Factor w/ 66 levels 01.02.2006,01.03.2006,..: 3 3 3 3 3 3 3 3 3 now I´d like use as.date on it - if I comprehend the instructions on http://finzi.psych.upenn.edu/R/library/base/html/format.Date.html it should

[R] Penalized L1 regression error in lasso2 package

Hi everbody, I need to apply lasso regression using the function l1ce from the lasso2 package: fr - l1ce( fitness_T ~ ., data = dr, absolute.t=TRUE, standardize=FALSE ); Where fitness_T is my response, . represents all the terms of my dataframe dr. This function fails when I use a lot of

[R] as.date - german date format

Hi, I have a data.frame with the following variable: $ xx :Factor w/ 66 levels 01.02.2006,01.03.2006,..: 3 3 3 3 3 3 3 3 3 now I´d like use as.date on it - if I comprehend the instructions on http://finzi.psych.upenn.edu/R/library/base/html/format.Date.html it should work like this:

[R] Two dependent variables in formula

Hello, I' m trying to change the formula in the rpart function. The format of a general formula is Answer ~ expression, where Answer is the dependent variable and expression is set of terms containing the independent variables and separated by operators. I want the response of the

[R] close connection, closeAllConnections()

close connection, closeAllConnections() Hello, For windows2000 and windowsXP, R.2.6.1 I have a little problem with the following lines socketConnection('127.0.0.1', port=7496, server=F, blocking=F, open='wb', encoding=''); description class mode text

[R] reading table

Hi, I am encountering a problem in reading a file, the file looks like that: T 3 0 -- -- --T -- -- -- 18.98 3 1 6.75 4.3939 -- -- -- 18.58 3 2 6.90 4.9043 -- -- -- 18.63 3 3

[R] An R is slow-article

Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more technically knowledgeable people explain why this is so?

Re: [R] Two dependent variables in formula

On Wed, 2008-01-09 at 13:57 +, Carla Rebelo wrote: Hello, I' m trying to change the formula in the rpart function. The format of a general formula is Answer ~ expression, where Answer is the dependent variable and expression is set of terms containing the independent

Re: [R] as.date - german date format

Uwe Ligges-3 wrote: Konga wrote: Hi, I have a data.frame with the following variable: $ xx :Factor w/ 66 levels 01.02.2006,01.03.2006,..: 3 3 3 3 3 3 3 3 3 now I´d like use as.date on it - if I comprehend the instructions on

Re: [R] An R is slow-article

fisher.test seems to use the .C calling convention in a couple of different places. for example: tmp - .C(fisher_sim, as.integer(nr), as.integer(nc), as.integer(sr), as.integer(sc), as.integer(n), as.integer(B), integer(nr * nc), double(n + 1),

Re: [R] An R is slow-article

Gustaf Rydevik wrote: Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more technically knowledgeable

[R] likelihood from test result

Is there any automatic mechanism for extracting a likelihood or test statistic distribution (PDF or CDF) from an object of class htest or from another object of a general class encoding a hypothesis test result? I would like to have a function that takes x, an object of class htest, as its only

Re: [R] An R is slow-article

On 1/9/2008 10:25 AM, Gustaf Rydevik wrote: Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more

Re: [R] Constrained minimization solver for nonlinear programming

On Jan 9, 2008 2:13 PM, tom soyer [EMAIL PROTECTED] wrote: Thanks Paul. I thought constrOptim does not do equality. I will check again. Indeed, constrOptim does not do equality constraints, but, trough penalties, one can add them. A concrete example for finding a solution based on a target

[R] Need help on distance matrix

Hi I have a data like this. 79 77.51 79.64 84.08 71.6 90.22 91.46 89.49 94.51 97.45 97.99 97.86 69.88 77.44 72.44 74.21 72.54 78.27 82.03 78.62 80.4 85.97 86.22 84.04 I try to do a distance matrix. I get error if I run the following program: D2 - matrix(0,n,n) for (i1

[R] Ransac implementation

Hi, is there an R-implementation of the RANSAC-algorithm? Thanks, Ralf __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide

Re: [R] An R is slow-article

Gustaf Rydevik wrote: Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more technically knowledgeable

Re: [R] An R is slow-article

Gustaf Rydevik wrote: Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm There are certainly situations where one would want to consider faster solutions than interpreted languages but, having been through these arguments a

Re: [R] An R is slow-article

Barry Rowlingson wrote: Gustaf Rydevik wrote: Hi all, Reading the wikipedia page on R, I stumbled across the following: http://fluff.info/blog/arch/0172.htm It does seem interesting that the C execution is that much slower from R than from a native C program. Could any of the more

Re: [R] likelihood from test result

You could create an S3 generic that does it. That is not initially any less work than the if statement but if you add new distribution no existing code need be modified. Just add a new method for each distribution to be supported: getDistr - function(x) { .Class -

Re: [R] An R is slow-article

I hazard to say that the author of that blog post isn't using the time he saved from writing his analyses in C very efficiently. I wonder how long it took him to write it in C in the first place, even to setup the testing of C against R, or to write the blog post. He didn't say. Jeff

Re: [R] labels to values

If I understand your question, you can do: x1 - as.factor(d[,'Y6']) levels(x1)[levels(x1) %in% attributes(x)[1]] - c(names(unlist(lapply(levels(x1), function(z)which(z==attributes(x)[[1]]) On 09/01/2008, Matthias Wendel [EMAIL PROTECTED] wrote: I couldn't find out how the following to

[R] The R book

I have just recieved The R book by Michael Crawley, and I am deeply impressed. Really. Chapter 2, Essentials of the R language taught me a lot. More than 900 pages of concentrated Information. Recommended! Tom -- ++ | Tom

Re: [R] An R is slow-article

[article: http://fluff.info/blog/arch/0172.htm ] Duncan Murdoch wrote: If I followed Blair's advice and did everything in C, then development would take much longer, the code would be much buggier (even his example has bugs, and he admits it!!) and all those cases where R is fast

Re: [R] likelihood from test result

David Bickel wrote: Is there any automatic mechanism for extracting a likelihood or test statistic distribution (PDF or CDF) from an object of class htest or from another object of a general class encoding a hypothesis test result? I would like to have a function that takes x, an object of

Re: [R] An R is slow-article

Hello Gustaf, List. Thanks Gustaf for your post! well I am working pretty intensively with fisher.test() right now, as some of you will know. The comparison is not fair: R's fisher.test() does a whole bunch of error checking and testing for the size of the input matrix and assessing of other

Re: [R] plotting help needed

maybe this is what you want: plot(all~c(1:2),type=b,col=blue,xlim=c(1,4),ylim=c(20,150),pch=c(a,b),yaxt=none) lines(all2~c(2:3),type=o,col=yellow,pch=c(d,e)) for some manuals, look at the contributed documents section at the R homepage Bart ran2 wrote: Dear all, i need some help

[R] use save.image inside a function?

Hi, All I'm trying to save the workspace as a Check Point for possible future come back. The save.image function works if the whole coding is in a main function: rm(list=ls()) t = 1 t = t+1 print(paste(before,t)) # [1] before 2 save.image(tt.RData) t = t+1 print(paste(after,t)) # [1] after 3

Re: [R] use save.image inside a function?

save.image() saves the global workspace: it does not save the environments of executing functions. If you want to save the latter, use the 'envir' argument of save(). On Tue, 8 Jan 2008, Hua Li wrote: Hi, All I'm trying to save the workspace as a Check Point for possible future come back.

[R] R help

Is there a number I can call to get started with R? I have some really basic questions that won't take more than 10 minutes. Sitadri This e-mail, including attachments, is intended for the person(s) or company named and may contain confidential and/or legally privileged

Re: [R] R help

On Jan 9, 2008 5:47 PM, [EMAIL PROTECTED] wrote: Is there a number I can call to get started with R? I have some really basic questions that won't take more than 10 minutes. Sitadri Try and write your questions down to this mailing list, and you're bound to get answers, /Gustaf

Re: [R] Constrained minimization solver for nonlinear programming

Thanks Paul. I will try it. On 1/9/08, Paul Smith [EMAIL PROTECTED] wrote: On Jan 9, 2008 2:13 PM, tom soyer [EMAIL PROTECTED] wrote: Thanks Paul. I thought constrOptim does not do equality. I will check again. Indeed, constrOptim does not do equality constraints, but, trough penalties,

Re: [R] as.date - german date format

Konga wrote: Uwe Ligges-3 wrote: Konga wrote: Hi, I have a data.frame with the following variable: $ xx :Factor w/ 66 levels 01.02.2006,01.03.2006,..: 3 3 3 3 3 3 3 3 3 now I´d like use as.date on it - if I comprehend the instructions on

Re: [R] R help

On Jan 9, 2008 11:57 AM, Gustaf Rydevik [EMAIL PROTECTED] wrote: On Jan 9, 2008 5:47 PM, [EMAIL PROTECTED] wrote: Is there a number I can call to get started with R? I have some really basic questions that won't take more than 10 minutes. Sitadri Try and write your questions

Re: [R] reading table

Read in lines using readLines, delete all T and G characters and reread using read.table: Lines.raw - T 3 0---- -- T ---- -- 18.98 3 1 6.75 4.3939 ---- -- 18.58 3 2 6.90 4.9043 ---- -- 18.63 3 3 7.07 5.3948 ----

[R] Distance matrix from a binary data frame

Hi, I am trying to calculate a distance matrix on a binary data frame using dist.binary() {ade4}. This is the code I run and the error I get: sjlc.dist - dist.binary(as.data.frame(data), method=2) #D = (a+d) / (a+b+c+d) Error in if (any(df 0)) stop(non negative value expected in df) :

Re: [R] as.date - german date format

Functions to convert between character representations and objects of class Date representing calendar dates. $ xx :Factor w/ 66 levels try as.character(xx) --- Konga [EMAIL PROTECTED] wrote: Hi, I have a data.frame with the following variable: $ xx :Factor w/ 66 levels

[R] formating ftable

Hi all, I am using ftable and xtabs to get total counts of species per location per hight category (understory, midstory and overstory). i can save the data in almost the format i would like it to be - but not quite. Here it is an example of what i get: x - is a dataframe with the

Re: [R] labels to values

There probably is an easier way but you put the value.labels and corresponding numbers into a data.frame, stick d[,'Y6] into a data frame and merge the two. Then just add or replace d[,Y6] in the original data.frame. Example # Set up basic data aa - 1:15 bb - letters[1:15] # Apply

Re: [R] An R is slow-article

Paul == Paul Gilbert [EMAIL PROTECTED] writes: Gustaf Rydevik wrote: The author also have some thought-provoking opinions on R being no-good and that you should write everything in C People used to say assembler, that's progress. From the FORTRAN Preliminary Report, IBM,

Re: [R] R help

--- [EMAIL PROTECTED] wrote: Is there a number I can call to get started with R? I have some really basic questions that won't take more than 10 minutes. Sitadri Probably not unless you know an R-user personally or there's someone at your firm or institution whom you can

[R] (no subject)

On 1/9/2008 4:28 PM, [EMAIL PROTECTED] wrote: I have a couple of simple questions. (a) Suppose that I have an Excel dataset stored in a file called dataset.xls located in some folder in my hard drive. Suppose that it has two columns called X and Y of equal length. After I click on

Re: [R] help with R

1) there are many ways to read data from excel into R, such as rodbc package. 2) check cran, or do a r search. On Jan 9, 2008 4:35 PM, [EMAIL PROTECTED] wrote: Folks, Two simple questions : (1) I have a data set (call it data.xls) in a folder in my hard drive. How do I perform a simple

[R] Question about putting multiple plots on the same page

Hi, I met a problem when trying to put multiple plots on the same page. I have a plotting function (e.g., myfunction()) that contains the lines of par(), layout(). Now I want to try four types of parameter combinations and put these four figures on the same page. I tried par(mfrow or mfcol) and

[R] Course*** R/S-Plus Advanced Programming ****by XLSolutions Corp

Happy New Year Our *** San Francisco *** R/Splus Advanced Programming is scheduled for January 24-25, 2008 Please email for earlybird rates: Payments due after the class. R/Splus Advanced Programming Course Outline: Day 1 - Overview of R/S fundamentals: Syntax and

Re: [R] help with R

Hi, please have a look at the posting guide (link is at the bottom of your message). Most (if not all) of your problems should be solved if you follow the advice given there. Anyway, please have a look below: [EMAIL PROTECTED] wrote: Folks, Two simple questions : (1) I have a data set

Re: [R] help with R

[EMAIL PROTECTED] wrote: Folks, Two simple questions : (1) I have a data set (call it data.xls) in a folder in my hard drive. How do I perform a simple regression between two variables from that data set? After I click on 'R', what exactly do I type in? Ideally, you shouldn't really

[R] pairwise cross tabulation tables

Hi, I have a huge number of categorical variables, say at least 1, and I put them into a matrix, each column is one variable. The question is: how can I make all of the pairwise cross tabulation tables efficiently? The straightforward solution is to use for-loops by looping two indexes on

Re: [R] help with R

Sitadri, What operating system are you using? Have you loaded R onto you computer? If not I suggest you do so. You can than enter the command ?lm which will give you information about lm command, the command used to perform linear regresssion. I would also suggest that you go to

[R] Subsetting Method [ Revisited

Hello Everyone: As usual, thanks in advance for any help. I was hoping to get some more advice on this question: I'm trying to write a subsetting routine for an S3 object I've created -- lets call it myObject. myObject has a few attributes basically of type string and numerics. Its atomic

Re: [R] help with R

Sitadri, I would also look at http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html a site that was pointed out in a recent posting to the listserve by John Kane. John Sitadri, What operating system are you using? Have you loaded R onto you computer? If not I suggest you do so. You can than enter

[R] general linear hypothesis glht() to work with lme()

Hi, I am trying to test some contrasts, using glht() in multcomp package on fixed effects in a linear mixed model fitted with lme() in nlme package. The command I used is: ## a simple randomized block design, ## type is fixed effect ## batch is random effect ## model with

Re: [R] Question about putting multiple plots on the same page

You need to provide commented, minimal, self-contained, reproducible code. The following code works fine for me: par(mfrow=c(2,2)) plot(0) plot(1) plot(2) plot(3) But I have no idea of how you are trying to use it, what operating system you have, what type of device you are going out to,

Re: [R] pairwise cross tabulation tables

On Wed, 9 Jan 2008, AndyZon wrote: Hi, I have a huge number of categorical variables, say at least 1, and I put them into a matrix, each column is one variable. The question is: how can I make all of the pairwise cross tabulation tables efficiently? The straightforward solution is to

Re: [R] Subsetting Method [ Revisited

print(Test) appears to be the last line of your [.myObject function, so its value will be returned by the function. This may not be what you want. Presumably you want some subset of the input object returned, so put that below the print(Test) line. You could use the invisible() function to

[R] how can i add a package that i want to use permanent

I want use a package(lattice) in R to do some work but everytime when i open R program ,this package is not loaded, so everytime i have to load it , who can tell me how to load this package permanent thanks!!! -- ºúÎIJ¨ TEL:15918732631 E-MAIL:[EMAIL PROTECTED] [EMAIL PROTECTED]

Re: [R] question on how to extract values from atomic vector

There are a couple of ways of getting the values: x - cbind(a=1:3, pi=pi) # simple matrix w/ dimnames attributes(x) $dim [1] 3 2 $dimnames $dimnames[[1]] NULL $dimnames[[2]] [1] a pi attributes(x)$dim [1] 3 2 attr(x, 'dim') [1] 3 2 So in your case, attr(Results, 'prob') or

Re: [R] how can i add a package that i want to use permanent

?Startup On Jan 9, 2008 10:28 PM, 文波胡 [EMAIL PROTECTED] wrote: I want use a package(lattice) in R to do some work but everytime when i open R program ,this package is not loaded, so everytime i have to load it , who can tell me how to load this package permanent thanks!!! -- ºúÎIJ¨

Re: [R] Question about putting multiple plots on the same page

Jim: Thanks for your response. Here is an example I took from graphics gallery ( http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=2 ). Now I want to place 4 plots into the same page (e.g., one for swiss, one for usa, and so on) by running the author's function plotacpclust() 4 times.

[R] diff in a dataframe

I have a dataframe say: date price_g price_s 0.340.56 0.360.76 . . . . . . and so on. say, 1000 rows. Is it possible to add two columns to this dataframe, by computing say

Re: [R] as.date - german date format

Thanks a lot, it works! Now I have to find out why - but I think I can/should do it on my own ;o) -- View this message in context: http://www.nabble.com/as.date---german-date-format-tp14712654p14728914.html Sent from the R help mailing list archive at Nabble.com.