[R] R Instance on Amazon EC2

I have built a few R servers on Amazon's EC2 infrastructure and rolled a pre-packaged instance of Ubuntu 64 with R ready to go. These instances are available with various levels technical support (for the server, not R itself). For those of you who want to get work done with R and don't want t

[R] User defined function's argument as Subset function's input

Dear R users, I have a data where I desire to subset according to certain conditions. However, the script is very messy as there are about 30 distinct conditions. (i.e. same script but with different conditions) I would like to make a user defined function so that I can input the desired conditi

Re: [R] How to call R routines in C++`

On 3 September 2009 at 20:41, lehe wrote: | Hi, | I have some results generated in my C++ program. I 'd like to call some R | functions that can test if two sample sets are from different distribution, | like Kolmogorov-Smirnov and other more sophisticated Tests. I also like to | draw the histogra

[R] How to call R routines in C++`

Hi, I have some results generated in my C++ program. I 'd like to call some R functions that can test if two sample sets are from different distribution, like Kolmogorov-Smirnov and other more sophisticated Tests. I also like to draw the histograms of the two sample sets in the same plot using R.

Re: [R] Re cursion is slow

Most of the time was being spent within the 'sapply' call. Here is a list from Rprof: 0 18.4 root 1. 18.4 system.time 2. . 12.9 A1 3. . . 12.9 sapply 4. . . . 12.9 lapply 5. . . . | 12.9 FUN 6. . . . | . 12.9 sapply 7. . . . | . . 12.9 lapply 8. . . . | . . . 12

[R] Windows 2x faster than linux x86_64?

I did a speed test with a colleague. We basically have identical Lenovo ThinkCentres. He has 8 vs my 4 G RAM, but I don't think that's the issue. code: length <- 2*10^6 a <- runif(length) b <- runif(length) print(summary(lm(a~b))) Running Arch x86_64 this takes about 16 to 17 seconds. I *think

Re: [R] Recursion is slow

Bill, Thanks for the great tips for speeding up functions in your response. Those are really useful for me. Even with the improvements the recursion is still many times slower than I need it to be in order to make it useful in R. I may just have to suck it up and call a compiled language. B

[R] Problem with locfit( ... , family="hazard")

I'm having difficulties with plot.locfit.3d, at least I think that is the problem. I have a large dataframe (about 4 MM cases) and was hoping to see a non-parametric estimate of the hazard plotted against two variables: > fit <- locfit(~surv.yr+ ur_protein + ur_creatinine, data=TRdta, cen

Re: [R] Easy way to get top 2 items from vector

it is speedier to use sort than a combination of [] and order: N<- 100 x <- runif(N) > system.time(x[order(x)[c(N-1,N)]]) user system elapsed 1.030.001.03 > system.time(sort(x)[c(N-1,N)]) user system elapsed 0.280.000.28 On Sep 4, 11:17 am, Noah Silverman wrot

Re: [R] Easy way to get top 2 items from vector

Phil, That's perfect. (For my application, I've never seen a tie. While possible, the likelihood is almost none.) Thanks! -- Noah On 9/3/09 4:29 PM, Phil Spector wrote: > Noah - >max(x[-which.max(x)] will give you the second largest value, > but it doesn't handle ties. >x[order(x,de

[R] predicting from segmented regression

Hello I'm having trouble figuring out how to use the output of "segmented()" with a new set of predictor values. Using the example of the help file: set.seed(12) xx<-1:100 zz<-runif(100) yy<-2+1.5*pmax(xx-35,0)-1.5*pmax(xx-70,0)+15*pmax(zz-.5,0)+rnorm(100,0,2) dati<-data.fra

Re: [R] Re moving redundant observations

Try this: # input data ID <- scan() 1 1 1 1 2 2 2 2 2 V2 <- scan() 23.9 NA 22.0 23.9 0.4 NA NA 3.0 2.4 # setup data frame DF <- cbind(ID, V2); DF # find unique pairs unique(DF) ### # Chi Yau # http://r-tutor.com ### Barbara-43 wrote: > > Hello R-helpers, >

[R] DOE in R?

Hello! This is not a topic I am well versed in but required to become well versed in...I welcome any assistance! Using R, I want to create an optimal design for an experiment. I'll be analyzing the results with logistic regression or some generalized linear model. I am thinking that the algdesi

[R] Removing redundant observations

Hello R-helpers, I am having a difficult time figuring out the following: I have a data frame with 24 variables. I need to remove redundant observations where, within the same values of ID, V2 is equal to another observation in V2. >ID V2 >123.9 >1NA >122.0 >1 23.9 >2 0.4

Re: [R] Zoomable graphs with multiple plots

On Thu, Sep 3, 2009 at 1:25 PM, Jim Porzak wrote: > Tim, > > I've had success (& user acceptance) simply plotting to a .pdf & > passing zoom functionality to Acrobat, or whatever. > > Worked especially well with large US map with a lot of fine print annotation. > > Of, course, will not replot axes

Re: [R] Easy way to get top 2 items from vector

Hi Noah, Next time try, please, send a short reproducible code/example. May be this can be (not so elegant but) helpfull myDF<-data.frame(cbind(a=runif(5),b=runif(5))) myDF N=2 a.order<-rev(order(myDF$a))[1:N] b.order<-rev(order(myDF$b))[1:N] myDF.max2a<-myDF[a.order,] myDF.max2a myDF.max2b<-m

Re: [R] Recursion is slow

Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Bryan Keller > Sent: Thursday, September 03, 2009 2:11 PM > To: r-help@r-project.org > Subject: [R] Recur

Re: [R] Rdonlp2 package question

Hi Richard, If not for your condition (d), which imposes nonlinear constraints, you could have used `constrOptim'. I have written a function called `constrOptim.nl" that can handle nonlinear inequality constraints, and it also improves upon `constrOptim' in a couple of aspects. Fortunately, y

Re: [R] Zoomable graphs with multiple plots

There is also playwith, if you're willing to go down the GTK+ route... 2009/9/3 Tim Shephard : > Hi folks, > > I was wondering if anyone could confirm/deny whether there exists any > kind of package to facilitate zoomable graphs with multiple plots (eg, >  plot(..) and then points(..)).    I've t

[R] Easy way to get top 2 items from vector

Hi, I use the max function often to find the top value from a matrix or column of a data.frame. Now I'm looking to find the top 2 (or three) values from my data. I know that I could sort the list and then access the first two items, but that seems like the "long way". Is there some way to a

Re: [R] [OT] book on Linux scripting

Hi, There are good books by O'Reilly for both sed and awk. That said, neither is what I would call a "complete" scripting language. Without knowing the details of your requirements, I STRONGLY suggest that you learn perl. It allows you do almost anything with data, fetch web pages, access a

Re: [R] Ability Estimates for Repeated Measurements in the eRm Package

Hello, Thank you very much for the tip. I think that the irt.ability() function is what I'm looking for but I'm not sure. To be more clear, I have obtained item parameters from the LLTM function in the eRm package which allows for repeated measurements. I have 10 items measured at 2 time point

Re: [R] variable selection in logistic

Thank you for all your suggestions. I will start with the chapter. Annie On Thu, Sep 3, 2009 at 1:50 PM, Don McKenzie wrote: > Frank may be too modest to suggest it, but a great place to start that > reading is in his book "Regression Modeling Strategies" chapter 4. > On Sep 3, 2009, at 1:45

Re: [R] Re cursion is slow

Bryan Keller wrote: > > The following recursion is about 120 times faster in C#. I know R is not > known for its speed with recursions but I'm wondering if anyone has a tip > about how to speed things up in R. > > #"T" is a vector and "m" is a number between 1 and sum(T) > > A <- function(T,

Re: [R] Party plots

> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of AnnieE > Sent: Thursday, September 03, 2009 12:57 PM > To: r-help@r-project.org > Subject: Re: [R] Party plots > > > > > Achim Zeileis wrote: > > > > > >>>You can easily plot i

[R] Recursion is slow

The following recursion is about 120 times faster in C#. I know R is not known for its speed with recursions but I'm wondering if anyone has a tip about how to speed things up in R. #"T" is a vector and "m" is a number between 1 and sum(T) A <- function(T,m) { lt <- length(T) if (lt == 1) {

Re: [R] variable selection in logistic

Frank may be too modest to suggest it, but a great place to start that reading is in his book "Regression Modeling Strategies" chapter 4. On Sep 3, 2009, at 1:45 PM, Frank E Harrell Jr wrote: > You'll need to do a huge amount of background reading first. These > stepwise options do not inco

Re: [R] Normalize data set

Are you looking for reshape()? HTH, Stephan Edward Chen schrieb: Hi all, I have a mxn matrix that consists of 28077 rows of features and 30 columns of samples. I want to normalize each row for the samples for each feature. I have tried normalize and scale functions but they don't seem to work

Re: [R] Normalize data set

On Sep 3, 2009, at 4:41 PM, Edward Chen wrote: Hi all, I have a mxn matrix that consists of 28077 rows of features and 30 columns of samples. I want to normalize each row for the samples for each feature. I have tried normalize and scale functions How? but they don't seem to work out

Re: [R] variable selection in logistic

You'll need to do a huge amount of background reading first. These stepwise options do not incorporate penalization. Frank annie Zhang wrote: Hi, Frank, If I want to do prediction as well as to select important predictors, which may be the best function to use when I have 35 samples and 35

[R] Normalize data set

Hi all, I have a mxn matrix that consists of 28077 rows of features and 30 columns of samples. I want to normalize each row for the samples for each feature. I have tried normalize and scale functions but they don't seem to work out the way I want to. Thank you -- Edward Chen Email: edche...@g

Re: [R] variable selection in logistic

Hi Annie, What kind of data (response and explanatory) you have? As a ecological modeller, I always think first what is my (our) mind models. After that I analyze a set of concorrent - *but with ecological meaning* - models. It helps me to test hypothesis as well as to discuss the results. If you

Re: [R] Zoomable graphs with multiple plots

Tim, I've had success (& user acceptance) simply plotting to a .pdf & passing zoom functionality to Acrobat, or whatever. Worked especially well with large US map with a lot of fine print annotation. Of, course, will not replot axes more appropriate for zoom level. HTH, Jim Porzak Ancestry.com

Re: [R] Help with GLM please!

(I haven't seen a response to this - might have missed it.) see inline Lars Bishop wrote: Dear experts, I have a few quick questions related to GLMs: 1) Suppose my response is of the type Yes/No, How can I control which response I'm modelling? By selecting the appropriate reference level. As

Re: [R] variable selection in logistic

Hi, Frank, If I want to do prediction as well as to select important predictors, which may be the best function to use when I have 35 samples and 35 predictors (penalized logistic with variable selection)? I saw there is a 'fastbw' function in the Design package. And there is a 'step.plr' function

Re: [R] Export objects

On Sep 3, 2009, at 4:03 PM, diana buitrago wrote: Hi, R users, How can I export an R object as a .txt file? As an example I have the result from a regression and I need to save this object in a .txt file ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt <- c(4.81,4.17,4.41,3.

[R] Neural networks

Dear list members. I am trying to make a sensitivity analysis (as derived by Zurada 1994, Engelbrecht 1995) of input parameters (gene expression data) when applying a neural network to classify different cancer subtypes. Since I am no expert in the field, (rather a newbie), I wonder if ther

Re: [R] extract and replace columns of matrices stored in a list

On Thu, Sep 3, 2009 at 4:34 PM, Henrique Dallazuanna wrote: > Try this: > > #1 > lapply(my.array, '[', , 3) > > this works! thank you a lot! > #2 > newThirdColumn <- sample(3) > lapply(my.array, replace, list = 7:9, values = newThirdColumn) > > i did not understand this last line, so far i could

[R] Export objects

Hi, R users, How can I export an R object as a .txt file? As an example I have the result from a regression and I need to save this object in a .txt file ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group <- gl(2,10,20, l

Re: [R] Party plots

Achim Zeileis wrote: > > >>>You can easily plot into a large PDF, e.g., something like this > >>> pdf(file = "foo.pdf", height = 15, width = 20) >>> plot(foo) >>> dev.off() > >>>and then view the PDF in an external viewer, zooming into parts of a tree >>>etc. Depending on the size of

[R] Output from as.windrose() in oce package baffles me

I'm having trouble understanding the output from as.windrose(). For one thing, data on a boundary between sectors seem to be left out of the counts. I assume that explains the missing point in the output below (angle 45). Shouldn't one side of each sector interval be open, to include values such

Re: [R] Rdonlp2 package question

Ravi & list, Here is a simplified example of the type of problem I need to solve. It's a constrained allocation problem of a finite population sample: Decision vars: n[h] , h=1:H, i.e an H-vector of stratum sample sizes Objective: Min the sum over h=1:H of ( W[h]^2 * S[h]^2 / n[h] ) w

Re: [R] Rdonlp2 package question

Hi Richard, Others have written to me about the non-availability of the Rdonlp2 package on CRAN and on package author's website. Some of these emails had expressed the hardships that thay are experiencing because a lot of their codes are dependent upon Rdonlp2. They had also expressed their f

Re: [R] Party plots

On Thu, 3 Sep 2009, AnnieE wrote: I'm pretty new to R, and not much of a progammer (yet). I'm having trouble navigating the graphical output for the party algorithm. Essentially, my tree is too large for the default page size so the nodes overlap and obscure one another. Anybody know how to c

Re: [R] Calling R from a Perl script: much slower?

On 09/03/2009 05:42 PM, j.delashe...@ed.ac.uk wrote: Hello list, I use R for microarray analysis. One procedure I use takes a large matrix, and loops through it looking for specific rows, does an operation with them, and outputs a result (single row) as a row of another matrix. The loop goes o

Re: [R] Calling R from a Perl script: much slower?

What operating system are you running under? You should take a look at the R process and see how much time it is using to see if there is a difference in the CPU time. Are you paging? Exactly how are you invoking the R script? Why are you using the GUI instead of Rterm? You might try to run Rpr

Re: [R] permutation test - query

You may find the multtest package helpful. It implements methods from Westfall and Young (Resampling based multiple testing). On Mon, Aug 31, 2009 at 5:37 AM, Yonatan Nissenbaum wrote: > Hi, > > My query is regarding permutation test and reshuffling of genotype/phenotype > data > I have been usi

Re: [R] Generating R plots via Ruby CGI - solved

My original problem was an inability to generate R plots using the following scenario: 1. HTML page sends data to Ruby CGI 2. Ruby CGI passes on data to R plotting script, which generates a plot 3. Ruby CGI passes plot back to user With help from Scott Sherrill-Mix on this list and from

Re: [R] Problem accessing functions in package 'roxygen'

Robert A. LaBudde wrote: I have Vista Home with R-2.9.0, and installed and tried to test the package 'roxygen': > utils:::menuInstallPkgs() trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.9/roxygen_0.1.zip' Content type 'application/zip' length 699474 bytes (683 Kb) opened

[R] wireframe - different axes on each panel

Hi, I would like to create wireframe plots conditional on 2 variables and use different limits for the 3-axes in each plot. I thought I could do this with subscripts and the panel.wireframe but I haven't been successful. I am getting this error "...multiple actual arguments..." so I definitel

Re: [R] Converting from "date strings" to internal POSIX format?

I assume you mean you wish to convert it from text to to the numeric representation that POSIXct uses: > options(digits = 20) > as.numeric(as.POSIXct("2009-06-16 09:28:17.746")) [1] 1245158897.746 If you just want convert it to POSIXct then omit the as.numeric part. On Thu, Sep 3, 2009 at 1:17 P

Re: [R] Differentiation on mathematical equation

Try this: ?numericDeriv On Thu, Sep 3, 2009 at 1:18 PM, FMH wrote: > Dear All, > > I was trying to compute the first and second order differentiation on a > number of mathematical equations, but never found any command in R to do this > operation. At present, i have almost 3000 different functi

[R] Converting from "date strings" to internal POSIX format?

I need to convert a date-style string: "2009-06-16 09:28:17.746" To its POSIX representation: 1245137297746 The function below converts my POSIX date to a string ... now I need to go backwards! render.t32 <- function(t32, tz = "CET") { timez <- ISOdatetime(1970,1,1,0,0,0, tz ="UTC")+t32/

[R] Differentiation on mathematical equation

Dear All, I was trying to compute the first and second order differentiation on a number of mathematical equations, but never found any command in R to do this operation. At present, i have almost 3000 different functions, consist of polynomial, harmonic and several other functions. Could some

Re: [R] variable selection in logistic

annie Zhang wrote: Thank you for all your reply. Actually as Bert said, besides predicion, I also need variable selection (I need to know which variables are important). As far as the sample size and number of variables, both of them are small around 35. How can I get accurate prediction as lo

[R] Problem accessing functions in package 'roxygen'

I have Vista Home with R-2.9.0, and installed and tried to test the package 'roxygen': > utils:::menuInstallPkgs() trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.9/roxygen_0.1.zip' Content type 'application/zip' length 699474 bytes (683 Kb) opened URL downloaded 683 Kb packa

Re: [R] variable selection in logistic

Thank you for all your reply. Actually as Bert said, besides predicion, I also need variable selection (I need to know which variables are important). As far as the sample size and number of variables, both of them are small around 35. How can I get accurate prediction as long as good predictors? A

Re: [R] dividing a dataframe column by different constants

Dear Ottorino-Luca, Here is a suggestion using ave(): df.mydata$PERCENTAGE <- with(df.mydata, ave(CONC, list(SAMPLE), FUN = function(x) x / max(x) )) df.mydata[1:5,] # CONC TIME SAMPLE PERCENTAGE # 1 1.01 A1.0 # 2 0.92 A0.9 # 3 0.83 A0.8 # 4

Re: [R] dividing a dataframe column by different constants

On Sep 3, 2009, at 12:17 PM, Ottorino-Luca Pantani wrote: Dear R users, today I've got the following problem. Here you are a dataframe as example. There are some SAMPLES for which a CONCentration was recorded through TIME. The time during which the concentration was recorded is not always

Re: [R] Alternative for correspondance analysis

You could try plotting them with a parallel plot. See ?parallel in lattice or ?ggpcp in ggplot2 On Thu, Sep 3, 2009 at 4:18 AM, Sannr wrote: > > I am looking for an alternative way to inspect my data, other than doing an > correspondance analysis. > > What I have is a list with 5 different measure

Re: [R] Zoomable graphs with multiple plots

Look at the zoomplot function in the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of T

Re: [R] to istall packages such as 'stats'

Hi Ajay, To install new packages try: install.packages("package_name", dependencies=T) But stats is part of base R. :-) bests miltinho On Thu, Sep 3, 2009 at 6:01 AM, Ajay Singh wrote: > Dear All, > I have to install 'stats' package in my windows machine, could you let me > know how to insta

Re: [R] to istall packages such as 'stats'

It should not require installation. It's part of the base distribution. What makes you think you do not have it as already? What does this report: installed.packages(priority="base") ? -- David On Sep 3, 2009, at 6:01 AM, Ajay Singh wrote: Dear All, I have to install 'stats' package in

[R] dividing a dataframe column by different constants

Dear R users, today I've got the following problem. Here you are a dataframe as example. There are some SAMPLES for which a CONCentration was recorded through TIME. The time during which the concentration was recorded is not always the same, 10 points for Sample A, 7 points for Sample B and 11 fo

[R] Confusion metaMDS and CA

Hello, I read a lot about ordination, but I am still confused... I have data on species presence/absence for 8 different sites and I would like to represent my species and the sites on an ordination plot to see if some species are associated with specific sites. I used metaMDS function, which disp

[R] Fwd: R package or function for ordinal predictors and continous response

Dear list, I have a microarray data in which gene expression is the response (dependent) variable. Can anybody tell me which package/function in R should I use to model the gene expression with an ordinal predictor (Independent Variable) Thanks, Shirley __

[R] Sweavelistingutil: Encoding problems

Hello, I am not sure whether this is a bug or lack of R experience. However, I am using your Sweavelistingutil package, which is very nice. Obviously I use it to create LaTeX files. These are encoded in utf8. However, when I use the Sweavelistingutil is uses some funky character for "`" and "'"

Re: [R] Problems with Boxplot

I'm posting answers to my own Q's here - as far as I have answers - first so that people don't spend time on them, and second in case the solutions are helpful to anyone else in future. 1) My first question is: is there a simple way of getting both dates along the x-axis and the "*100" calculatio

[R] Alternative for correspondance analysis

I am looking for an alternative way to inspect my data, other than doing an correspondance analysis. What I have is a list with 5 different measurements of a person and ratings that that person gave to a number of objects, so: person1.name, person1.score1, person1.score2, person1.score3, person1

[R] to istall packages such as 'stats'

Dear All, I have to install 'stats' package in my windows machine, could you let me know how to install the package? Look forward to your assistance, Ajay. - Ajay Singh, Ph.D. |Tel: +91-22 25764785 Research Scien

[R] Two-ways anova / interaction

When I perform a two-way anova on my dataframe "pin", I can't get any indication about the interaction among the two factors "gen" and "con" while the statistics about the significance relative to the two factors alone is correct. I wrote this: *pvalues_genotipo<-sapply(pin[,1:(length(pin)-2)],FUN

[R] Party plots

I'm pretty new to R, and not much of a progammer (yet). I'm having trouble navigating the graphical output for the party algorithm. Essentially, my tree is too large for the default page size so the nodes overlap and obscure one another. Anybody know how to change the plot parameters to either:

Re: [R] putting reference lines or grids into the background of a plot

Hi, You may find some inspiration here: http://wiki.r-project.org/rwiki/doku.php?id=tips:graphics-misc:ggplot2theme_inbase HTH, baptiste 2009/9/3 RINNER Heinrich > Dear R-community, > > using R.2.9.1, how do you put reference lines or grids into the > _background_ of a plot? > For example:

[R] Calling R from a Perl script: much slower?

Hello list, I use R for microarray analysis. One procedure I use takes a large matrix, and loops through it looking for specific rows, does an operation with them, and outputs a result (single row) as a row of another matrix. The loop goes on about 25000 times. When I run the loop direct

Re: [R] variable selection in logistic

But let's be clear here folks: Ben's comment is apropos: ""As many variables as samples" is particularly scary." (Aside -- how much scarier then are -omics analyses in which the number of variables is thousands of times the number of samples?) Sensible penalization (it's usually not too sensitiv

Re: [R] How to do rotation for polygon?

The my.symbols and ms.polygon functions in the TeachingDemos package may help. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.

[R] putting reference lines or grids into the background of a plot

Dear R-community, using R.2.9.1, how do you put reference lines or grids into the _background_ of a plot? For example: barplot(3:1) abline(h = seq(0.5, 2.5 ,0.5), col = "red", lty = "dashed") -> The lines are before the bars (and the line parts going through the bars might be considered as "ch

[R] Rdonlp2 package question

Previous versions have this question have partially bounced. I apologize if parts of this are showing up multiple times on the list. Another try ... There was at one time an R package called Rdonlp2 for solving constrained nonlinear programming problems. Both the objective function and the const

Re: [R] Moving Rterm.exe to another location

uwe that is brilliant - i was not aware of that command. the solution is now apparent: as you suggest, i can access that PID, write it to a file, then search for that file, reads it contents, etc. thanks. dennis Dennis Fisher MD P < (The "P Less Than" Company) Phone: 1-866-PLessThan (1-86

Re: [R] Moving Rterm.exe to another location

Dennis Fisher wrote: Colleagues, I have encountered the following situation in R (2.9.0) with Windows XP. I have an application that calls Rterm.exe. In certain situations, the application terminates but fails to close R. Then, the next time that the application runs, there are replicated

Re: [R] extract and replace columns of matrices stored in a list

Try this: #1 lapply(my.array, '[', , 3) #2 newThirdColumn <- sample(3) lapply(my.array, replace, list = 7:9, values = newThirdColumn) On Thu, Sep 3, 2009 at 11:16 AM, Carlos Hernandez wrote: > Dear All, > I created a list (of length Z) in the following way: > > my.array <- vector("list", Z) >

[R] Moving Rterm.exe to another location

Colleagues, I have encountered the following situation in R (2.9.0) with Windows XP. I have an application that calls Rterm.exe. In certain situations, the application terminates but fails to close R. Then, the next time that the application runs, there are replicated copies of R running -

[R] extract and replace columns of matrices stored in a list

Dear All, I created a list (of length Z) in the following way: my.array <- vector("list", Z) then i assigned a matrix (of T rows by N columns) in each of the elements of the list my.array in the following way: my.array[[i]] <- matrix.data ##( matrix.data has dimensions TxN, and i repeated this

Re: [R] encoding problem using xml package

You can convert back to UTF-8: value <- unlist(xpathApply(doc,"//MESSUNG/BEZEICHNUNG", xmlValue)) Encoding(value) <- "UTF-8" On Thu, Sep 3, 2009 at 7:56 AM, Dominik Bänninger wrote: > Dear list > I tried to read an xml file using the xml package. Unfortunately, some > encoding problems occure.

Re: [R] goodness of "prediction" using a model (lm, glm, gam, brt, regression tree .... )

There are many ways to measure prediction quality, and what you choose depends on the data and your goals. A common measure for a quantitative response is mean squared error (i.e. 1/n * sum((observed - predicted)^2)) which incorporates bias and variance. Common terms for what you are looking for

Re: [R] Zoomable graphs with multiple plots

This is what I've done. Just capture two identifies and then replot. If the identifies are right left, I zoom out. Works quite well. Still, can't wait for iplot xtreme. Cheers, Tim. On Thu, Sep 3, 2009 at 5:03 AM, Jim Lemon wrote: > Tim Shephard wrote: >> >> Hi folks, >> >> I was wondering

Re: [R] abind, but on lists?

Peter, Thank you for the dput values. Kenn points out that result <- cbind(data1[,,1], data2[,,1]) dim(result) <- c(3,3,1) gets what you want. We wrote abind to bind atomic arrays and/or data.frames. The list feature, which is interfering with your usage, was designed to simplify calling se

Re: [R] variable selection in logistic

>>  You mean the backward and forward stepwise selection is bad? You also >> suggest the penalized logistic regression is the best choice? Is there any >> function to do it as well as selecting the best penalty? >>  Annie > > All variable selection is bad unless its in the context of penalization.

Re: [R] Zoomable graphs with multiple plots

Tim Shephard wrote: Hi folks, I was wondering if anyone could confirm/deny whether there exists any kind of package to facilitate zoomable graphs with multiple plots (eg, plot(..) and then points(..)).I've tried zoom from IDPmisc, and iplot from the iplot and iplot extreme packages, but as

[R] Odp: How can I appoint a small part of the whole data

Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) & (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: > Dear all, >

[R] encoding problem using xml package

Dear list I tried to read an xml file using the xml package. Unfortunately, some encoding problems occure. E.g. german Umlaut will be red correctly. I assume that the occurs due to (internal?) conversion to utf-8. To illustrate the problem, I have wrote to xml files. File Test 1 ---

[R] Help with GLM please!

Dear experts, I have a few quick questions related to GLMs: 1) Suppose my response is of the type Yes/No, How can I control which response I'm modelling? 2) How can I perform Type III tests? Is it with -> drop1(mymodel, test="Chisq") ? 3) I have a numerical variable which I converted to an ord

[R] "Iterated cumulative sums of squares algorithm" in R ?

Dear R Users, Is the "iterated cumulative sums of squares algorithm" implemented in any package in R ? A simple search yields no results but perhaps it is named something else. Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including o

[R] How can I appoint a small part of the whole data

Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b<-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990

[R] R: "biplot" graphical options?

Thanks Andris, Michael and Petr for your prompt and kind feedbacks. I will try generating my own biplot from low-level graph commands... I hope it will work. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Re

Re: [R] abind, but on lists?

On Thu, Sep 3, 2009 at 5:50 AM, Peter Meilstrup wrote: > I'm trying to massage some data from Matlab into R. The matlab file has a > "struct array" which when imported into R using the R.matlab package, > becomes an R list with 3+ dimensions, the first of which corresponds to the > structure fiel

Re: [R] Subsetting Data Frame based On Specified K Value

Is this what you want? > dat <- read.table("http://dpaste.com/88988/plain/";, comment.char="", header = TRUE) > names(dat) [1] "X.ID" "VALUE" "FREQUENCY" > subset(dat, X.ID %in% 0:2 & !duplicated(X.ID)) X.ID VALUE FREQUENCY 1 0 0.00 3 321 0.67 1 65

Re: [R] Help with sub-setting data.frame

Your subset problem has been solved already but i'd like to add a comment on this: > I want all rows where TTE is equal to 0.024657534 Comparing floating point numbers for equality with '==' is problematic so a simple df[df$TTE == 0.024657534, ] can easily fail. have a look at help("=="), especi