[R] [R-pkgs] Version 1.3.0 of apcluster package on CRAN

Dear colleagues, This is to inform you that Version 1.3.0 of the R package apcluster has been released on CRAN yesterday. We did a major extension and overhaul of the package. Most importantly, we added Leveraged Affinity Propagation in fulfillment of multiple users requests. It should now be

Re: [R] Problem getting loess tricubic weights

Thank you Mr Gunter! I will look into it. On Wed, Jan 9, 2013 at 11:59 AM, Bert Gunter gunter.ber...@gene.com wrote: As this does not seem to have been answered... I believe you may misunderstand how loess works. The tricube weights are part of the smoothing algorithm and change with each

Re: [R] plot residuals per factor

Hi, I forgot to mention: levels(dat1$d) #[1] 1 2 3 4 5 Suppose, if I use different levels library(car) dat1$d1-recode(dat1$d,1='A';2='B';3='C';4='D';5='E')  levels(dat1$d1) # check the order of the levels #[1] A B C D E mypath-file.path(/home/arun/Trial1,paste(catalin_,LETTERS[1:5],.jpg,sep=))  

[R] How to use 'glmnet' or 'lars' package to select features?

Hi all, I am a newbie of statistics. I want to make lasso feature selection on a bioinfomatics data set. I know I can use 'glmnet' or 'lars' package to do that. However, the glmnet() and lars() function return a model object. I don't know how to use this object to make feature selection. What

[R] t-test behavior given that the null hypothesis is true

Dear all, I observer a strange behavior of the pvalues of the t-test under the null hypothesis. Specifically, I obtain 2 samples of 3 individuals each from a normal distribution of mean 0 and variance 1. Then, I calculate the pvalue using the t-test (var.equal=TRUE, samples are independent). When

Re: [R] Applying a user-defined function

Hi Pradip, I didn't check the mode at that time.   It generated a matrix test1$newcols- sapply() You can do this: test2-data.frame(test1[,-7],test1$newcols) str(test2) #'data.frame':    51 obs. of  9 variables: # $ ObtMj_P   : num  49.6 55 52.5 50.5 51.1 55.1 56.3 53.6 53.5 52.7 ... # $

Re: [R] plot x-axis DateTime NOT evenly spaced

Thanks! it was really helpful. soichi 2013/1/7 arun smartpink...@yahoo.com Hi, Try this: dat1-read.table(text=1 2012-07-01 00:57:54 +0900156 2 2012-07-01 01:07:41 +0900587 3 2012-07-01 01:09:31 +0900110 4 2012-07-01 01:18:42 +0900551 5 2012-07-01 01:39:01 +09001219

Re: [R] how to label two figures in the same chunk independently with knitr

Dear Yihui, thanks a lot for your kind reply. Your solution is very elegant and versatile. However, there is a point that is obscure to me and I didn't manage to fully understand them after looking at the Knitr manual and graphic manual. The issue concerns the hook: *knit_hooks$set(par =

[R] deparse substitute

Hi, I'm writing a function that needs the input names (as characterstrings) as part of the output. With deparse(substitute( ) ) that works fine, until I replace all zeros with 0.001 (log is calculated at some time): tf - function(input) { input[input==0] - 0.001 ;

Re: [R] t-test behavior given that the null hypothesis is true

On 09-Jan-2013 08:50:46 Pavlos Pavlidis wrote: Dear all, I observer a strange behavior of the pvalues of the t-test under the null hypothesis. Specifically, I obtain 2 samples of 3 individuals each from a normal distribution of mean 0 and variance 1. Then, I calculate the pvalue using the

[R] select partial name and full name columns

Hi, I have the following function: getDataFromDVFileCustom - function (file, hasHeader = TRUE, separator = \t) { DVdatatmp - as.matrix(read.table(file, sep = \t, fill = TRUE, comment.char = #, as.is = TRUE, stringsAsFactors = FALSE, na.strings = NA)) DVdatatmper - as.matrix(DVdatatmp[ ,

Re: [R] deparse substitute

On 13-01-09 5:03 AM, Berry Boessenkool wrote: Hi, I'm writing a function that needs the input names (as characterstrings) as part of the output. With deparse(substitute( ) ) that works fine, until I replace all zeros with 0.001 (log is calculated at some time): tf - function(input) {

[R] R-Forge package check error. Package dependencies on linux platform

Dear All, I've got an error in R-Forge package check. when it checks with windows and mac platform it doesn't give an error except one note which is regarding to maintainer. However, it doesn't check correctly regarding to Linux platform and gives me the following error. Due to this error I

Re: [R] error in a abline loop

Hi -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of arun Sent: Tuesday, January 08, 2013 3:30 PM To: Elaine Kuo Cc: R help Subject: Re: [R] error in a abline loop HI Elaine, In the data you sent to me, it had 5 levels

[R] update.packages problem

I've updated to R-devel on my development machine and have lots of packages. The update.packages() script ends up with 33 failures, all due to out-of-order reloading. That is, if package abc depends on package xyz, then the reinstall of abc fails with a message that version of xyz is built

Re: [R] update.packages problem

On 09/01/2013 12:52, Terry Therneau wrote: I've updated to R-devel on my development machine and have lots of packages. The update.packages() script ends up with 33 failures, all due to out-of-order reloading. That is, if package abc depends on package xyz, then the reinstall of abc fails with

Re: [R] problems regarding the latest version of the package BRugs

I think we a much clearer statement of the problem This link provides some suggestions on how to frame the problem https://github.com/hadley/devtools/wiki/Reproducibility John Kane Kingston ON Canada -Original Message- From: mcmoumi...@gmail.com Sent: Wed, 9 Jan 2013 08:55:25

[R] Need an advise for bayesian estimate

Hi R bayesians, I need an advise how to resolve the two different estimates applying a traditional glm (TG) and a bayes glm (BG), and different results depending on the data formats of response data and the prior specs using bayesglm in R. I'm not familiar with bayes estimate and my colleague

Re: [R] how to count A, C, T, G in each row in a big data.frame?

forgot the data. this will count the characters; you can add logic with 'table' to count groups x - structure(list(name = c(Gga_rs10722041, Gga_rs10722249, Gga_rs10722565, Gga_rs10723082, Gga_rs10723993, Gga_rs10724555, Gga_rs10726238, Gga_rs10726461, Gga_rs10726774,

Re: [R] t-test behavior given that the null hypothesis is true

Ah! You have aqssigned a parameter equal.var=TRUE, and equal.var is not a listed paramater for t.test() -- see ?t.test : t.test(x, y = NULL, alternative = c(two.sided, less, greater), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) Try it instead with

Re: [R] how to count A, C, T, G in each row in a big data.frame?

If test is the structure, will test2-sapply(test[,-c(1:4)],function(x){table(t(x))}) to what you want? On 09.01.2013, at 15:48, jim holtman wrote: forgot the data. this will count the characters; you can add logic with 'table' to count groups x -

Re: [R] Need an advise for bayesian estimate

Hi Kyong, Even if it is not -as can be inferred from what you said- a homework or assignment related query (and the group has clear policy against such requests), the questions you posed have nontheless very little to do specifically with R. Instead, they are about statistics. In this respect,

[R] Reminder: useR meetup group in Munich, Germany

Dear all, this is a short reminder for the Meetup Munich useR group. Next week Wednesday (16th January 2013) we have our first meeting with two talks about Reporting and Reproducible Research with R and some ideas for an R certification. More information at

[R] Basic loop programming

Hi all, newbie question: I am trying to set up a very simple loop without succeeding. Let's say I have monthly observation of two variables for a year - Sales_2012_01, Sales_2012_02, Sales_2012_03, (total sales for jan 2012,feb 2012, etc.) - Customers_2012_01, Customers_2012_02,

Re: [R] Basic loop programming

Hi -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Paolo Donatelli Sent: Wednesday, January 09, 2013 5:03 PM To: r-help@r-project.org Subject: [R] Basic loop programming Hi all, newbie question: I am trying to set up a

Re: [R] Basic loop programming

Hi Paolo, You say you have monthly observations of two variables, say Sales and Customers. Then, what you should have is something like this: Year Month Sales Customer 2012Jan ss_12.1 cc_12.1 2012Feb ss_12.2 cc_12.2 ... ... ... ... 2013Jan

Re: [R] rJava Error

On Jun 27, 2012, at 12:16 AM, fabin.ittiachan wrote: Hi, I'm receiving an error when I am trying to install rJava. I have posted the error below. Your R was not compiled with --enable-R-shlib so you can't use JRI (see http://rforge.net/rJava). You can either disable JRI (if you don't

Re: [R] Java, rJava, and Windows x64

On Oct 29, 2012, at 11:17 AM, Robert Baer wrote: When running [1] R version 2.15.1 (2012-06-22) x86_64-pc-mingw32, rJava fails. I have installed both the 32-bit and 64-bit versions of Java 7 update 9. library(rJava) Error : .onLoad failed in loadNamespace() for 'rJava', details: call:

[R] weighted factor analysis

hello there, I am trying to use a weight variable in a factor analysis but apparently the factanal command does not have a weight option. Any way to this? Thanks for your suggestions, V [[alternative HTML version deleted]] __

Re: [R] select partial name and full name columns

Hi Arun, thank-you for your suggestion. I made a mistake previously when I suggested that there was a prefix in front of 00060_3 possibly suggesting that it was a string of characters rather than numbers. The prefix in front of 00060_3 is actually two numbers, see the examples below:

Re: [R] how to count A, C, T, G in each row in a big data.frame?

Sorry, you wanted rows, i wrote for columns #rows would be: test2-apply(test[,-c(1:4)],1,function(x){table(t(x))}) #find single values in a row sapply(test2,function(row){ allVars-paste(names(row),collapse=) u - unique(strsplit(allVars,)[[1]])

Re: [R] Integrating Java, C++ and R

On Jan 4, 2013, at 11:41 AM, Dirk Eddelbuettel wrote: On 4 January 2013 at 16:57, Suzen, Mehmet wrote: | On 4 January 2013 11:36, Royden Fernandes roydens...@gmail.com wrote: | Hi, | | I am able to integrate C++ and R through RInside library. However when I | | Questions regarding

Re: [R] select partial name and full name columns

Hi Arun, thanks again for your assistance. Previously I did not read the files with the headers so I could not search for those prefixed names. I corrected my mistake and the code that you suggested does work. Irucka -Original Message- From: arun [smartpink...@yahoo.com] Sent: 1/9/2013

[R] R encrypt/decrypt

Hello, I am working on a web system (php) that uses R in the backend, and we need some basic fast encryption/decryption for the underlying mysql database that can be used by both R AND php. It does not need to be top-of-the-line, but just provide some basic level of fast

Re: [R] select partial name and full name columns

Hi, May be this is creating the problem: set.seed(15)

[R] problem adding curve/abline

Hey, I'm stuck on something I already did before (just a different kind of database), and whatever I try, it doesn't work anymore. So thanks for your help. Here's how my data approximately looks like: year season replicate sizefreq weight 2000 summer

Re: [R] Basic loop programming

HI, If you have more than one observation per month, you could do this: dat1-read.table(text= Year Month    Sales    Customer 2011    Jan    150 35 2011    Jan    125 40 2011    Feb    130 45 2011    Feb    135 25 2012    Jan    100 25 2012    Jan    150 35 2012    Feb   

Re: [R] Applying a user-defined function

Hi Pradip, Another way to get the results would be:  res-cbind(test1,do.call(data.frame,lapply(test1[,seq(1,6,2)],CutQuintiles)))  colnames(res)[7:9]-paste(newcols_,colnames(res)[7:9],) sapply(res,is.factor)  #  ObtMj_P   ObtMj_SE   ExpPrevMed_P   #  

Re: [R] select partial name and full name columns

Hi, You can use the same code: set.seed(15)   dat1-data.frame(sample(1:10,5,replace=TRUE),sample(20:30,5,replace=TRUE),sample(1:15,5,replace=TRUE),sample(1:8,5,replace=TRUE),datetime=as.POSIXct(paste(rep(6/3/2011,5),c(0:00,0:30,0:35,0:40,0:45)),format=%m/%d/%Y %H:%M))  

Re: [R] R encrypt/decrypt

Dear All, I am wondering if there is a script in R or Python that can convert shape files to KML oKMZ files. I used a free online shp2kml.exe file my locations all went to Africa. But, I know they are in the USA. Thanks, Alemu [[alternative HTML version deleted]]

Re: [R] [solved] t-test behavior given that the null hypothesis is true

Hi Ted, yes this was the problem. Thank you very much. best idaios On Wed, Jan 9, 2013 at 4:51 PM, Ted Harding ted.hard...@wlandres.netwrote: Ah! You have aqssigned a parameter equal.var=TRUE, and equal.var is not a listed paramater for t.test() -- see ?t.test : t.test(x, y = NULL,

Re: [R] Using objects within functions in formulas

Hello, Try the following. It uses argument 'data' to pass the data.frame w2. In the function below, I've changed the pastes to two lines of code because the first one changes the way the formula is put together. test1 - function(x2, y2, w2) { #print(str(w2)) p1 - paste((1|,

Re: [R] how to label two figures in the same chunk independently with knitr

Hi Francesco, This is an advanced topic in knitr; it is called a chunk hook: http://yihui.name/knitr/hooks Sorry for the confusion on the name par; you can call it anything, e.g. mypar knit_hooks$set(mypar = function(before, options, envir) { if (before) par(mar = c(4, 4, .1, .1)) })

Re: [R] Using objects within functions in formulas

On Jan 9, 2013, at 8:53 AM, Aidan MacNamara wrote: Dear all, I'm looking to create a formula within a function to pass to glmer() and I'm having a problem that the following example will illustrate: library(lme4) y1 = rnorm(10) x1 = data.frame(x11=rnorm(10), x12=rnorm(10), x13=rnorm(10)) x1

[R] writing to .xlsx

Dear r helpers; I'm interested in reading from and writing to large .xlsx files fairly regularly. (Why, the naysayers may ask - and the answer is basically colleagues and clients who prefer that format). I've tried out the XLConnect and xlsx libraries, but the java implementation they use just

[R] Need help setting up a mirror

Hello. I am trying to follow the instructions herehttp://mirror.fcaglp.unlp.edu.ar/CRAN/ to set up a mirror at my company as my developers are not allowed to go outside our firewall to download R packages. I am not having much success in getting this to work. Here is how I configured my

Re: [R] writing to .xlsx

Can you use '.xls' format files? If so, XLConnect works pretty good for those. If you are using '.xlsx' format (zip files internally), XLConnect takes much more CPU and memory to handle them. On Wed, Jan 9, 2013 at 2:19 PM, Benjamin Caldwell btcaldw...@berkeley.edu wrote: Dear r helpers; I'm

Re: [R] R encrypt/decrypt

I suggest looking at mcrypt. There is a PHP module, and you could either call out from R to the mcrypt program or use libmcrypt and C calls.It supports AES, and other standard things. There's no real saving of effort in using weaker ciphers, and you really don't want to be implementing the

Re: [R] weighted factor analysis

It depends on what sort of weights you have, but one approach is to construct a weighted covariance matrix and then run factanal() on it. That's what svyfactanal() in the survey package does. The difficult part is the tests: you need to specify the sample size, and in the presence of weights it

[R] Sweave, Texshop, and sync with included Rnw file

Hello everyone. I am in the process of writing a book in Latex with Texshop, on Mac. This book contains a lot of R code, hence the need to use Sweave. I was able to compile Rnw files, and to sync back and forth from the pdf to the source Rnw. My problem now is that the book is divided in

[R] We've posted our 2013***R Courses*** by XLSolutions Corp at 9 USA Cities: San Francisco, New York, Washington DC, Houston, Boston, Las Vegas, Seattle, etc

Happy New Year ! XLSolutions January-February 2013 R courses schedule is now available online at 9 USA cities for with 13 new courses: *** Suggest a future course date/city (1) R-PLUS: A Point-and-Click Approach to R (2) S-PLUS / R : Programming Essentials. (3) R/S+ Fundamentals and Programming

[R] Random Rectangles

Hi, Just curious. Has anyone out there ever written a script to generate 100 random rectangles such as the ones shown on this page? http://www2.math.umd.edu/~jlh/214/Random%20Rectangles.pdf Thanks. D. -- View this message in context:

Re: [R] R encrypt/decrypt

On 9 January 2013 18:59, Ramiro Barrantes ram...@precisionbioassay.com wrote: I am working on a web system (php) that uses R in the backend, and we need some basic fast encryption/decryption for the underlying mysql database that can be used by both R AND php. It does not need to be

Re: [R] writing to .xlsx

On Wed, Jan 9, 2013 at 2:19 PM, Benjamin Caldwell btcaldw...@berkeley.edu wrote: Dear r helpers; I'm interested in reading from and writing to large .xlsx files fairly regularly. (Why, the naysayers may ask - and the answer is basically colleagues and clients who prefer that format). I've

[R] graphical distance matrix

Dear R-family, I made a distance matrix of about 2000 stations. its extremely hard to visualize the details of that matrix. I heard that there is a way in R to represent the details of distance matrix graphically. more precisely, different sections of our distance matrix can be presented in

Re: [R] R encrypt/decrypt

Dear Suzen, Thank you for your reply. What I meant was that some fields in the database will be encrypted (the data for those fields will be entered via php web interface and then encrypted and stored on the mysql db), and then I will use R to read such database and do appropriate

Re: [R] Sweave, Texshop, and sync with included Rnw file

I believe RStudio has done a fairly good job in terms of the synchronization. If you have to stick to TeXShop, I do not have any ideas on how to make it work with Sweave child documents. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of

Re: [R] incrementation within ifelse

Damien, You don't give an example of what your data frame looks like or what you want the new column to look like (given that example data), but I created an example data frame for z, and wrote a few lines of code to add a new column. Check it out and see if it comes close to doing what you

[R] How to estate the correlation between two autocorrelated variables

Dear R users, In my data, there are two variables t1 and t2. For each observation of t1 and t2, two location indicators (x, y) were provided. The data format is #x y t1 t2 Since the both t1 and t2 are depended on x and y, t1 and t2 are autocorrelated variables. My question is how to

Re: [R] Sweave, Texshop, and sync with included Rnw file

Hi Yihui, yes, RStudio works flawlessly with synchronization, but working with it I will lose all the features of a full-fledged tex editor, first of all BibDesk integration. Texworks can also do two-way sync in Rnw, and I tried to switch configurations but with no luck. In texworks I am using

Re: [R] R encrypt/decrypt

Hello Ramiro, I am still not sure why do you need to encrypt/decrypt data in R. One can encrypt/decrypt data in the SQL server side. https://dev.mysql.com/doc/refman/5.5/en/encryption-functions.html If your concern is on the web traffic, again, sql servers supports SSL

Re: [R] Basic loop programming

Yes, R is a different language, and has different syntax and different built-in functions, so, yes it works differently. If you want to do it the same way in R as in that other language, you have to use a different method for constructing the variable names inside the loop. Here's an example,

Re: [R] GLMM post- hoc comparisons

El día 08/01/2013 a las 12:40, Silvina Velez sve...@mendoza-conicet.gob.ar escribió: Hi All, I have data about seed predation (SP) in fruits of three differents colors (yellow, motted, dark) and in two fruiting seasons (2007, 2008). I performed a GLMM (lmer function, lme4 package) and the

Re: [R] Sweave, Texshop, and sync with included Rnw file

Hi Perhaps you need to make a master file and call the chapter files from it eg (just copying the relevant section from my master GClimate12.Rnw file) latex preliminaries + R options + begin % plots \SweaveInput{GClimate12RX.Rnw} % Soil 300 % 15

Re: [R] Using objects within functions in formulas

David Winsemius dwinsemius at comcast.net writes: On Jan 9, 2013, at 8:53 AM, Aidan MacNamara wrote: I'm looking to create a formula within a function to pass to glmer() and I'm having a problem that the following example will illustrate: library(lme4) y1 = rnorm(10) x1 =

Re: [R] writing to .xlsx

On Jan 9, 2013, at 2:45 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Wed, Jan 9, 2013 at 2:19 PM, Benjamin Caldwell btcaldw...@berkeley.edu wrote: Dear r helpers; I'm interested in reading from and writing to large .xlsx files fairly regularly. (Why, the naysayers may ask -

Re: [R] How to estate the correlation between two autocorrelated variables

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Zhiqiu Hu Sent: Wednesday, January 09, 2013 1:45 PM To: r-help@r-project.org Subject: [R] How to estate the correlation between two autocorrelated variables Dear R users,

Re: [R] writing to .xlsx

Folks, Thanks for your input. I'm pretty comfortable with the options for writing to .xls; I'm interested in 1. Something that can write to .xlsx for the larger supported dimensions, as Marc guessed; but of course he's right that .csv would work very well if that was the main goal. I'm really

Re: [R] how to count A, C, T, G in each row in a big data.frame?

In fact I want to calculate the gene frequency of each SNP. The key problems are that: 1. my data.frame is large ,about 50,000 rows. So it is so slow to split() it by row 2 .The allele in each SNP (each row) are different.Some are A/G, some are G/C. It is a little bit embarrassed for me to

Re: [R] how to count A, C, T, G in each row in a big data.frame?

Thanks a lot. The problem is that I don't know how to handle the output list as I want calculate the frequency of A or G or T or C by row. Yao He 2013/1/10 Jessica Streicher j.streic...@micromata.de: Sorry, you wanted rows, i wrote for columns #rows would be:

Re: [R] how to count A, C, T, G in each row in a big data.frame?

Can you get what you need from the following, where 'd' is your data.frame, the first four columns of which are irrelevant to this problem? dd - d[,-(1:4)] ; table(rownames(dd)[row(dd)], unlist(dd)) AA AG CC CT GA GG GT TC TG TT 27412 29 10 0 0 13 1 0 0 0 0

Re: [R] how to count A, C, T, G in each row in a big data.frame?

It is really a good output. Maybe I could go on with this output. Everytime I understand R further from your help. The first four cols are irrelevant. It is a negligence 2013/1/10 William Dunlap wdun...@tibco.com: Can you get what you need from the following, where 'd' is your data.frame, the

[R] SRS, Stratified, and Cluster sampling

Hi, Has anyone done (or know of) any nice R activities that help introductory students ( and teachers :) ) better understand the concepts of simple vs stratified vs cluster sampling? Any links? David -- View this message in context:

[R] piece-wise linear regression nls function

windows 7, R 2.12 I am trying to run a piecewise linear regression with a single knot, i.e. a regression composed of two straight lines where the two lines intersect at an x value given by the variable knot. I wish to estimate the slope of both lines, the value of knot, the x value where the

Re: [R] multiple versions of function

On Jan 9, 2013, at 1:00 PM, ivo welch wrote: mea culpa. f - function(...) { ## parse out the arguments and then do something with them } ## all of these should result in the same actions f(2,3) ## interprets a to be first and b to be second f(a=2,b=3) f(b=3,a=2)

Re: [R] Sweave, Texshop, and sync with included Rnw file

On 13-01-09 3:25 PM, michele caseposta wrote: Hello everyone. I am in the process of writing a book in Latex with Texshop, on Mac. This book contains a lot of R code, hence the need to use Sweave. I was able to compile Rnw files, and to sync back and forth from the pdf to the source Rnw. My

Re: [R] piece-wise linear regression nls function

On Jan 9, 2013, at 5:33 PM, John Sorkin wrote: windows 7, R 2.12 I am trying to run a piecewise linear regression with a single knot, i.e. a regression composed of two straight lines where the two lines intersect at an x value given by the variable knot. I wish to estimate the slope of

Re: [R] Random Rectangles

On 01/10/2013 07:37 AM, David Arnold wrote: Hi, Just curious. Has anyone out there ever written a script to generate 100 random rectangles such as the ones shown on this page? http://www2.math.umd.edu/~jlh/214/Random%20Rectangles.pdf Hi David, There are a number of ways to generate random

Re: [R] graphical distance matrix

On 01/10/2013 07:50 AM, eliza botto wrote: Dear R-family, I made a distance matrix of about 2000 stations. its extremely hard to visualize the details of that matrix. I heard that there is a way in R to represent the details of distance matrix graphically. more precisely, different sections

Re: [R] how to count A, C, T, G in each row in a big data.frame?

Hi arun Then how could spilt them and get a table of letters count such as: id AA AG CC CT GA GG GT TC TG TT id A T C G #1 27412 81 0 0 25 #2 27413 0 77 29 0 Thanks 2013/1/10 arun smartpink...@yahoo.com: Hi Yao, You could also use: library(reshape2) dd-dat1[,-(1:4)]

Re: [R] how to count A, C, T, G in each row in a big data.frame?

Here is one option (not the best, but does the job): foo - function(x) table(factor(unlist(strsplit(as.character(x), )), levels = c('A','C','G','T'))) t(apply(d[, -c(1:4)], 1, foo)) What's wrong with Jim Holtman's solution? HTH, Jorge.- On Thu, Jan 10, 2013 at 3:46 PM, Yao He wrote: Hi

[R] ./R: error while loading shared libraries

Hi,   I have installed R on linux using a non root account.   I am getting this error when trying to use it : ./R: error while loading shared libraries: libRblas.so: cannot open shared object file: No such file or directory   Linux version I am using : Linux version 2.6.32-131.17.1.el6.x86_64

[R] Determining sample size from power function

Hello, I am trying to get the power function to report the sample size rather than the power. My goal is to input a variety of values for theta and then for the power function to report the corresponding sample sizes. I haven't had much luck trying to create my own function, something along

Re: [R] multiple versions of function

mea culpa. f - function(...) { ## parse out the arguments and then do something with them } ## all of these should result in the same actions f(2,3) ## interprets a to be first and b to be second f(a=2,b=3) f(b=3,a=2) f(data.frame(a=2,b=3)) f(data.frame(b=3,a=1)) On Tue, Jan 8, 2013 at

[R] Interpreting Rasch models

I'm testing an education assessment (evaluating quantitative skills in biology students) for reliability. I used cronbach's alpha, but got a really low alpha which I think is likely due to my small number of questions (12) and the fact that the questions are of varying difficulty. After a lot of

[R] Parameter estimates for each observation (ordered choice)

I have several demographic variables with which I want to explain the ordered choice of individuals within a survey in an ordered choice (probit or logit, this is not important) framework. Standard ordered choice estimations of course just give me aggregate/average parameter estimates. For my task

Re: [R] Determining sample size from power function

Dear Kaveh, Take a look at http://www.statmethods.net/stats/power.html HTH, Jorge.- On Thu, Jan 10, 2013 at 3:21 PM, Kaveh Zakeri wrote: Hello, I am trying to get the power function to report the sample size rather than the power. My goal is to input a variety of values for theta and