[R] Passing command line parameters to a script

Hi, Does any one know if it is possible to create an R script that can use command line parameters. I can execute an R script from the command line, but I cannot figure out how to pass parameters to the script. The only resources I have found seem somewhat involved or incomplete. Any help is

Re: [R] Passing command line parameters to a script

Does system(command -arguments) works for you? Xiaohui akintayo holder wrote: Hi, Does any one know if it is possible to create an R script that can use command line parameters. I can execute an R script from the command line, but I cannot figure out how to pass parameters to the script.

Re: [R] Passing command line parameters to a script

probably you're looking for ?commandArgs(). I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web:

Re: [R] Identifying points in a plot that have duplicate values

David Lloyd wrote: I have code like this: - #--- -- x=scan() 0 0 0 0 0 1 2 3 4 y=scan() 1 1 1 2 2 1 3 4 5 plot(x,y) identify(0,1,3) #Allows me to select

[R] Estimating parameters of 2 phase Coxian using optim

Hi, My name is Laura. I'm a PhD student at Queen's University Belfast and have just started learning R. I was wondering if somebody could help me to see where I am going wrong in my code for estimating the parameters [mu1, mu2, lambda1] of a 2-phase Coxian Distribution.

[R] Estimating parameters of 2 phase Coxian using optim

Hi, My name is Laura. I'm a PhD student at Queen's University Belfast and have just started learning R. I was wondering if somebody could help me to see where I am going wrong in my code for estimating the parameters [mu1, mu2, lambda1] of a 2-phase Coxian Distribution. cox2.lik-function(theta,

Re: [R] Mixed effects multinomial regression and meta-analysis

Here is my suggestion. Let P_i denote the true proportion in the ith study and p_i the corresponding observed proportion based on a sample of size n_i. Then we know that p_i is an unbiased estimate of P_i and if n_i is sufficiently large, we know that p_i is approximately normally distributed

[R] Quick question on Cochran-Mantel-Haenszel test

Dear List, I am looking for what B.S.Everitt refers to as Cochrane Method for testing independence in combined 2x2 contingency tables. Is it the same method as the Cochran-Mantel-Haenszel Chi-Squared Test for Count Data in R? Thanks, Serguei [[alternative HTML version deleted]]

Re: [R] Estimating parameters of 2 phase Coxian using optim

Hi There, Perhaps the problem is the line loglik-log(p %*% expm(Q * y(i)) %*% q) You mention that y is a vector but here you're treating it as a function. Maybe try loglik-log(p %*% expm(Q * y[i]) %*% q) ? Don't have a clue about the correctness of the contents of

[R] expm()

Can the expm function be used to calculate the exponential of a matrix where the matrix is multiplied by a vector in a data frame? For example for (i in 1:length(y)){ expmN-expm(Q*y[i]) Q-Matrix(c(1, 2, 3, 4), 2, 2) return(expmN) } Sorry I am new to R and I have been

[R] dispersion_parameter_GLMM's

Hi all, I was wondering if somebody could give me advice regarding the dispersion parameter in GLMM's. I'm a beginner in R and basically in GLMM's. I've ran a GLMM with a poisson family and got really nice results that conform with theory, as well with results that I've obtained previously

Re: [R] Quick question on Cochran-Mantel-Haenszel test

Hello, The R function mantelhaen.test implements the generalized method for IxJxK tables (not only 2x2xK). If I remember well, Mantel-Haenszel test is more accurate than the Cochran approximation. Regards, Le mardi 06 mars 2007 10:28, Serguei Kaniovski a écrit : Dear List, I am looking for

Re: [R] Is there a quick way to count the number of times each element in a vector appears?

Dylan Arena wrote: I'm writing a function that calculates the probability of different outcomes of dice rolls (e.g., the sum of the highest three rolls of five six-sided dice). You know there are simpler ways to do this, don't you? Alberto Monteiro

Re: [R] Mixed effects multinomial regression and meta-analysis

I just realized that the example I used in my previous posting today is incorrect because it is a binary response, not a multilevel response (small, medium, large) such as my real life problem has. I apologize for the confusion. The example is incorrect, but the multinomial problem is

[R] The plot of qqmath

Hello, I would like to inlude the Q-Q plot by qqmath into a panel with other plots, say, using par(mfrow=c(1,2)). How can this be done given that qqmath refreshes the plotting window and there seems to be no series coming out of it? Thanks Serguei [[alternative HTML version deleted]]

Re: [R] Is there a quick way to count the number of times each element in a vector appears?

El lun, 05-03-2007 a las 22:16 -0800, Dylan Arena escribió: So here is my question in a nutshell: Does anyone have ideas for how I might efficiently process a matrix like that returned by a call to combinations(n, r, rep=TRUE) to determine the number of repetitions of each element in each row

Re: [R] Identifying points in a plot that have duplicate values

A very simple solution is given in: help(sunflowerplot,package=graphics) ##If you want to see it in action: example(sunflowerplot) El mar, 06-03-2007 a las 19:55 +1100, Jim Lemon escribió: David Lloyd wrote: I have code like this: -

[R] Generate random numbers up to one

Dear all, I would like to know if there is a simple way to generate random numbers with the constrain that they sum up to one. I am new using R... Thanks in advance, Núria _ Acepta el reto MSN Premium: Correos más divertidos con

Re: [R] dispersion_parameter_GLMM's

That amount of overdispersion would make the use of a poisson model very questionable, and will very likely result in estimated standard errors that are too low, hence the change in statistical significance when you switch to quasipoisson. On 06/03/07, Cristina Gomes [EMAIL PROTECTED] wrote: Hi

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Re: [R] The plot of qqmath

qqmath is in the lattice package, which is not compatible with the conventional graphics parameter. Why not using qqnorm and qqline instead? If you want to combine qqmath with other lattice plots you should look at the documentation of the lattice and grid packages. If you read carefully in

Re: [R] expm()

On 3/6/07, Laura Hill [EMAIL PROTECTED] wrote: Can the expm function be used to calculate the exponential of a matrix where the matrix is multiplied by a vector in a data frame? I don't quite understand the question. The exponential of a matrix is only defined for square matrices. For

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Re: [R] Generate random numbers up to one

Núria Martínez napsal(a): Dear all, I would like to know if there is a simple way to generate random numbers with the constrain that they sum up to one. I am new using R... Thanks in advance, Núria You need to specify what 'random' means. If you have any numbers, you can always

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Re: [R] Generate random numbers up to one

Petr Klasterecky wrote: You need to specify what 'random' means. If you have any numbers, you can always make them add-up to 1: x - rnorm(100) #runif(100), rpois(100) etc. x - x/sum(x) sum(x) I see a slight problem that may occur with dividing by sum(x) in certain cases Barry

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Re: [R] Generate random numbers up to one

Núria Martínez wrote: Dear all, I would like to know if there is a simple way to generate random numbers with the constrain that they sum up to one. I am new using R... The easiest way is to generate them by whatever method and divide by their sum. e.g. as (s-rexp(100))/sum(s) Are

[R] how to edit my R codes into a efficient way

Hello, Everyone, I am a student an a new learner of R and I am trying to do my homework in R. I have 10 files need to be read and process seperately. I really want to write the codes into something like macro to save the lines instead of repeating 10 times of similar work. The following is part

Re: [R] Generate random numbers up to one

Barry Rowlingson napsal(a): Petr Klasterecky wrote: You need to specify what 'random' means. If you have any numbers, you can always make them add-up to 1: x - rnorm(100) #runif(100), rpois(100) etc. x - x/sum(x) sum(x) I see a slight problem that may occur with dividing by sum(x)

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[R] sem: standardized covariance estimates

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[R] help using non-separable space time covariance model

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[R] Distinct combinations for bootstrapping small sets

Small data sets (6-12 values, or a similarly small number of groups) which don't look nice and symmetric are quite common in my field (analytical chemistry and biological variants thereof), and often contain outliers or at least stragglers that I cannot simply discard. One of the things I

Re: [R] how to edit my R codes into a efficient way

Xuhong Zhu napsal(a): Hello, Everyone, I am a student an a new learner of R and I am trying to do my homework in R. I have 10 files need to be read and process seperately. I really want to write the codes into something like macro to save the lines instead of repeating 10 times of similar

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Re: [R] sem: standardized covariance estimates

Dear Mike, I don't believe that I've provided a way to get these correlations automatically, but you can, of course, just divide the covariance by the product of the standard deviations. I hope this helps, John John Fox Department of Sociology McMaster

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Re: [R] how to edit my R codes into a efficient way

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Re: [R] Package RODBC

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[R] Off topic:Spam on R-help increase?

Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Thanks. Bert Gunter Genentech

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[R] Question

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Re: [R] Distinct combinations for bootstrapping small sets

On Tue, 2007-03-06 at 15:54 +, S Ellison wrote: Small data sets (6-12 values, or a similarly small number of groups) which don't look nice and symmetric are quite common in my field (analytical chemistry and biological variants thereof), and often contain outliers or at least stragglers

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Re: [R] Matrix/dataframe indexing

On Mon, 2007-03-05 at 12:49 -0500, Guenther, Cameron wrote: Hi all, I am hoping someone can help me out with this: If I have dataframe of years and ages and the first column and first row are filled with leading values: Df- age1age2age3 Yr1 1 0.4

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Re: [R] How to utilise dual cores and multi-processors on WinXP

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Re: [R] Off topic:Spam on R-help increase?

Dear Gunter, I am having the same problem at my email box. Bert Gunter escreveu: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the

[R] Estimation near boundary

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Re: [R] Off topic:Spam on R-help increase?

Bert Gunter wrote: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Martin

[R] Recalling and printing multiple graphs. Is there something in the HISTORY menu that will help?

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Re: [R] how to edit my R codes into a efficient way

Again, thanks a lot. Xuhong On 3/6/07, Petr Klasterecky [EMAIL PROTECTED] wrote: Xuhong Zhu napsal(a): Hello, Everyone, I am a student an a new learner of R and I am trying to do my homework in R. I have 10 files need to be read and process seperately. I really want to write the codes

Re: [R] Off topic:Spam on R-help increase?

On 3/6/07, Bert Gunter [EMAIL PROTECTED] wrote: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? There has indeed been

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Re: [R] Generate random numbers up to one

On 06-Mar-07 Petr Klasterecky wrote: Barry Rowlingson napsal(a): Petr Klasterecky wrote: You need to specify what 'random' means. If you have any numbers, you can always make them add-up to 1: x - rnorm(100) #runif(100), rpois(100) etc. x - x/sum(x) sum(x) I see a slight problem that

Re: [R] Off topic:Spam on R-help increase?

On Tue, 2007-03-06 at 08:23 -0800, Bert Gunter wrote: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel

Re: [R] Off topic:Spam on R-help increase?

Not in the past 2 days, but only today I've received already more than 40 spams from R-help and R-sig-* too. Rarely I received a spam from these lists... Fernando Mayer. Bert Gunter escreveu: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others

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Re: [R] Off topic:Spam on R-help increase?

Dear Mark, If you are using an email program like thunderbird or any other you can filter your emails by key (not very amusing) words at the source. Best regards, Carlos Mark W Kimpel escreveu: me too. Over 50% of messages are spam. I also noted the same thing on ESS-help. Carlos Guerra

Re: [R] Off topic:Spam on R-help increase?

Bert Gunter wrote: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Thanks.

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Re: [R] Off topic:Spam on R-help increase?

me too. Over 50% of messages are spam. I also noted the same thing on ESS-help. Carlos Guerra wrote: Dear Gunter, I am having the same problem at my email box. Bert Gunter escreveu: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others

Re: [R] Off topic:Spam on R-help increase?

Carlos Guerra wrote: Dear Gunter, I am having the same problem at my email box. Our warmest thanks to Martin Maechler who managed to keep us free from spam for so many years on the R mailing lists!!! Uwe Ligges Bert Gunter escreveu: Folks: In the past 2 days I have seen a large

[R] optim(), nlminb() and starting values

Hi all ! I've been trying to maximize a likelihood using optim( ) function, but it seems that the function has several local maxima. I've tried in my algorithm with different starting values and depending on them optim obtains different results... I use the L-BFGS-B method setting the lower

Re: [R] delete selecting rows and columns

A one-dimensional delete might be faster: n - 4000 m - 0.01 matr - matrix(1:(n^2), n, n) excl_r - sample(n, m*n) incl_r - setdiff(1:n, excl_r) excl_c - sample(n, m*n) incl_c - setdiff(1:n, excl_c) system.time(matr[-excl_r, -excl_c]) system.time( { m4 - matr[outer(incl_r, incl_c, function(i, j) i

Re: [R] Off topic:Spam on R-help increase?

On 3/6/07, Peter Dalgaard [EMAIL PROTECTED] wrote: Bert Gunter wrote: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem

[R] Question about the smooth.Pspline

Hello, Everyone, I want to use the smooth.Pspline to smooth my data but R give me the error message as follows: Error in smooth.Pspline(sort.e$time, sort.e$cuff, method = 3) : X not strictly increasing my data looks like the following: id cuff time patient ... 2783

[R] mixed exponential distribution

Hi all, I have a 15min rainfall intensity dataset. I would like to fit a mixture of two exponential distributions to this dataset, and then extract certain quantiles from it. Is there a package in R that will allow me to get maximum likelihood estimates for the paramters, do goodness of fit

[R] R plug in for Eclipse

Hello, Is there any R plug-in available for Eclipse other than StatET? StatET doesn't seem to work with the latest release of Eclipse properly, i.e. syntax highlighting isn't enabled for R commands. I already contacted the author some time ago, but have not yet received a response. Would also

Re: [R] Generate random numbers up to one

Ted Harding wrote: And, specifically (to take just 2 RVs X and Y), while U = X/(X+Y) and V = Y/(A+Y) are two RVs which summ to 1, the distribution of U is not the same as the distribution of X conditional on (X+Y = 1). This question appeared in October 2006, and the answer was the Dirichlet

[R] 私を狂わせたあの日の体験

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Re: [R] Recalling and printing multiple graphs. Is there something in the HISTORY menu that will help?

Here is a function that I have used to write the files on my Windows machine. I put this function call after each graph that I produce and it will write out a new file and tell me what the file name is. I can then go back and copy the files into a document or a PowerPoint presentation. f.plot

Re: [R] Recalling and printing multiple graphs. Is there somethingin the HISTORY menu that will help?

See FAQ for Windows 5.2 and the referenced README. ?win.metafile and ?replayPlot might allow you to replay the saved plot history (by default in .SavedPlots) into a file in emf or wmf format, I think, but I haven't actually tried this -- don't know if it will work for multiple graphs. Let us

Re: [R] R and SAS proc format

See ?cut for continuous variables, and ?factor, ?levels for the others. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of lamack lamack Sent: Tuesday, March 06, 2007 12:49 PM To: R-help@stat.math.ethz.ch Subject: [R] R and SAS proc format Dear all,

Re: [R] Recalling and printing multiple graphs. Is there something in the HISTORY menu that will help?

options(graphics.record=TRUE) can be used to switch the recording on (MS Windows, not sure about other platforms). See ?options To set this option as default, use .Rprofile It is however quite annoying to examine and save all the graphs manually... You might find functions like postscript(),

Re: [R] R and SAS proc format

The down side to R's factor solution: The numerical values of factors are always 1 to number of levels. Thus, it can be tough and requires great care to work with studies that have both numerical values different from this and value labels. This situation is currently not well-supported by R.

[R] cluster analysis

Dear R-help, In performing cluster analysis (packages: hopach, cluster, boot, and many others), I got these errors: makeoutput(kidney, gene.hobj, bobj, file= kidney.out, gene.names= gene.acc) Error: could not find function makeoutput boot2fuzzy(kidney, bobj, gene.hobj, array.hobj,

Re: [R] Generating R plots through Perl - Solution

Hello, I tried what you suggested (i.e. combine the separate plot creation commands into one command from Perl to R), and it worked. The syntax is as follows: $R-send(qq (xVal - c(1,2,3,4,5,6))); $R-send(qq (yVal - c(3,5,2,6,1,5))); $R-send(qq (c(pdf(C:/Test Environment/R/perlPlotTest.pdf),

[R] Memory Limits in Ubuntu Linux

I am an R user trying to get around the 2Gig memory limit in Windows, so here I am days later with a working Ubuntu, and R under Ubuntu. But - the memory problems seem worse than ever. R code that worked under windows fails, unable to allocate memory. Searching around the web, it appears that

Re: [R] R and SAS proc format

lamack lamack wrote: Dear all, Is there an R equivalent to SAS's proc format? Best regards J. Lamack Fortunately not. SAS is one of the few large systems that does not implicitly support value labels and that separates label information from the database [I can't count the number of

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