Re: [R] help on Venn's diagram

On 01/31/2010 02:13 PM, Zoppoli, Gabriele (NIH/NCI) [G] wrote: Hello! I have this problem: I want to create a Venn's diagram with three lists of genes'names. The first is all the genome, the second a subset of it comprising all mitochondrial genes, and the third including all genes that

Re: [R] graph help

On 01/31/2010 07:04 AM, Rob Manley wrote: Hello, I'm fairly new to R and having trouble displaying my data graphically to a publishable quality. I have a multivariate data-set (columns all the same length), 8 environmental variables and 3 species diversity variables. I'm simply trying to

Re: [R] format

how about round? ?round -- View this message in context: http://n4.nabble.com/format-tp1457899p1457938.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] drawing a line that shifts from solid to broken

On 01/31/2010 02:33 AM, Jamie Smith wrote: I am graphing longitudinal data from three time points. I'd like to draw a solid line from point 1 to point 2, and then a dashed line from point 2 to point 3. It works if I do it in two steps: first.vector- c(mean(year1$variable1),

[R] RCurl : limit of downloaded Urls ?

Dear Rexperts, I am using R to query google. I am getting different results (in size) for manual queries and queries sent through getForm of RCurl. It seems that RCurl limits the size of the text retrieved (the maximum I could get is around 32 k bits). Any idea how to get around this ?

Re: [R] accessing column and row numbers inside splom in lattice

Roger Levy-2 wrote: When using splom() in the lattice package, I would like to be able to access the row and column number of each individual pairs plot , I found this rather tricky, but Deepayan's http://markmail.org/message/mxbevsxc5orbweu6 might help. Dieter -- View this

Re: [R] format

maybe you are looking for: format(x,drop0trailing=TRUE) Bart -- View this message in context: http://n4.nabble.com/format-tp1457899p1457952.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

Re: [R] For loop into a vectorized form?

Exactly, thanks! -jrara 2010/1/30 David Winsemius dwinsem...@comcast.net: On Jan 29, 2010, at 9:31 AM, johannes rara wrote: How to vectorize this for loop and how can I assign result to vector instead of using print function? as.vector( sapply(mylist$a, function(x)                        

Re: [R] Solving an optimization problem: selecting an optimal subset

Dimitri Shvorob wrote: Same request to Hans: I am afraid I need a little more spoon-feeding following I sent a GAMS script modeling this problem to the NEOS solvers Thanks a lot! If you have access to CPLEX (I mean the commercial program, not Rcplex which is just an interface to

Re: [R] More than on loop??

hello, i appreciate your help, your help, comments, and suggestion really are so helpful to develop not only my R skills, but also my programming language sense. as i said, i am not breaking any academic rules, and this is a softwar i have to develop to deal with my project after two months

Re: [R] RCurl : limit of downloaded Urls ?

Alexis-Michel Mugabushaka wrote: Dear Rexperts, I am using R to query google. I believe that Google would much prefer that you use their API rather than their regular HTML form to make programmatica search queries. I am getting different results (in size) for manual queries and queries

[R] Reshaping matrix of vectors as dataframe

Dear R people, I have to deal with the output of a function which comes as a matrix of vectors. You can reproduce the structure as given below: x - list(c(1,2,4),c(1,3,5),c(0,1,0), c(1,3,6,5),c(3,4,4,4),c(0,1,0,1), c(3,7),c(1,2),c(0,1)) data - matrix(x,byrow=TRUE,nrow=3)

[R] Package ismev, gpd.fit, and interpretation for statistics of extreme values

Dear All, I have a question about package ismev, its function gpd.fit, and interpretation of the results. I used the package ismev to do an extreme value analysis on a fire dataset. Two variables are used in the analysis. The focal variable is acreage burned per fire, ranging from 1 to

Re: [R] Solving an optimization problem: selecting an optimal subset

Thank you very much, Erwin. If I may ask some follow-up questions 1. GAMS R, ad it's just not entirely clear how to move the soltion to R. (At most trivial, how do I bring in the subsettable vector into the solver?) 2. The quadratic objective can be replaced by a linear one by minimizing the

Re: [R] Solving an optimization problem: selecting an optimal subset

To replace an absolute value by two binary variables is an old trick in optimization modeling. I am having trouble Googling it: can anyone suggest a reference, or just explain? Thank you. -- View this message in context:

[R] RBloomberg on Mac Leopard

Hi, I'm running R 2.10.1 GUI 1.31 Leopard build 64-bit (5537). I cannot install RBloomberg on my Mac. After I type: install.packages(RBloomberg, repos=http://R-Forge.R-project.org;) I get the following message: Warning in install.packages(RBloomberg, repos = http://R-Forge.R-project.org;) :

[R] linear models with variance in dependent and independent variables

Dear list, I need to fit a multiple regression in which individual data point in the independent and the dependent variables have an associated variance or standard deviation. To make things clear, instead of having just a table of dependent (X) and independent (Y1, Y2) variable values like

Re: [R] FracSim set.seed

I think you may be out of luck. The randomization is in the C-code of the function. You could recode that and build your own version of the package. Or perhaps the authors would be receptive to a request to make a suitable change. -Peter Ehlers Selwyn McCracken wrote: Hi, I am using the

Re: [R] Reshaping matrix of vectors as dataframe

On Jan 31, 2010, at 9:53 AM, Oliver Gondring wrote: Dear R people, I have to deal with the output of a function which comes as a matrix of vectors. If that is so, then the object below does not represent it, because that is a matrix of _lists_. You can reproduce the structure as

Re: [R] RBloomberg on Mac Leopard

What made you think it was available for the Mac? The R-forge page says: • Intended Audience: Developers • License: GNU General Public License (GPL) • Natural Language: English • Operating System: Windows • Programming Language: R • Topic: Data

Re: [R] Reshaping matrix of vectors as dataframe

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Oliver Gondring Sent: Sunday, January 31, 2010 6:53 AM To: r-help@r-project.org Subject: [R] Reshaping matrix of vectors as dataframe Dear R people, I have to deal with

[R] permutation analysis with randomly chosen subsets of a matrix

Hello, here is the problem: I want to demonstrate that, on average, the Pearson's correlations of a specified subset of genes from a huge list (18,000 columns) are higher than any randomly chosen subset of that list. I would therefore like to do a number of tests between that specified subset

[R] How to split data frame into groups by a list of factors?

Dear R users: I am dealing a data frame x as followings: Date trade_day IV.b IV.a 1 2003-03-0219 0.1724818 0.1815687 2 2003-03-0218 0.1733542 0.1763827 3 2003-03-0219 0.1753308 0.1783653 4 2003-03-0316 0.1751217 0.1781624 5 2003-03-0316

[R] R performance

Dear R Fans, I was recently asking myself how quick R is in code execution. I have been running simulations lately that need quite a time for execution and I was wondering if it is reasonable at all to do more computational extensive projects with R. Of course, it is possible to compare

[R] combining data frames in a list - how do I add breaks?

I'm a week-old R user, and have become stuck trying to create usable CSV outputs for post-processing. I am using the package Rioja, which provides small datasets of results. I am running several analyses in a loop and iteratively adding the results to a *list* (combined). Within each iteration I

[R] (With trepidation): Evaluating expressions with sub expressions again

(For R language geeks only) Folks: I think the best solution for the issue in the Subject line(see 29 January thread on this for details) was the one Jennifer and Gabor previously arrived at: (essentially)don't use R; instead, use a computer algebra system that you can access through an R

Re: [R] R performance

On Sun, Jan 31, 2010 at 7:55 PM, Marc Jekel feuerw...@gmx.de wrote: Dear R Fans, I was recently asking myself how quick R is in code execution. R can be a million times quicker than C code. Badly written C code. Next question... I have been running simulations lately that need quite a time

Re: [R] combining data frames in a list - how do I add breaks?

How about posting your complete set of code that is manipulating the list. Normally when I am using a list, each list element is the result from a test/iteration and then I can use something like 'rbind' at the end. I would not expect the output you are getting with the results extending to the

Re: [R] How to split data frame into groups by a list of factors?

This seems to work fine for me: x - read.table(textConnection( Date trade_day IV.b IV.a + 1 2003-03-0219 0.1724818 0.1815687 + 2 2003-03-0218 0.1733542 0.1763827 + 3 2003-03-0219 0.1753308 0.1783653 + 4 2003-03-0316 0.1751217 0.1781624 + 5

Re: [R] combining data frames in a list - how do I add breaks?

I have several questions on your goals. Why are you planning to post-processing outside of R? Why use CSV files when there are usually better ways to maintain the structure of the data? Why do you want to flatten your tables? It looks like a three-dimensional array would better capture the

Re: [R] permutation analysis with randomly chosen subsets of a matrix

On Jan 31, 2010, at 2:19 PM, Zoppoli, Gabriele (NIH/NCI) [G] wrote: Hello, here is the problem: I want to demonstrate that, on average, the Pearson's correlations of a specified subset of genes from a huge list (18,000 columns) are higher than any randomly chosen subset of that list. I

[R] ggplot2: ... seem to be overwriting each other

Dear list A week ago Dennis Murphy helped me out by showing me some nice ggplot2 tricks . Now I got stuck in a new problem that I can't solve (I have ordered the ggplot2-book). My problem is that I can't add my spline (or geom_smooth) and at the same time control the grid (using

Re: [R] ggplot2: ... seem to be overwriting each other

While I have never used ggplot2, it looks to me like the minimal reproducible code that replicates your problem is: plot - 1 plot + 2 plot + 3 HTH Ray Brownrigg On Mon, 01 Feb 2010, Eric Fail wrote: Dear list A week ago Dennis Murphy helped me out by showing me some nice ggplot2 tricks .

[R] Help with R in ubuntu

Dear R users: Maybe it is a silly question, but I'm don't understand what am I doing wrong. In a new karmik koala ubuntu installation I compile the last patched 2.10.1 version of R. Every thing was right (I install all the dev libraries I need). First I type: ./configure --enable-R-shlib

[R] Help with R in ubuntu (more organized)

Dear R users: Maybe it is a silly question, but I'm don't understand what am I doing wrong. In a new karmik koala ubuntu installation I compile the last patched 2.10.1 version of R. Every thing was right (I install all the dev libraries I need). First I type: ./configure --enable-R-shlib

[R] Help with R in ubuntu (more organized 2)

Dear R users: Maybe it is a silly question, but I'm don't understand what am I doing wrong. In a new karmik koala ubuntu installation I compile the last patched 2.10.1 version of R. Every thing was right (I install all the dev libraries I need). First I type: ./configure --enable-R-shlib

Re: [R] Solving an optimization problem: selecting an quot;optimalquot; subset

Dimitri Shvorob dimitri.shvorob at gmail.com writes: Thank you very much, Erwin. If I may ask some follow-up questions 1. GAMS R, ad it's just not entirely clear how to move the soltion to R. (At most trivial, how do I bring in the subsettable vector into the solver?) 2. The quadratic

Re: [R] (With trepidation): Evaluating expressions with sub expressions again

On Sun, 31 Jan 2010, Bert Gunter wrote: (For R language geeks only) Folks: I think the best solution for the issue in the Subject line(see 29 January thread on this for details) was the one Jennifer and Gabor previously arrived at: (essentially)don't use R; instead, use a computer algebra

[R] Using apply function on duplicates in a data.frame

Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0 pSysX_49_8_1 pSysX_49 pSysX_49 4042 3843 0

Re: [R] Using apply function on duplicates in a data.frame

On Jan 31, 2010, at 6:05 PM, Sunny Srivastava wrote: Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like ProbeUID ControlType ProbeName GeneName SystematicName 1665 1577 0 pSysX_50_22_1 pSysX_50 pSysX_50 5422 5147 0

[R] Installling source package

Hi R users, Im trying to install XML source package (in window platform) using the following command. *install.packages(pkgs = C:\\Documents and Settings\\skang\\Desktop\\Softwares\\R\\Library\\XML_2.6-0.tar.gz, repos = NULL, type = source)* and get the following result. gzip: stdin: unexpected

Re: [R] ggplot2: ... seem to be overwriting each other

Hi Dennis (cc Lucien Lemmens and the r-help) Thank you for your help. I got help from Mr. Lucien Lemmens as well, and thanks to him to (again). The thing is, if, my working example, is run line by line, it overwrites ... or one thing overwrites the next. However both you and Lucien

Re: [R] combining data frames in a list - how do I add breaks?

With Jim's help, the solution is as follows... -Original Message- From: jim holtman [mailto:jholtman * at sign * gmail.com] Sent: Sunday, January 31, 2010 5:41 PM To: Euan Reavie Subject: Re: [R] combining data frames in a list - how do I add breaks? Your 'combined' was a 'list of a

Re: [R] Installling source package [SEC=UNCLASSIFIED]

Steven, Package 'XML_2.6-0.tar.gz' is the Linux version, it doesn't unpack in Windows. For Windows you need to download and instal: 'XML_2.6-0.zip'. Which is available from: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10/ Cheers, Augusto

Re: [R] (With trepidation): Evaluating expressions with sub expressions again

Thankyou Thomas. Yes, I was motivated by bquote(). It is so slick (to some extent, still too slick for me). I wanted to do it nonrecursively because it's both clearer (I think) and maybe even more efficient (though I doubt this is detectable in any case). Bert Gunter Genentech Nonclinical

[R] Is there a way to make blocks of code independent from each other?

I'm wondering if there is a way to make blocks of code independent from each other. Please see the following example for what I mean. x=1 ## is there a way to make the following assignment not affect the above x? ## in C++, I can use {} to make the effect local. Is there an equivalent construct

Re: [R] Is there a way to make blocks of code independent from each other?

Put in a function what you would have put in the {} and execute the function x=1 myf=function() { x=3 do something with new value of x ... } myf() print(x) # it will be 1 On 1/31/2010 5:56 PM, Peng Yu wrote: I'm wondering if there is a way to make blocks of code independent from each

[R] Loading data from folder

Hi, I am trying to load csv type data from a folder. However, rather than syntax that simply loads one file at a time I was wondering if there is a method that loads all data from a specific folder. For instance, I have the following data files in a folder nebraskaStats:

Re: [R] Is there a way to make blocks of code independent from each other?

Use 'local' x - 1 local({ + x - 3 + print(x) + }) [1] 3 print(x) [1] 1 On Sun, Jan 31, 2010 at 8:56 PM, Peng Yu pengyu...@gmail.com wrote: I'm wondering if there is a way to make blocks of code independent from each other. Please see the following example for what I mean. x=1

Re: [R] Loading data from folder

Something like the following might work. YOu can use 'choose.dir()' to get the directory: files - list.files(path=yourDir) result - do.call(rbind, lapply(files, read.csv)) On Sun, Jan 31, 2010 at 9:10 PM, Mark Altaweel maltaw...@anl.gov wrote: Hi, I am trying to load csv type data from a

Re: [R] Loading data from folder

Hi, looks like the list.files() method was the key to my problem. With that, I was able to just loop through the files variable and get the file names to load Thanks for your help. Mark On Jan 31, 2010, at 8:23 PM, jim holtman wrote: Something like the following might work. YOu can use

[R] String Comparison

a - as.character(c(a, b, c, d, e)) b - as.character(c(d, a, c, e, f, b)) How would I get a list of only the unique values of these two character vectors. I would like the output a b c d e f there is no reason to have these in order. I am looking at to character vectors of genes and I would like

Re: [R] Loading data from folder [SEC=UNCLASSIFIED]

Hi Mark, You can use: all_files - dir(pattern=Data) One_file - all_files[1] Is this what you want? Cheers, Augusto Augusto Sanabria. MSc, PhD. Mathematical Modeller Risk Impact Analysis Group Geospatial Earth Monitoring Division Geoscience

Re: [R] String Comparison

How about union() ? a - as.character(c(a, b, c, d, e)) b - as.character(c(d, a, c, e, f, b)) union(a,b) [1] a b c d e f HTH, Jorge On Sun, Jan 31, 2010 at 10:31 PM, stephen sefick wrote: a - as.character(c(a, b, c, d, e)) b - as.character(c(d, a, c, e, f, b)) How would I get a list of

Re: [R] Using apply function on duplicates in a data.frame

On Sun, Jan 31, 2010 at 5:05 PM, Sunny Srivastava research.b...@gmail.com wrote: Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like     ProbeUID ControlType     ProbeName GeneName SystematicName 1665     1577           0 pSysX_50_22_1 pSysX_50       pSysX_50 5422  

Re: [R] Dear professor

This is the R-help list, not the list for S-Plus. And note that you are using a 6 year old version of the Design library. Note that if you ever use R, use the rms package in place of Design. Frank Tian Xu wrote: Dear professor： When I used s-plus to run a Buckley-James Multiple Regression

[R] How to globally enable warning messages or stop the program if NA is encountered?

By default, my R functions run silently if NA is encountered? I would like them to give me some message when NA is encountered by default. Note that I could check each intermediate variable by something like is.na(). But this is not manageable for big programs, so I'd like a way to check NA

Re: [R] Using apply function on duplicates in a data.frame

Thanks a lot. All the three approaches work for me! On Sun, Jan 31, 2010 at 10:43 PM, hadley wickham h.wick...@gmail.comwrote: On Sun, Jan 31, 2010 at 5:05 PM, Sunny Srivastava research.b...@gmail.com wrote: Dear R-Helpers, I have a data.frame (df) and the head of data.frame looks like

[R] Merging vector data into one file

Hi, I had another question. If you had say a vector (e.g., called data) with 235 elements and each element looked like the following data[[1]] Column A-BColumn Z-SColumn A-S 1 25 ... data[[2]] Column Z-BColumn A-S

[R] Hierarchical data sets: which software to use?

Dear R-helpers, I’m writing for advice on whether I should use R or a different package or language. I’ve looked through the R-help archives, some manuals, and some other sites as well, and I haven’t done too well finding relevant info, hence my question here. I’m working with hierarchical data

Re: [R] Installling source package

Most likely you have a corrupted tarball, so I would compare its size with that on the CRAN master (which to me looks like 680366 bytes). Note though that you need to get XML to work on Windows - to get appropriate versions of libxml2 and its dependencies iconv and zlib. - to make changes to

Re: [R] Merging vector data into one file

Altaweel, Mark R. wrote: I had another question. If you had say a vector (e.g., called data) with 235 elements and each element looked like the following data[[1]] Column A-BColumn Z-SColumn A-S 1 25 ... data[[2]]