Re: [R] Boxplot- input the median point and the median value

On 01/02/2010 12:53 PM, elaine kuo wrote: Dear, I am a newbie to R. Now I am learning to draw boxplot using graphics(). I want to highlight the median position with a round point and the value left (or on the top of)to the point. Hi Elaine, For your boxplot questions, I'll use the

Re: [R] How to use read.table with Hebrew column names ?

Hi David, Thank you for responding, but it didn't work. I get the following error: [1] X. 0 rows (or 0-length row.names) Warning messages: 1: In read.table(http://www.talgalili.com/files/aa.txt;, header = T, : invalid input found on input connection '

[R] [Off-topic] problem with Tinn-R editor

This is not directly related with R however I would like to ask for a solution for my TINN-R editor because, I feel that lot many people perhaps use it as a reliable R editor and secondly I could not find any other forum only deals with TINN over net to discuss with. For quite sometime I have

[R] Run R in server web

Colleagues, I have a web server (appache Tomcat), and my web application (java-jsp..) run on it, how i can run R on server example, i want running R on server, and save output on server Thanks -- View this message in context: http://n4.nabble.com/Run-R-in-server-web-tp997126p997126.html

Re: [R] using optim

On 01/01/2010 11:45 PM, Erin Hodgess wrote: Dear R People: I know that you can use optim for a function with several parameters. Is there an equivalent for 2 functions, please? Or should I put together a finite difference type of matrix, etc., please? What is the goal? optim optimizes a

Re: [R] suppress output for meta in package tm

Can you wrap your call in capture.output(..., file=...)? -Peter Ehlers Amber Jaycocks wrote: Hello, I am using the tm package and wish to suppress the output for meta. I am defining another variable for one of the tags and don't want the value printed on the screen. Any help would be

Re: [R] to discriminate AUC of different models

Hello Elaine, Time to learn about search facilities: RSiteSearch(AUC, restrict=functions) #too many hits? RSiteSearch(DeLong, restrict=functions) -Peter Ehlers elaine kuo wrote: Dear, Regarding the methodology comparing the power of AUC generated by differernt models, please kindly

Re: [R] using optim

Duncan Murdoch wrote: On 01/01/2010 11:45 PM, Erin Hodgess wrote: Dear R People: I know that you can use optim for a function with several parameters. Is there an equivalent for 2 functions, please? Or should I put together a finite difference type of matrix, etc., please? What is the

[R] Question on Reduce + rollmean

Hello useRs, I'd like to perform a moving average on the dataset, xx. I've tried combining the functions Reduce and rollmean but it didn't work. r - function(n) rollmean(n, 2) # where 2 = averaging interval output - Reduce(r, x) Error in f(init, x[[i]]) : unused argument(s) (x[[i]]) Is

Re: [R] Question on Reduce + rollmean

Dear M.Rahiz, Unfortunatelly I can't reproduce your example. PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html bests milton On Sat, Jan 2, 2010 at 9:26 AM, Muhammad Rahiz muhammad.ra...@ouce.ox.ac.uk wrote: Hello useRs,

Re: [R] Question on Reduce + rollmean

Let me rephrase; Given x as x [[1]] V1 V2 V3 [1,] 1 1 1 [2,] 2 2 2 [3,] 3 3 3 [[2]] V1 V2 V3 [1,] 4 4 4 [2,] 5 5 5 [3,] 6 6 6 [[3]] V1 V2 V3 [1,] 7 7 7 [2,] 8 8 8 [3,] 9 9 9 I'd like to calculate the moving average (interval = 2) i.e. ( x[[1]] + x[[2]] )

[R] scatterplot matrix question

I would like a scatterplot matrix and a correlation matrix for the following set-up. The data (dataframe d) are like this: angle resp -90 182 -60 137 -30 ...etc 0 30 60 90 ...etc I would like each cell in the matrix to be the scatterplot of the responses for each pair of angles (

[R] Regexp: extract first occurrence of date in string

I would like to extract first date from a string: txt - first date is 05.12.2009. Second date is 06.12.2009. txt [1] first date is 05.12.2009. Second date is 06.12.2009. I tried: sub(^.*?\\s(\\d{1,2}\\.\\d{1,2}\\.\\d{4}), \\1, txt, extended=T, perl=T) [1] 05.12.2009. Second date is

Re: [R] Question on Reduce + rollmean

Try apply: library(zoo) # rollmean # test data m - matrix(1:3, 3, 3) x - list(m, m+3, m+6) # convert to array a - array(unlist(x), c(3, 3, 3)); a # apply rollmean and permute to desired form aa - apply(a, 1:2, rollmean, k = 2) aperm(aa, c(2, 3, 1)) The last line outputs: aperm(aa, c(2, 3,

Re: [R] Regexp: extract first occurrence of date in string

Try this which uses a slightly simpler regexp: library(gsubfn) strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]] [1] 05.12.2009 or we could convert it to Date class at the same time where we have assumed month.day.year: strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*, ~ as.Date(x,

Re: [R] Regexp: extract first occurrence of date in string

Thanks, is the same possible using basic gsub/sub/grep etc. functions? -J 2010/1/2 Gabor Grothendieck ggrothendi...@gmail.com: Try this which uses a slightly simpler regexp: library(gsubfn) strapply(txt, (\\d{1,2}\\.\\d{1,2}\\.\\d{4}).*)[[1]] [1] 05.12.2009 or we could convert it to Date

Re: [R] Regexp: extract first occurrence of date in string

Use regexpr to get the offset into the string and its length and then use substr to pick extract it. On Sat, Jan 2, 2010 at 10:43 AM, johannes rara johannesr...@gmail.com wrote: Thanks, is the same possible using basic gsub/sub/grep etc. functions? -J 2010/1/2 Gabor Grothendieck

Re: [R] Regexp: extract first occurrence of date in string

Thanks for the hint, ie. something like this works in this case: txt - first date is 05.12.2009. Second date is 06.12.2009. txt [1] first date is 05.12.2009. Second date is 06.12.2009. l - regexpr(\\d{1,2}\\.\\d{1,2}\\.\\d{4}, txt, perl=T) substr(txt, l, l+9) [1] 05.12.2009 But your

Re: [R] caculate the frequencies of the Amino Acids

Hi fadialnaji, Take a look at the Biostring package in Bioconductor [1] It might be an alternative to do what you want. HTH, Jorge [1] http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html On Fri, Jan 1, 2010 at 11:59 PM, che wrote: may some one please help me to sort

Re: [R] Building static HTML help pages in R 2.10.x on Windows

Steve Rowley wrote: Heinz Tuechler wrote: At 21:40 22.12.2009, Steve Rowley wrote: (a) how to build the static HTML help pages of all currently installed packages under Windows, [...] At least two ways: Way 1: reinstall all those packages from sources using R CMD INSTALL --html Way

Re: [R] How to calculate density function of Bivariate binomial distribution

Thanks milton, I checked some of them, and actually none is what I want. So instead, I wrote a small function for the density of bivariate binomial. Thanks, nykee milton ruser wrote: Hi Nykee, I checked out ??bivariate on my R installed libraries, and found about a hundred of

[R] Query: sampling from a multivariate normal distribution using the singular value decomposition

Dear R-list users, this question is not strictly related to R, but hopefully somebody will be able to answer. In a schematic way, which is the algorithm to sample from a multivariate normal distribution using the singular value decomposition? thank you for your help Stefano AVVISO IMPORTANTE:

Re: [R] scatterplot matrix question

On Sat, 2 Jan 2010, William Simpson wrote: I would like a scatterplot matrix and a correlation matrix for the following set-up. The data (dataframe d) are like this: angle resp -90 182 -60 137 -30 ...etc 0 30 60 90 ...etc I would like each cell in the matrix to be the

[R] filehash - multiple indices via '[' not allowed when using RDS format

Hi, I have been using filehash for a while. It has performed very well. However, recently I found filehash gives an error when I need to do something like db[c(a, b)] when the db is in RDS format. Does any one know a way to get around that? The code below reproduces the error thanks Jeff

Re: [R] scatterplot matrix question

On Sat, Jan 2, 2010 at 4:55 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Sat, 2 Jan 2010, William Simpson wrote: I would like a scatterplot matrix and a correlation matrix for the following set-up. The data (dataframe d) are like this: angle resp -90 182 -60 137 -30

Re: [R] help with for loop

If I understand the query, z - outer(x,x,-) z[lower.tri(z)] ## is what you want. ?outer and ?lower.tri will tell you how to interpret what you get. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org

Re: [R] scatterplot matrix question

William Simpson wrote: On Sat, Jan 2, 2010 at 4:55 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Sat, 2 Jan 2010, William Simpson wrote: I would like a scatterplot matrix and a correlation matrix for the following set-up. The data (dataframe d) are like this: angle resp -90 182

Re: [R] suppress output for meta in package tm

Hi, Peter. Thanks. This works but is not ideal to have an external file. The main reason I want to suppress the output is to speed up the processing time, which capture.output does indeed do. It is a great work around for now. I am using the output to match items in a corpa to a file that

Re: [R] scatterplot matrix question

Now that we are able to help with some more detailed view of your data (although you could have helped helping by making it easier for us to import your data into R), the answer is: I am preparing for the data analysis, writing the code (knowing I may have to modify it later) while the data are

Re: [R] suppress output for meta in package tm

I don't know anything about pkg:tm, but I'll make a couple of comments below. Amber Jaycocks wrote: Hi, Peter. Thanks. This works but is not ideal to have an external file. The main reason I want to suppress the output is to speed up the processing time, which capture.output does indeed do.

Re: [R] scatterplot matrix question

On Jan 2, 2010, at 1:49 PM, William Simpson wrote: Now that we are able to help with some more detailed view of your data (although you could have helped helping by making it easier for us to import your data into R), the answer is: I am preparing for the data analysis, writing the code

Re: [R] scatterplot matrix question

OK thanks David Thanks very much, Uwe. I will try this (on artificial data). I think reshape() requires a library [reshape?]. No. In fact, the reshape package does not have a reshape function. -- David Winsemius, MD Heritage Laboratories West Hartford, CT

Re: [R] suppress output for meta in package tm

Actually if you just use 'capture.output' without specifying a 'file' it will return a character vector with the output which you can just ignore. On Sat, Jan 2, 2010 at 1:51 PM, Peter Ehlers ehl...@ucalgary.ca wrote: I don't know anything about pkg:tm, but I'll make a couple of comments

Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

Your data set has 217 predictors and 166 samples. If you read the vignette on feature selection for this package, you'll see that the default ranking mechanism that it uses for linear models requires a linear model fit. The note that: prediction from a rank-deficient fit may be misleading

[R] Ordering variables in a parallel coordinates plot

Hello all, I am searching for a way in R to re-order variables before presenting them in a parallel coordinates plot. So far I didn't find anything within a R related context on how to do this. I did find some texts talking about how it should be done in general, here is such example:

[R] Rscript: how to suppress all output

How can I suppress ALL output when running Rscript in Terminal? ~/DocumentsRscript test.r I tried options --slave, --vanilla with no success. I get these Loading required package: methods ..etc.. and other output as well. -J sessionInfo() R version 2.9.2 (2009-08-24) i386-apple-darwin8.11.1

Re: [R] suppress output for meta in package tm

Thanks Jim and Peter. Ignoring the filename worked. The process is still slow but a bit improved. I had to slightly modify the substring to match across the two objects. n_corp_file - capture.output(meta(corpa[[n]], URI),file=) n_char - nchar(n_corp_file[1]) n_char_dir - nchar(corpa_dir) #

Re: [R] Rscript: how to suppress all output

Try this on Windows: Rscript test.r 1NUL 2NUL On Sat, Jan 2, 2010 at 3:27 PM, johannes rara johannesr...@gmail.com wrote: How can I suppress ALL output when running Rscript in Terminal? ~/DocumentsRscript test.r I tried options --slave, --vanilla with no success. I get these Loading

Re: [R] Questions bout SVM

Hi, On Fri, Jan 1, 2010 at 1:03 PM, Nancy Adam nancyada...@hotmail.com wrote: Hi everyone, Can someone please help me in these questions?: 1)if I use crossvalidation with svm, do I have to use this equation to calculate RMSE?:      mymodel - svm(myformula,data=mydata,cross=10)      

[R] xyplot: several plots in one creates y-scale problem

Hello, I've been looking for a solution to this problem for some time now but I seem unable to solve it.. so this is the case: I want to plot 4 time series in the same graph using xyplot(). When I do this with xyplot(mydata[,2]+mydata[,3]+mydata[,4]+mydata[,5] ~ mydata[,1], data = mydata,

[R] xyplot: problems with column names legend

Hello! one more question about xyplot. If I have data which have space in the column names, say xyz 123. How do I create a working graph where this text is displayed in the legend key? Now when I try something like xyplot(xyz 123 ~ variable1, data = mydata, ...) I get nothing. Also, is it

Re: [R] Questions bout SVM

Hi Steve, Thanks a lot for your reply.1)I’m still confused which equation (1- sqrt(mean(mymodel$MSE)) OR 2- mean(sqrt(mymodel$MSE)) )is equivalent to sqrt(mean(error**2))?I just want to compute the typical RMSE that is usually used for measuring the performance of regression systems. 2)I’m

Re: [R] xyplot: problems with column names legend

On Jan 2, 2010, at 6:51 PM, Jay wrote: Hello! one more question about xyplot. If I have data which have space in the column names, say xyz 123. How do I create a working graph where this text is displayed in the legend key? Now when I try something like xyplot(xyz 123 ~ variable1, data =

Re: [R] caculate the frequencies of the Amino Acids

Thanks very much the code is working perfectly, but I hope guys that you can help me to do the same thing but by using the loop structure, i want to know if i am doing right, i want to use the loop structure to scan each sequence from the file sequence.txt (the file is attached) to get the

Re: [R] caculate the frequencies of the Amino Acids

On Jan 3, 2010, at 12:28 AM, che wrote: Thanks very much the code is working perfectly, but I hope guys that you can help me to do the same thing but by using the loop structure, i want to know if i am doing right, i want to use the loop structure to scan each sequence from the file

Re: [R] Rscript: how to suppress all output

On Sat, 2 Jan 2010, johannes rara wrote: How can I suppress ALL output when running Rscript in Terminal? ~/DocumentsRscript test.r Rscript test.r /dev/null or equivalent in your shell. But note that Rscript produces no output itself: tystie% touch test.r tystie% Rscript test.r tystie%

[R] Help with function fitdistr in MASS

Hi, R users: I want to fit my data into a normal distribution by using the command fitdistr in MASS. I changed my data class from ts to numeric by class(mydata)=numeric but after using fitdistr, I got the result below fitdistr(mydata,normal) meansd NA NA (NA) (NA) the help

Re: [R] Help with function fitdistr in MASS

I check my data again, and find that: 1. when the class of mydata is ts, I can't compute the sd of it. R returns 'NA'. 2. when I change the class from ts into numeric, R still can't compute the sd of the data. Any suggestion? -- View this message in context:

Re: [R] Help with function fitdistr in MASS

And when I used the command below: fitdistr(mydata, normal, na.rm=TRUE) the result is still the same. -- View this message in context: http://n4.nabble.com/Help-with-function-fitdistr-in-MASS-tp997609p997615.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Please help me!!!! Error in `[.data.frame`(x, , retained, drop = FALSE) : undefined columns selected

thanks, I have reduce the number of descriptors, and the erroe is none, my major is qsar, but what is the criterion to select descritors, and how many descriptors should be selected, It is a problem, I calculate my descriptors troungh E-dragon, and apply the wonderful package caret,but my

[R] Anova in 'car': SSPE apparently deficient rank

I have design with two repeated-measures factor, and no grouping factor. I can analyze the dataset successfully in other software, including my legacy DOS version BMDP, and R's 'aov' function. I would like to use 'Anova' in 'car' in order to obtain the sphericity tests and the H-F