[R] bootstrapping error message "Error in t.star[r, ] <- statistic(data, i[r, ], ...) : number of items to replace is not a multiple of replacement length"

Hi, I am trying to run some bootstraps with the boot package. When I run it with 400 replicates it does it ok, but then I need to run the same analysis but with 89, 86, 102 and 106 samples (for four different environments), and then is when I get the error message: > mybootstrap <- boot(Da

Re: [R] Reading from Google Docs

On 7/8/2009 3:18 PM, Gabor Grothendieck wrote: To my mind its pretty serious that Rtools can make other software not work and the importance of using the word find in the tools is close to zero. Most people never even look at the scripts. You didn't read what I wrote. It could be called anyth

Re: [R] Reading from Google Docs

I understand what you wrote. Its just that I don't agree that that is a reasonable solution. What is wanted is something that works safely out of the box, not something with a built in danger that every single person that uses it must fix (and know about it to fix) in order to maintain the integri

Re: [R] Reading from Google Docs

To my mind its pretty serious that Rtools can make other software not work and the importance of using the word find in the tools is close to zero. Most people never even look at the scripts. Why don't you just rename find.exe to find2.exe, say, in Rtools and adjust the other files accordingly. F

[R] nested model with random factors

I am really having trouble with getting the right syntax for my model. Here is a truncated version of my data: > data Ind Treatment Order DatePC1 1 PER14SC 3rd 4-May-09 0.5704611 2 PER14SH 1st 26-Apr-09 0.5329025 3 PER14AC 2nd 29-Apr-09 2.139

Re: [R] print() to file?

?sink -- 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 Steve Jaffe > Sent: Wednesday, July 08, 2009 1:03 PM >

[R] What is cast telling me?

Hi, What is cast telling me when it says the following? Aggregation requires fun.aggregate: length used as default What is 'length'? I've taken a small subset of data and wondered what EnTime vs ExTime might look like. cast is kind enough to give me a table but I don't understand the value

Re: [R] Reading from Google Docs

On 7/8/2009 3:39 PM, Gabor Grothendieck wrote: I understand what you wrote. Its just that I don't agree that that is a reasonable solution. What is wanted is something that works safely out of the box, not something with a built in danger that every single person that uses it must fix (and know

Re: [R] matching each row

On Jul 8, 2009, at 12:17 PM, tathta wrote: From an email suggestion, here are two sample datasets, and my ideal output: dataA <- data.frame(unique.id=c("A","B","C","B"),x=11:14,y=5:2) dataB <- data .frame(unique.id=c("A","B","A","B","A","C","D","A"),x=27:20,y=22:29) ## mystery operation(

Re: [R] What is cast telling me?

That you have non-unique rows in your data (as identified by the identifying variables). - Original message - From: "Mark Knecht" To: "r-help" Date: Wed, 8 Jul 2009 12:41:28 -0700 Subject: [R] What is cast telling me? Hi, What is cast telling me when it says the following? Aggre

Re: [R] heatmap.2: question regarding the "raw z-score"

Hi Chrysanthi, Chrysanthi A. wrote: Hi, I am analysing gene expression data using the heatmap.2 function in R and I was wondering what is the formula of the "raw z-score" bar which shows the colors for each pixel. According to that post: https://mailman.stat.ethz.ch/pipermail/r-help/2006-Septem

Re: [R] What is cast telling me?

On Wed, Jul 8, 2009 at 12:58 PM, wrote: > > That you have non-unique rows in your data (as identified by the identifying > variables). > Humm...OK - so I cast it with PL_Pos which has (in this data subset) a unique value for each experiment in this set. there are 25 experiments and there are 25

Re: [R] Reading from Google Docs

No one really knows how many people are being affected. Also one can minimize the impact like this: 1. In Rtools, change find.exe to find2.exe. 2. In R, create a 'find' a variable in any script using find and at the top check for find2 and if found set the find variable to find2 otherwise set it

[R] Unix commands on R

I am using R on unix. While in R how do I execute the unix shell commands? Is there a way to do it? I am executing a function in R and the matrix resulting from the function has to be passed on as an input to unix command. Any directions will be helpful. Thanks, Suman [[alternative HTML

[R] rgtk2 colorbutton

How do you retrieve the color from a GtkColorButton in rgtk2? There seems to be a promising function gtkColorButtonGetColor However, the function doesn't return the current color, instead it *sets* a color that you pass to it. The function header looks like gtkColorButtonGetColor(color_button, c

Re: [R] R2WinBUGS under Linux/WINE fails

Harlan Harris wrote: Hi, I'm running wine-1.0.1, OpenBUGS 3.0.3, R 2.9.0, and R2WinBUGS on a Redhat Enterprise Linux machine. Following various peoples' suggestions... This works perfectly (yay!): wine Z:/opt/OpenBUGS/winbugs.exe Within R, however, I get this: (setup the example from ?bugs

Re: [R] Unix commands on R

?system ?shQuote On Wed, Jul 8, 2009 at 4:36 PM, suman Duvvuru wrote: > I am using R on unix. While in R how do I execute the unix shell commands? > Is there a way to do it? I am executing a function in R and the matrix > resulting from the function has to be passed on as an input to unix command.

Re: [R] Unix commands on R

Le mercredi 08 juillet 2009 à 16:36 -0400, suman Duvvuru a écrit : > I am using R on unix. While in R how do I execute the unix shell commands? > Is there a way to do it? I am executing a function in R and the matrix > resulting from the function has to be passed on as an input to unix command. >

Re: [R] system() how to make a program run a specific file - RUN and Output directory issues

Paulo E. Cardoso wrote: I have a particular case where the program I'm calling needs a additional instructions, to click a RUN button and set a output directory. Could these options be controlled with system() function? system() just calls the program as started from the operating system's

Re: [R] how to read point shp file to R?

On 8/07/2009, at 6:28 AM, Sunny wrote: I am new with R and want do some analysis with a point vector data file. Any help is appreciate. Sunny See the vignette ``Handling shapefiles in the spatstat package'' from the spatstat package on CRAN. cheers, Rolf Turne

[R] truncated regression out-of-sample predictions

Dear all, I am trying to implement Simar & Wilson's (2007) second algorithm and have the following question: If I use a truncated regression on the mmailto:r-help-boun...@r-project.org] On Behalf Of Karina Boege Sent: Wednesday, July 08, 2009 11:18 AM To: r-help@r-project.org Subject: [R] bootstr

Re: [R] R2WinBUGS under Linux/WINE fails

Uwe, thanks for helping! After some poking around, I realized that the problem was that I had installed OpenBUGS instead of WinBUGS. I did an additional installation of WinBUGS, which also runs fine under Wine, and now everything seems to work! Thanks! To clarify: both the OpenBUGS and WinBUGS dis

Re: [R] R2WinBUGS under Linux/WINE fails

Harlan Harris wrote: Uwe, thanks for helping! After some poking around, I realized that the problem was that I had installed OpenBUGS instead of WinBUGS. I did an additional installation of WinBUGS, which also runs fine under Wine, and now everything seems to work! Thanks! To clarify: both the

Re: [R] \dQuote in packages

The difference you are experiencing is the new Rd2 parser that is more picky now (but also prevents to produce wrong documentation files). If you make the code of the Rd available, someone might be able to help. Are you really under R-2.1.1 ??? That is really ancient! Best, Uwe Ligges Rebe

[R] A Lattice Question

To the Lattice expert - I am new to the lattice package and I would like to add a curve to the xyplot(). I know that I need to use panel function to add it. But it doesn't work. Is there anyone can help me out on how to transfer the data into the function? The following is my code and I would

[R] R Help Question

Hi, I am currently working on reading large files into R. My files are text documents with four columns and around 10 million lines. Each line is set up as: string|integer|string|integer I have been trying to use read.table to read in the file, but I think I am reading too much into memory and t

Re: [R] Unix commands on R

?system On Wed, Jul 8, 2009 at 4:36 PM, suman Duvvuru wrote: > I am using R on unix. While in R how do I execute the unix shell commands? > Is there a way to do it? I am executing a function in R and the matrix > resulting from the function has to be passed on as an input to unix command. > > > An

[R] subsetting a dataframe with a string logical expression

Hi, I am trying to subset a dataset based on a filter defined by a user... I prompt the user for input.. resulting in a string logical expression ("X1 < 3"). I have tried using subset, but it is looking for a logical expression, not a character string. I keep getting the error: 'subset' must

Re: [R] Two-way ANOVA gives different results using anova(lm()) than doing it by hand

the following works. i don't exactly what happens here. I guess "lm" might treat S1 and S2 as quantitative variables, not qualitative variables. cheers, Zhiliang S1 <- as.character(Data[,1]) S1 <- as.factor(S1) S2 <- as.character(Data[,2]) S2 <- as.factor(S2) data <- data.frame(S1=S1, S2=S2, ExM=

[R] Substituting numerical values using `apply'

Hello, I wish to perform a substitution of certain numerical values in a data matrix with the corresponding column name. For instance, if I have a data matrix V1 V2 V3 201 012 150 500 I want to substitute the `1' and the `2' for the corresponding column name,

[R] How to deploy statistical models built in R in real-time?

I am framing this as a question since I would like to know how folks are currently deploying the models they build in R. Say, you want to use the results of your model inside another application in real-time or on-demand, how do you do it? How do you use the decisions you get back from your

Re: [R] Tex fonts in R plots

Hi KARAVASILIS GEORGE wrote: Hello, R users. I would like to display the font of Math Mode of MikTex 2.3, WinEdt 5.4 in R plots, e.g. in xlab, ylab or legend. How can I do that? Thank you in advance. See http://www.stat.auckland.ac.nz/~paul/R/CM/CMR.html and "Non-standard fonts in PostScript

[R] Getting value rather than formula in RGoogleDocs

Is there an easy way to read the value of the cells rather than the formula?So for instance in a cell whose value was created by simply using the value from the cell immediately to the left in the Google spreadsheet I would prefer to get the value rather than =RC[-1] When one exports with Google

Re: [R] Substituting numerical values using `apply'

Dear Olivella, Assuming that x is your data, here is one possible way to do what you want: t( apply(x, 1, function(x){ index <- x %in% c(1,2) x[index] <- cls[index] x[!index] <- NA x

Re: [R] Substituting numerical values using `apply'

Arggg! Forgot to add "cls" before the code. Here is the (hopefully) complete version: # column names cls <- colnames(x) # Transformation res <- t( apply(x, 1, function(x){ index <- x %in% c(1,2) x[index] <- cls[index]

Re: [R] Getting value rather than formula in RGoogleDocs

Farrel Buchinsky wrote: Is there an easy way to read the value of the cells rather than the formula?So for instance in a cell whose value was created by simply using the value from the cell immediately to the left in the Google spreadsheet I would prefer to get the value rather than =RC[-1] W

Re: [R] subsetting a dataframe with a string logical expression

Try this: subset(x, eval(parse(text=filter))) On Wed, Jul 8, 2009 at 4:46 PM, Tracey Frescino wrote: > Hi, > > I am trying to subset a dataset based on a filter defined by a user... > I prompt the user for input.. resulting in a string logical expression > ("X1 < 3"). > > I have tried using su

Re: [R] nested model with random factors

Jeff DaCosta wrote: > > I am really having trouble with getting the right syntax for my > model. Here is a truncated version of my data: > > > data > Ind Treatment Order DatePC1 > 1 PER14SC 3rd 4-May-09 0.5704611 > 2 PER14SH 1st 26-Apr-09 0.5329025

Re: [R] R Help Question

How big is the entire text file? What is the length of an average line? Have you tried to use 'scan' to read in the data? How much memory do you have? Are you paging? Here was a quick test I did with a file with about 5M lines (12|this is some text|12345|more test): > system.time(x <- scan('/

[R] tkrplot installation problems

Hello, I'm running R 2.8.1 on Ubuntu Hardy. I'm trying to install tkrplot. Using r-cran-tkrplot from the repository, I'm getting the following error: > library(tkrplot) Loading required package: tcltk Loading Tcl/Tk interface ... done Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk")

[R] Best way to export values from a function?

Maybe there is a great website out there or white paper that discusses this but again my Google skills (or lack there of) let me down. I would like to know the best way to export several doubles from a function, where the doubles are not an array. Here is a contrived function similar to my n

Re: [R] Best way to export values from a function?

You can return a list, vector, or any other object: The last value is the return value unless you do an explicit return() On Wed, Jul 8, 2009 at 8:34 PM, Jason Rupert wrote: > > Maybe there is a great website out there or white paper that discusses this > but again my Google skills (or lack ther

Re: [R] Best way to export values from a function?

> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Jason Rupert > Sent: Wednesday, July 08, 2009 5:35 PM > To: R-help@r-project.org > Subject: [R] Best way to export values from a function? > > > Maybe there is a great website o

Re: [R] Best way to export values from a function?

On Wed, Jul 8, 2009 at 8:34 PM, Jason Rupert wrote: > > Maybe there is a great website out there or white paper that discusses this > but again my Google skills (or lack there of) let me down. Yeah, R is difficult to search for - I've had partial success with rseek.org, though. > > I would like

Re: [R] Best way to export values from a function?

On Wed, Jul 8, 2009 at 5:34 PM, Jason Rupert wrote: > > Maybe there is a great website out there or white paper that discusses this > but again my Google skills (or lack there of) let me down. > > I would like to know the best way to export several doubles from a function, > where the doubles are

[R] Dantzig Selector

Hi, I was wondering if there was an R package or routines for the Dantzig Selector (Candes & Tao, 2007). I know Emmanuel Candes has Matlab routines to do this but I was wondering if someone had ported those to R. Thanks, T ---Reference--- @article{candes2007dantzig, title={{The Dantzig selec

[R] Picante package 0.7 on mac

Hello, I tried to run the package but it shows me the following error: In addition: Warning message: package 'picante' was built under R version 2.10.0 Error in library(picante) : .First.lib failed for 'picante' What could I do to run picante in mac R version? ___

[R] Sampling a dataframe based on the length of a subset of observations within

Thank you in advance for your consideration. I have a dataframe of 2000+ observations with repeated measures across approximately 300 unique individuals An event either does or does not happen (1,0) and there is a suit of independent variables associated with the event. A simplified represen

Re: [R] \dQuote in packages

That's good to know. I have attached three Rd files that gave errors (others gave identical errors). I would love to know what is wrong with them. I'm using 2.1.1 because that is what is installed on the Linux computer I have access to. (I haven't bothered figuring out how to assemble a packa

[R] Mysteriously vanishing LD_LIBRARY_PATH

Using R-2.8.0 and R-2.8.1, I get behaviour like this: R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [] > Sys.getenv("LD_LIBRARY_PATH") LD

Re: [R] Best way to export values from a function?

On Wed, Jul 8, 2009 at 5:55 PM, Mark Knecht wrote: > On Wed, Jul 8, 2009 at 5:34 PM, Jason Rupert wrote: >> >> Maybe there is a great website out there or white paper that discusses this >> but again my Google skills (or lack there of) let me down. >> >> I would like to know the best way to export

Re: [R] Mysteriously vanishing LD_LIBRARY_PATH

R respects LD_LIBRARY_PATH, see /usr/lib/R/etc/ldpaths where it prepends its own path to any value in the environment when R is invoked: if test -z "${LD_LIBRARY_PATH}"; then LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}" else LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}" fi export LD_LIBR

Re: [R] Mysteriously vanishing LD_LIBRARY_PATH

On Jul 8, 2009, at 8:45 PM, p_conno...@slingshot.co.nz wrote: Using R-2.8.0 and R-2.8.1, I get behaviour like this: R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [] Sys.getenv("LD_LIBRARY_PATH") LD_LIBRARY_PATH "/

Re: [R] Mysteriously vanishing LD_LIBRARY_PATH

Quoting Godmar Back : R respects LD_LIBRARY_PATH, see /usr/lib/R/etc/ldpaths where it prepends its own path to any value in the environment when R is invoked: if test -z "${LD_LIBRARY_PATH}"; then LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}" else LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${LD_LIBRARY

Re: [R] Substituting numerical values using `apply'

Try this: sapply(names(DF), function(n)ifelse(DF[,n] %in% c(1, 2), n, NA)) Where DF is your data.frame On Wed, Jul 8, 2009 at 5:25 PM, Olivella wrote: > > Hello, > > I wish to perform a substitution of certain numerical values in a data > matrix with the corresponding column name. For instance

Re: [R] Reading from Google Docs

Farrel Buchinsky wrote: > Boy oh boy that process of getting source to binary was super painful. Now that I have the package as binary I can share the whole folder with my coworker and she is able to use RGoogleDocs. I intend to use the same process for the other two windows machines

Re: [R] Best way to export values from a function?

Mark and Jason, At 7:23 PM -0700 7/8/09, Mark Knecht wrote: On Wed, Jul 8, 2009 at 5:55 PM, Mark Knecht wrote: On Wed, Jul 8, 2009 at 5:34 PM, Jason Rupert wrote: Maybe there is a great website out there or white paper that discusses this but again my Google skills (or lack there of) le

Re: [R] Best way to export values from a function?

Hi, On Jul 8, 2009, at 8:34 PM, Jason Rupert wrote: Maybe there is a great website out there or white paper that discusses this but again my Google skills (or lack there of) let me down. I would like to know the best way to export several doubles from a function, where the doubles are

[R] splint

I am trying to understand idea for splint, but it use Fortran code. Does anyone know how to see that Fortran code? Is splint a not-knot spline method? Thanks, jfm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https

[R] change capital to small letters?

Hello R users, I have a string of characters in capital letters and I need to convert it in small letters, is there an easy way to do it? Thanks a lot Wapita _ Découvrez toutes les possibilités de communication avec vos

Re: [R] change capital to small letters?

ok, find! ?toupper ?tolower sorry!!! (but you have perhaps learned something...) From: wap...@hotmail.com To: r-help@r-project.org Subject: change capital to small letters? Date: Thu, 9 Jul 2009 03:07:35 + Hello R users, I have a string of characters in capital letters and I

Re: [R] R regular expression to extract words with the query string.

The solution below does not include the pid: string before it. This modification works: > strapply(i, paste("[^ ]*", "ENSP", "[^ ]*", sep = ""), c, simplify = unlist) [1] "pid:ENSP12345" On Wed, Jul 8, 2009 at 10:08 AM, Gabor Grothendieck wrote: > Try this: > > library(gsubfn) > i <- "transcr

Re: [R] R Help Question

You could try something like this: library(sqldf) DF <- read.csv.sql("myfile.txt", sep = "|", header = FALSE) or possibly this, which is the same except instead of using an "in memory" database it uses an external database: DF <- read.csv.sql("myfile.txt", sep = "|", header = FALSE, dbname = "te

Re: [R] Reading from Google Docs

Dear Duncan On my home computer I was able to use install.packages("RGoogleDocs", repos = "http://www.omegahat.org/R";) But, alas it would not read the data in the spreadsheet. It went back to its nasty ways Error in !includeEmpty : invalid argument type That is what I was getting with version 0

[R] Save rgl plot3d Graph as Image

Dear Users: I wish to save 3d scatter plots I have generated using the plot3d command in the rgl package. Any image format such as .tiff would work. Can anyone tell me how to do this? Thank you [[alternative HTML version deleted]] __ R-help@r-p

[R] Population pyramids

Hi, I hope somebody can help me with this issue: I am doing population pyramids using the barplot command, so in the left side I have male age structure and in the right side the female age structure. To plot the male age structure I put the data in negative numbers. Now, I want to change the si

Re: [R] Population pyramids

Hi Victor, See http://bm2.genes.nig.ac.jp/RGM2/R_current/library/plotrix/man/pyramid.plot.html HTH, Jorge On Thu, Jul 9, 2009 at 12:24 AM, Victor Manuel Garcia Guerrero < vmgar...@colmex.mx> wrote: > Hi, I hope s

Re: [R] Population pyramids

have you tried the pyramid function in the epicalc package? best, daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Victor Manuel Garcia

Re: [R] Population pyramids

Thanks Jorge, this is a very good library, but I have been trying with barplot because I am doing population pyramids with confidence intervals. So, the pyramid function does not work with more than two colum matrix. -Mensaje original- De: Jorge Ivan Velez [mailto:jorgeivanve...@gmail.c

[R] Converting indices of a matrix subset

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I have two matrices: > m1 <- matrix(1,4,4) > m1 [,1] [,2] [,3] [,4] [1,]1111 [2,]1111 [3,]1111 [4,]1111 > m2 <- matrix(0,3,3) > diag(m2) <- 1 > m2 [,1] [,2] [,3] [1,]10

Re: [R] Population pyramids

Yes, but my issue is because I need to plot a pop pyramid with confidence intervals, and the pyramid function does not work in that way. Thanks Daniel. -Mensaje original- De: Daniel Malter [mailto:dan...@umd.edu] Enviado el: mié 08/07/2009 11:36 Para: Victor Manuel Garcia Guerrero; r-hel

Re: [R] Population pyramids

Can you provide a self-contained example of what you did so far (i.e. code for simulating some data and code for the plot)? That would greatly help to help you find a solution. Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht---

Re: [R] RDCOMClient: how to close Excel process?

Thanks again. That did not work either. I get > library(RDCOMClient) > xl <- COMCreate("Excel.Application") > wk <- xl$Workbooks() > sh <- wk$Open(normalizePath("sample_file.xls"))$Sheets()$Count() > > wk$Close() [1] TRUE > xl$Quit() NULL > and there is still Excel process open in the Task manag

Re: [R] Population pyramids

Yes the code is the next: par(mfrow=c(1,2),bty="n",mai=c(0.5, 0.25, 0.25, 0.25)) barplot(height=t(icNM2005.dat), width = 0.825, space = NULL, names.arg = NULL, legend.text = NULL, beside = FALSE, horiz = TRUE, density = NULL, angle = 0, col = c("yellow","Blue","orange"), b

Re: [R] bigglm() results different from glm()+Another question

That was definitely helpful. "if you change your seq to: seq(chunksize, 1-chunksize, chunksize) then you won't get the error messages" Even previously, I was not getting any error messages or warnings at all, i.e., "update" removes the extra NA rows silently, for example: set.seed(1) xx =

Re: [R] Extracting a column name in loop?

If df is your dataframe then names(df) contains the column names and so names(df)[i] is the name of i-th column. --- On Thu, 9/7/09, mister_bluesman wrote: > From: mister_bluesman > Subject: [R] Extracting a column name in loop? > To: r-help@r-project.org > Received: Thursday, 9 July, 2009,

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