Re: [R] Creating bibtex file of all installed packages?

2009-12-10 Thread Achim Zeileis
On Fri, 11 Dec 2009, Rainer M Krug wrote: Hi is there an easy and fast way, to generate a BibTeX file of all installed / loaded packages and R? I know about toBibtex(citation()) to extract the BibTeX for a single package, but how can I generate a file containg citations for all installed / loa

[R] Creating bibtex file of all installed packages?

2009-12-10 Thread Rainer M Krug
Hi is there an easy and fast way, to generate a BibTeX file of all installed / loaded packages and R? I know about toBibtex(citation()) to extract the BibTeX for a single package, but how can I generate a file containg citations for all installed / loaded packages? Cheers, Rainer -- NEW GERMA

Re: [R] incorrect multiple outputs

2009-12-10 Thread bawan03
Apologies, I didn't explain this clearly. The Rscript is called by a perl script, which creates "input_file.txt" by inserting 288 lines of (reformatted) data for each data file in the directory. So the Rscript will (and is doing) run the loop a number of times equal to the number of files the p

[R] How to draw three line on the same picture ?

2009-12-10 Thread z_axis
The following is sampling data: No V1 V2 V3 1 0.23 0.12 0.89 2 0.11 0;56 0.12 ... I just want to draw three lines on same picture according to value of V1, V2 and V3. I am a R newbie, so any suggestion is appreciated ! -- View this message in context: http://n4.nabble.com/How

[R] Recoding factor labels that are lists into first element of list

2009-12-10 Thread Jennifer Walsh
Hi all, I've Googled far and wide but don't think I know the correct terms to search for to find an answer. I have a massive dataset where one of the factors is made up of both individual items and lists of items (for example, "cat" and "cat, dog, bird"). I would like to recode this facto

[R] Reducing the "dimension" of a list object

2009-12-10 Thread Bogaso
Please consider following code : set.seed(1) res <- vector("list") for (i in 1:5) { res1 <- vector("list") res1[[1]] <- letters[1:5] res1[[2]] <- rnorm(5) res1[[3]] <- rnorm(5); res[[i]] <- res1 } res[[1]] # Now I want to reduce the dimension of "res" through creating a data frame li

Re: [R] How to get rid of NULL in the result of apply()?

2009-12-10 Thread hadley wickham
> Is there a version of apply that returns a list without NULL's? > > I try to remove NULL elements in the following example, but neither > for loops work. Would you please let me know what the correct way is? Try this function: compact <- function(x) Filter(Negate(is.null), x) compact(x) Hadley

Re: [R] How to get rid of NULL in the result of apply()?

2009-12-10 Thread Peng Yu
On Thu, Dec 10, 2009 at 10:00 PM, Marc Schwartz wrote: > On Dec 10, 2009, at 9:44 PM, Peng Yu wrote: > >> The following code returns a list with the 2nd element as NULL. I'm >> wondering what the best way to get rid of NULL element in an >> 'apply()'s result. >> >>> lapply(1:3, function(x) { >> >>

Re: [R] Combining 3D/2D plots

2009-12-10 Thread Deepayan Sarkar
On Thu, Dec 10, 2009 at 8:44 PM, Bruno Goncalves wrote: > Thank you very much.  Your link to the lattice webpage was extremely > helpful. > Now I just need to pour over the wireframe, panel.3d, etc... documentation > and try to figure out a way of combining 13.7 and 13.9 :) You should also consid

[R] library(survival)-- cluster

2009-12-10 Thread sayan dasgupta
dear all Can you please throw some light on this .I am getting som error when I use library(survival) model <- survreg(Surv(time, status) ~ rx + cluster(litter), rats) Error in rowsum.default(resid(fit, "dfbeta"), cluster) : 'x' must be numeric Why does it throw up error ? Thanks and Regar

Re: [R] How to profile an R program?

2009-12-10 Thread Sharpie
Peng Yu wrote: > > Is there a way to profile an R program similar to valgrind > (valgrind.org), in the sense that I can easily see which function is > the bottleneck of an R program? > See writing R-Extensions, Section 3 "Tidying and Profiling R Code": http://cran.r-project.org/doc/manuals/

Re: [R] Combining 3D/2D plots

2009-12-10 Thread Bruno Goncalves
Thank you very much. Your link to the lattice webpage was extremely helpful. Now I just need to pour over the wireframe, panel.3d, etc... documentation and try to figure out a way of combining 13.7 and 13.9 :) Best, Bruno *** Bruno Miguel Tavares Gonçalve

[R] [R-pkgs] ggplot2: version 0.8.4

2009-12-10 Thread Hadley Wickham
ggplot2 ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (l

Re: [R] How to get rid of NULL in the result of apply()?

2009-12-10 Thread Marc Schwartz
On Dec 10, 2009, at 9:44 PM, Peng Yu wrote: The following code returns a list with the 2nd element as NULL. I'm wondering what the best way to get rid of NULL element in an 'apply()'s result. lapply(1:3, function(x) { + if(x==2) { + return(NULL) + } else { + return

[R] readHTML within tm package

2009-12-10 Thread Peter O'Donnell
I'm hoping to work with the tm package with some html documents. In the documentation and in the the tutorial material it says that there is a readHTML routine that can be used to read HTML documents into a corpus. However, when I try to use that routine I get an error. When I run getReaders (belo

[R] How to get rid of NULL in the result of apply()?

2009-12-10 Thread Peng Yu
The following code returns a list with the 2nd element as NULL. I'm wondering what the best way to get rid of NULL element in an 'apply()'s result. > lapply(1:3, function(x) { + if(x==2) { + return(NULL) + } else { + return(x) + } + } + ) [[1]] [1] 1 [[2]

Re: [R] Combining 3D/2D plots

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 9:09 PM, David Winsemius wrote: Take a look at Figure 13.7 in Sarkar's Lattice book, all of whose figures are on the web page for the book, I believe. ... yep... http://lmdvr.r-forge.r-project.org/figures/figures.html (tried to extract the link to that page but you w

[R] How to profile an R program?

2009-12-10 Thread Peng Yu
Is there a way to profile an R program similar to valgrind (valgrind.org), in the sense that I can easily see which function is the bottleneck of an R program? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do re

Re: [R] How to get the runtime as well as the result?

2009-12-10 Thread Peng Yu
On Thu, Dec 10, 2009 at 7:03 PM, Dirk Eddelbuettel wrote: > > On 10 December 2009 at 18:12, Peng Yu wrote: > | If I use system.time() to measure the runtime of an expression, I will > | not get the result. Is there a way to measure the runtime and get the > | result as well? > > Use an assignment

Re: [R] About R memory management?

2009-12-10 Thread Peng Yu
Thatis was not my original question. My original questions was how memory is managed/allocated in R? On Thu, Dec 10, 2009 at 6:08 PM, jim holtman wrote: > If you really want to code like a C++ coder in R, then create your own > object and extend it when necessary: > > # take a variation of this;

Re: [R] Combining 3D/2D plots

2009-12-10 Thread David Winsemius
Take a look at Figure 13.7 in Sarkar's Lattice book, all of whose figures are on the web page for the book, I believe. ... yep... http://lmdvr.r-forge.r-project.org/figures/figures.html (tried to extract the link to that page but you will need to navigate the page yourself. On Dec 10,

[R] Combining 3D/2D plots

2009-12-10 Thread Bruno Goncalves
Dear All, This is my first post to this mailing list (and yes, I did read http://www.r-project.org/posting-guide.html ) so please forgive any faux pas. I'm trying to make a visualization that looks like this http://www.gradient-da.com/img/temperature%20surface%20plot%20470x406.JPG(found through go

Re: [R] How to get the runtime as well as the result?

2009-12-10 Thread Dirk Eddelbuettel
On 10 December 2009 at 18:12, Peng Yu wrote: | If I use system.time() to measure the runtime of an expression, I will | not get the result. Is there a way to measure the runtime and get the | result as well? Use an assignment inside system.time(): R> system.time( m <- max(rnorm(1e6)) )

[R] How to get the runtime as well as the result?

2009-12-10 Thread Peng Yu
If I use system.time() to measure the runtime of an expression, I will not get the result. Is there a way to measure the runtime and get the result as well? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] About R memory management?

2009-12-10 Thread jim holtman
If you really want to code like a C++ coder in R, then create your own object and extend it when necessary: # take a variation of this; preallocate and then extend when you read a limit x <- numeric(2) for (i in 1:100){ if (i > length(x)){ # double the length (or whatever you want)

Re: [R] incorrect multiple outputs

2009-12-10 Thread jim holtman
If I rad you code right, file.rows is equal to 1 and your 'for' loop will only iterate once. Is that what you were expecting? No reproducible code provided, so that is my best guess. >file.rows<- c(nrow(file)/288) # "input_file.txt" contains 288 reformatted lines for each original data file ...

Re: [R] non-linear regression

2009-12-10 Thread Katharine Mullen
You did not provide the data or a way of generating it. I would guess that Excel finds the same solution (the same residual sum-of squares) as nls but that it uses a weak convergence criterion and/or does not give you information regarding why it terminates. Regarding the step size: you can set

[R] R CMD SHLIB requesting makefile. Is a makefile required?

2009-12-10 Thread Mark Kimpel
A few years ago I used the following to compile a shared object that I wanted to call from R and it worked just fine. R CMD SHLIB -o ~/my_C/R.shared.so/cocite.mat.so cocite.mat.c Now when it is executed I receive the following error message: make: *** No rule to make target `cocite.mat.o', needed b

Re: [R] Labeling plot points

2009-12-10 Thread Doug Hill
Thanks, Greg, downloading now! Doug Greg Snow-2 wrote: > > There are 2 functions in the development version of the TeachingDemos > package (the version on R-forge, not CRAN yet) that do just what you > describe. The functions are HWidentify which only works on windows > machines and HTKident

Re: [R] Open user's R function

2009-12-10 Thread Lisa
It works. Thank you for your help. Lisa David Winsemius wrote: > > > On Dec 10, 2009, at 5:19 PM, Lisa wrote: > >> >> Dear all, >> >> How can I open my own function in the R console window? For example, >> I have >> a function called my.function.r saved at the following directory >> >> >>

Re: [R] Open user's R function

2009-12-10 Thread David Winsemius
Except when you are using regular expressions. On Dec 10, 2009, at 5:51 PM, Tal Galili wrote: > Two backslashes... > > > > Contact > Details:--- > Contact me: tal.gal...@gmail.com | 972-52-7275845 > Read me: www.talgalili.com

Re: [R] Open user's R function

2009-12-10 Thread Tal Galili
Two backslashes... Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -

[R] R CMD check glitch (resolved)

2009-12-10 Thread Prof. John C Nash
Today I wanted to update one of my r-forge packages (optimx) and when I ran the usual R CMD check optimx I got all sorts of odd errors with Latex (and a very slow R CMD check). I thought I had managed to damage the Rd file, which indeed I had changed. Since I recently started using Ubuntu 9.0

Re: [R] mutlidimensional in.convex.hull (was multidimensional point.in.polygon??)

2009-12-10 Thread Charles C. Berry
On Thu, 10 Dec 2009, Keith Jewell wrote: Hi All (especially Duncan and Baptiste), Summary (of lengthy bits below): I will have a convex hull in multiple (3 to 10) dimensions derived from many (thousands) of points by geometry::convhulln. I will need to categorise other 'test' points as inside/o

Re: [R] Open user's R function

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 5:19 PM, Lisa wrote: Dear all, How can I open my own function in the R console window? For example, I have a function called my.function.r saved at the following directory Try: source(file="E:/My documents/R files/my.function.r") Note that I changed the backslash

[R] Open user's R function

2009-12-10 Thread Lisa
Dear all, How can I open my own function in the R console window? For example, I have a function called my.function.r saved at the following directory E:\My documents\R files Now I want to input a command in the R console window to open my.function.r. How can I do it? Thank you in advance. Lis

Re: [R] Need help to forecasting the data of the time series .

2009-12-10 Thread G. Jay Kerns
Dear R-help, This thread was started by a graduate student that I am supervising who is supposed to know how to do this already. I would appreciate it if the readers of this list would please refrain from any further responses to him; he was supposed to complete this project on his own to satis

Re: [R] barplot and cumulative curve using ggplot2 layers

2009-12-10 Thread hadley wickham
Hi Sunita, To get the bars, you want: ggplot(mydata, aes(x = factor(jobno), y = recruits)) + geom_bar() and to add the cumulative sum, first add it to the data: mydata$cum_ recruits <- cumsum(mydata$recruits) and then add another layer: + geom_line(aes(y = cum_recruits, group = 1)) Hadley O

Re: [R] problem with data processing in R

2009-12-10 Thread Tal Galili
Hi Maxim, Yes, it is possible. Please review the information here: http://www.statmethods.net/management/subset.html In short, you need to read in your file at one chunk (maybe using read.table) and then subset and plot it however you want. If this was a bigger job I would send you to learn the p

Re: [R] Labeling plot points

2009-12-10 Thread Greg Snow
There are 2 functions in the development version of the TeachingDemos package (the version on R-forge, not CRAN yet) that do just what you describe. The functions are HWidentify which only works on windows machines and HTKidentify which uses the tcltk package. Hope this helps, -- Gregory (Gr

Re: [R] vector help

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 3:47 PM, Steve Lianoglou wrote: Hi Ramya, On Dec 10, 2009, at 3:29 PM, David Winsemius wrote: On Dec 10, 2009, at 2:55 PM, Ramya wrote: I have tow vectors one is the subset of another x is a subset of X Both are vectors with n elements X[X %in% x] would give me x ag

[R] Labeling plot points

2009-12-10 Thread Doug
Hi, all. I've been searching for a while to find out how to create an scatterplot which would let a user interact with it, specifically by hovering the mouse over a point and having a pop-up appear with data about the point. The pop-up would disappear when the mouse moved away. I've included a moc

Re: [R] MLE for a t distribution

2009-12-10 Thread Barbara Gonzalez
Thank you. I actually found fitdistr() in the package MASS, that "estimates" the df, but it does a very bad job. I know that the main problem is that the t distribution has a lot of local maxima, and of course, when k->infty we have the Normal distribution, which has nice and easy to obtain MLEs.

Re: [R] MLE for a t distribution

2009-12-10 Thread Albyn Jones
k -> infinity gives the normal distribution. You probably don't care much about the difference between k=1000 and k=10, so you might try reparametrizing df on [1,infinity) to a parameter on [0,1]... albyn On Thu, Dec 10, 2009 at 02:14:26PM -0600, Barbara Gonzalez wrote: > Given X1,...,Xn ~ t

Re: [R] vector help

2009-12-10 Thread Steve Lianoglou
Sender: r-help-boun...@r-project.org On-Behalf-Of: mailinglist.honey...@gmail.com Subject: Re: [R] vector help Message-Id: <2154bd29-add9-4cfc-8447-ba5eea3a3...@gmail.com> Recipient: yingmei.la...@magnetar.com --- Begin Message --- Hi Ramya, On Dec 10, 2009, at 3:29 PM, David Winsemius wrote: >

Re: [R] vector help

2009-12-10 Thread Steve Lianoglou
Sender: microsoftexchange329e71ec88ae4615bbc36ab6ce411...@magnetar.com On-Behalf-Of: mailinglist.honey...@gmail.com Subject: Re: [R] vector help Message-Id: <118a120f-a549-4bbe-86a4-8157e6529...@journal.report.generator> Recipient: 20...@boyersesf.com --- Begin Message --- Sender: r-help-boun..

Re: [R] vector help

2009-12-10 Thread Steve Lianoglou
Hi Ramya, On Dec 10, 2009, at 3:29 PM, David Winsemius wrote: > > On Dec 10, 2009, at 2:55 PM, Ramya wrote: > >> >> I have tow vectors one is the subset of another >> >> x is a subset of X Both are vectors with n elements >> >> X[X %in% x] would give me x again rite because it is a subset bu

[R] January 2010***R Courses*** by XLSolutions Corp at 9 USA Cities: San Francisco, New York, Washington DC, Houston, Boston, Las Vegas, Seattle, etc

2009-12-10 Thread Sue Turner
Happy New Year ! XLSolutions January 2010 R courses schedule is now available online at 9 USA cities for *** R/Splus Fundamentals and Programming Techniques and R Advanced Programming***courses in January 2010. www.xlsolutions-corp.com/courselist.asp * New York City ** January

Re: [R] vector help

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 2:55 PM, Ramya wrote: I have tow vectors one is the subset of another x is a subset of X Both are vectors with n elements X[X %in% x] would give me x again rite because it is a subset but i want all those are not in x from X. X[which(X != x)] should this do that Per

[R] Need help creating multiple datasets using loops or vectorization

2009-12-10 Thread Anderson, Chris
I am trying to create multiple dataset by group like the following using either a loop or vectorization: vocallGp1<-subset(vocallsub, Group==1) vocallGp2<-subset(vocallsub, Group==2) vocallGp3<-subset(vocallsub, Group==3) vocallGp4<-subset(vocallsub, Group==4) vocallGp5<-subset(vocallsub, Group

[R] non-linear regression

2009-12-10 Thread AneSR
I have a non-linear regression with 8 parameters to solve however it does not converge ... easily solves the excel ... including the initial estimates used in the R were found in the excel ... Another question is how to establish the increments of R by the parameters in the search .. qx.sua

[R] Is there a variant of findInterval() such that v[i[j]] < x[j] <= v[i[j] + 1]?

2009-12-10 Thread Peng Yu
In findInterval's help page, it says 'v[i[j]] <= x[j] < v[i[j] + 1]'. I'm wondering if there is a variant of it such that 'v[i[j]] < x[j] <= v[i[j] + 1]'. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read th

[R] MLE for a t distribution

2009-12-10 Thread Barbara Gonzalez
Given X1,...,Xn ~ t_k(mu,sigma) student t distribution with k degrees of freedom, mean mu and standard deviation sigma, I want to obtain the MLEs of the three parameters (mu, sigma and k). When I try traditional optimization techniques I don't find the MLEs. Usually I just get k->infty. Does anybod

Re: [R] Moving Averages in ggplot2

2009-12-10 Thread Gabor Grothendieck
You probably want to use a time series package for this. There are plotting facilities specifically aimed at time series in zoo, xts, quantmod, timeSeries and latticeExtra. We illustrate with zoo which has classic graphics and lattice graphics methods: devAskNewPage(TRUE) library(zoo) set.seed(

Re: [R] How to figure out which the version of split is used?

2009-12-10 Thread Peng Yu
On Thu, Dec 10, 2009 at 3:46 AM, Karl Ove Hufthammer wrote: > On Wed, 9 Dec 2009 19:20:47 -0600 Peng Yu wrote: >> Is there a way to figure out which of these variants is actually >> dispatched to when I call split? I know that if the argument is of the >> type data.frame, split.data.frame will be

[R] vector help

2009-12-10 Thread Ramya
I have tow vectors one is the subset of another x is a subset of X Both are vectors with n elements X[X %in% x] would give me x again rite because it is a subset but i want all those are not in x from X. X[which(X != x)] should this do that Thanks Ramya -- View this message in context: http

Re: [R] Assigning variables into an environment.

2009-12-10 Thread Rolf Turner
Thanks to Gabor Grothendieck, Duncan Murdoch, Hadley Wickham, and Bert Gunter for their useful input. I'm beginning to get a glimmering of understanding, and I think I now have enough to make some progress. cheers, Rolf Turner #

Re: [R] .Rhistory in R.app

2009-12-10 Thread Rolf Turner
On 11/12/2009, at 8:30 AM, Maria Gouskova wrote: Renaming the .Rhistory file to .Rosxhistory didn't solve the problem for me--the file is still empty. And I have confirmed that it is a problem specific to R.app--running R from Terminal works fine, adding records to the existing .Rhistory file.

Re: [R] How to scale a histogram

2009-12-10 Thread Rolf Turner
On 11/12/2009, at 4:01 AM, terry johnson wrote: If I want to scale a histogram ie multiply by a constant how would I do this? Thanks This question is pretty vague. Please read the posting guide. If you want to rescale the y-axis you could do something like: > set.seed(333) # Only half ev

Re: [R] .Rhistory in R.app

2009-12-10 Thread Maria Gouskova
Renaming the .Rhistory file to .Rosxhistory didn't solve the problem for me--the file is still empty. And I have confirmed that it is a problem specific to R.app--running R from Terminal works fine, adding records to the existing .Rhistory file. Too bad there is no apparent workaround. Thanks, eve

Re: [R] Help with beanplot fromatting

2009-12-10 Thread James Widman
Sorry for the previous error. Dear Helpful R Users, I am graphing some data using the beanplot, but I am having trouble getting the output I desire. I have five tanks (A-E) and 2 groups for each tank grp1 or grp2, except tank C where there is only grp1. (I only changed the grouprep to "C grp1

Re: [R] global variables in a function

2009-12-10 Thread Gray Calhoun
Hi Keith, A more specific example of what you're looking for might be helpful--ie do you want to read global variables or set them? You probably want to look at environments and closures; ?"<<-" and ?assign are good starting points (the latter has an example of "Global Assignment within a function

Re: [R] Need help to forecasting the data of the time series .

2009-12-10 Thread stephen's mailinglist account
On Thu, Dec 10, 2009 at 12:34 AM, nivas wrote: > > Hi, > This is the time series data collected from 2001 to 2008 by every > month.so,there are 96 entries.I have done basic statistics.I need to find a > model fitted to forecast this data.This is the mixedpaper collection for > recycling in the cam

[R] Moving Averages in ggplot2

2009-12-10 Thread fruminator
Hello all, Have some time series data stored in a data.frame, and am plotting it with ggplot2 (which is totally awesome). I have explored the documentation and mailing list archives, and I can't see any way to plot a 'smoother' that is just the K-step moving average. For example, imagine I had

Re: [R] [R-pkgs] survey package (3.18)

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 1:41 PM, Brad Fulton wrote: Does the survey package have a function similar to prop.test() Or is there a way to use svyciprop() to perform a Chi-square test to see if the difference in proportions is significant? That would only give you CIs around the separate propo

Re: [R] simple data manipulation question

2009-12-10 Thread Bert Gunter
Scratch my suggestion. You have a data frame of variables which is what aggregate() is for. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Greg Snow Sent: Thursday, December 10, 2

Re: [R] [R-pkgs] survey package (3.18)

2009-12-10 Thread Brad Fulton
Does the survey package have a function similar to prop.test() Or is there a way to use svyciprop() to perform a Chi-square test to see if the difference in proportions is significant? I'm comparing liberal congregations with conservative congregations in their sponsorship of HIV/AIDS programs.

Re: [R] simple data manipulation question

2009-12-10 Thread Bert Gunter
... or perhaps simpler is ?ave Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Greg Snow Sent: Thursday, December 10, 2009 9:48 AM To: dolar; r-help@r-project.org Subject: Re: [R] si

[R] option for multi thread or multi core machines

2009-12-10 Thread Anderson, Chris
I notice that R basic installation does not take advantage of multi-thread or multi-core processors. Is there an option for multi-threaded processors? I currently run all of my analysis on thinkpad laptop and most processing is very quick, however, when I run stepAIC with interaction terms it c

Re: [R] simple data manipulation question

2009-12-10 Thread Greg Snow
?aggregate -- 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 dolar > Sent: Wednesday, December 09, 2009 5:51 PM

Re: [R] plotting with varying dot sizes

2009-12-10 Thread Greg Snow
The symbols function may work better than plot for this situation. -- 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 Beha

[R] mutlidimensional in.convex.hull (was multidimensional point.in.polygon??)

2009-12-10 Thread Keith Jewell
Hi All (especially Duncan and Baptiste), Summary (of lengthy bits below): I will have a convex hull in multiple (3 to 10) dimensions derived from many (thousands) of points by geometry::convhulln. I will need to categorise other 'test' points as inside/outside that convex hull . e.g. given:

Re: [R] updating arguments of formulae

2009-12-10 Thread Moreno Ignazio Coco
Michael, Thanks a lot for your reply, I have now understood how to fiddle around with the formulae updates...my question (see my previous e-mail where I was sketching this problem out) about LME models remains open... whether: depM ~ (1 |Sb2) + OS + (1 + OS | Sb2) + VR + (1 + VR | Sb2) is

[R] incorrect multiple outputs

2009-12-10 Thread biscuit
HI, I'm having trouble with a piece of Rscript which keeps outputting incorrectly. it's something like this: the code reads in from a file which contains (reformated) input >file<-read.table(file="input_file.txt",sep="\t")[,c(1,3:5)] > >file.rows<- c(nrow(file)/288) # "input_file.txt" contains

Re: [R] PH Model assumption

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 12:11 PM, Ashta wrote: Hi all, I was trying to test the assumption of proportional hazards assumption, I used the cox.zph function cox.zph(coxfit6) Results are: rhochisqp x1 -0.03961.397 2.37e-01 x2 0.11079.715

Re: [R] About R memory management?

2009-12-10 Thread Peng Yu
I have a situation that I can not predict the final result's dimension. In C++, I believe that the class valarray could preallocate some memory than it is actually needed (maybe 2 times more). The runtime for a C++ equivalent (using append) to the R code would still be C*n, where C is a constant a

Re: [R] About R memory management?

2009-12-10 Thread hadley wickham
For the case below, you don't need to know anything about how R manages memory, but you do need to understand basic concepts algorithmic complexity. You might find "The Algorithm Design Manual", http://www.amazon.com/dp/1848000693, a good start. Hadley On Thu, Dec 10, 2009 at 10:26 AM, Peng Yu

Re: [R] About R memory management?

2009-12-10 Thread Henrik Bengtsson
Related... Rule of thumb: Pre-allocate your object of the *correct* data type, if you know the final dimensions. /Henrik On Thu, Dec 10, 2009 at 8:26 AM, Peng Yu wrote: > I'm wondering where I can find the detailed descriptions on R memory > management. Understanding this could help me understa

Re: [R] Assigning variables into an environment.

2009-12-10 Thread Bert Gunter
V&R's S PROGRAMMING has a lucid (to me) discussion of environments/lexical scoping starting on p. 63. I am unable to judge whether it is sufficiently complete to satisfy Rolf's (or others') needs, however. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-b

[R] PH Model assumption

2009-12-10 Thread Ashta
Hi all, I was trying to test the assumption of proportional hazards assumption, I used the cox.zph function >cox.zph(coxfit6) Results are: rhochisqp x1 -0.03961.397 2.37e-01 x2 0.11079.715 1.83e-03 x3 -0.08857.7435.39

Re: [R] Have you used RGoogleDocs and RGoogleData?

2009-12-10 Thread Farrel Buchinsky
That would be fantastic. How about an option whereby all the worksheets are downloaded and read into dataframes and appear as a a list of dataframes? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Thu, Dec 10, 2009 at 10:38, Adrian Dragulescu wrote: > > I will try to have something in pla

Re: [R] Statistical question and implementation

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 10:59 AM, Santosh wrote: Dear R/Statistics-gurus! I tried to find answer to my hypothetical question and in vain. Sorry, I don't have a dataset that fits into this hypothetical question and pardon me if my explanations/use of statistical terms are not accurate. It doe

Re: [R] Avoid for-loop in creating data.frames

2009-12-10 Thread Henrique Dallazuanna
Try this: lapply(1:ncol(set2), function(idx)set2[is.na(set2[,idx]),idx, drop = FALSE]) On Thu, Dec 10, 2009 at 2:33 PM, Andreas Wittmann wrote: > Hi babtiste, > > thank you very much for your fast answer. your solution is very good, but i > also need the dimnames as in the for-loop for further c

Re: [R] Avoid for-loop in creating data.frames

2009-12-10 Thread Andreas Wittmann
Hi babtiste, thank you very much for your fast answer. your solution is very good, but i also need the dimnames as in the for-loop for further calculations. best regards Andreas baptiste auguie wrote: Hi, Is the following close enough? apply(set2, 2, function(x) x[is.na(x)]) HTH, bap

[R] About R memory management?

2009-12-10 Thread Peng Yu
I'm wondering where I can find the detailed descriptions on R memory management. Understanding this could help me understand the runtime of R program. For example, depending on how memory is allocated (either allocate a chuck of memory that is more than necessary for the current use, or allocate th

Re: [R] heatmap/image from csv data

2009-12-10 Thread Liat
This worked :o) Thanks very much! Liat wrote: > > Hi all, > I'm trying to use heat.map to display some data. > The data is originally in csv format and when I read it in R using > read.table I get: > a b c d e > 1 A 1 1 1 1 > 2 B 1 0 1 1 > 3 C 0 1 0 1 > 4 D 1 1 1 0 > 5 E 1 0 0 0 > The problem

Re: [R] Avoid for-loop in creating data.frames

2009-12-10 Thread baptiste auguie
Hi, Is the following close enough? apply(set2, 2, function(x) x[is.na(x)]) HTH, baptiste 2009/12/10 Andreas Wittmann : > Dear R-users, > > after several tries with lapply and searching the mailing list, i want to > ask, wheter and how it is possibly to avoid the for-loop in the following > pie

Re: [R] global variables in a function

2009-12-10 Thread Gabor Grothendieck
I think you are looking for a macro facility. See defmacro in gtools which is based on Thomas Lumley's function of the same name whose article you can find in back issues of R News. On Thu, Dec 10, 2009 at 11:00 AM, Keith Jones wrote: > Y'all, > > I would like to have most of the variables in m

[R] Avoid for-loop in creating data.frames

2009-12-10 Thread Andreas Wittmann
Dear R-users, after several tries with lapply and searching the mailing list, i want to ask, wheter and how it is possibly to avoid the for-loop in the following piece of code? set2<-as.data.frame(matrix(rnorm(9),ncol=3)) set2[1,1] <- NA set2[3,2] <- NA set2[2,1] <- NA dimnames(set2)[1] <-

[R] Statistical question and implementation

2009-12-10 Thread Santosh
Dear R/Statistics-gurus! I tried to find answer to my hypothetical question and in vain. Sorry, I don't have a dataset that fits into this hypothetical question and pardon me if my explanations/use of statistical terms are not accurate. It does sound a weird question, but I want to rule out that

[R] global variables in a function

2009-12-10 Thread Keith Jones
Y'all, I would like to have most of the variables in my function to be global instead of local. I have not found any references that tell me now to do that. If I have missed a reference please excuse me and tell me what I have missed. Thanks, Keith Jones __

Re: [R] Help with missing values in the dataset

2009-12-10 Thread Nikhil Kaza
?merge use all=L On 10 Dec 2009, at 6:06AM, Venkatesh.P wrote: Dear all, I am facing problem with inserting the scheduled day of Observation in the dataset. In the dataset I have only relative time (table 1) and not scheduled day of observation (day 1, 4, 8, 15, 22, 29, 36, 43). I would

[R] Help with beanplot fromatting

2009-12-10 Thread James Widman
Dear Helpful R Users, I am graphing some data using the beanplot, but I am having trouble getting the output I desire. I have five tanks (A-E) and 2 groups for each tank grp1 or grp2, except tank C where there is only grp1. (I only changed the grouprep to "C grp1" for the example) When I plot

Re: [R] Fwd: Evaluating a function within a pre-defined environment?

2009-12-10 Thread hadley wickham
On Wed, Dec 9, 2009 at 4:48 PM, David Reiss wrote: > Ideally I would like to be able to use the function f (in my example) > as-is, without having to designate the environment as an argument, or > to otherwise have to use "e$x" in the function body. e <- new.env() e$x <- 3 f <- function(xx) x <<-

[R] Graph for finding patterns

2009-12-10 Thread Sunitap22
Hello I am searching for a graph for finding the patterns in writing of Authors. I have around 8 to 10 Authors for whom we have tabulated their writing times. for e.g the data is as follows: Author TimeofWriting A 2009-09-16:57:35:45 A

Re: [R] Have you used RGoogleDocs and RGoogleData?

2009-12-10 Thread Adrian Dragulescu
I will try to have something in place by Monday to allow you to download a specific sheet not default to the first. I will let you know. Adrian On Thu, 10 Dec 2009, Farrel Buchinsky wrote: Thank you Adrian. Your response was very informative. ?downloadDocument filled me with excitement un

Re: [R] heatmap/image from csv data

2009-12-10 Thread David Winsemius
On Dec 10, 2009, at 10:19 AM, Liat wrote: I have looked at the help for data.matrix. But didn't find a solution. data.matrix only gets two arguments the data and a logical rownames.force - I have tried to change this logical to TRUE but that doesn't help. Any advice would be greatly appreci

[R] barplot and cumulative curve using ggplot2 layers

2009-12-10 Thread Sunitap22
Hello My dataset is as follows: jobno recruits 1100 18 1200 1 1850 5 2100 190 2789 25 3000 1 .. .. the dataset has 130 rows I want to plot barplot from left side and cumulative curve from ri

Re: [R] simple data manipulation question

2009-12-10 Thread Felipe Carrillo
Or like this: d = data.frame(gender=c("m","f","unkown"), x=rnorm(300)) ddply(d,"gender",summarise,mean=mean(x)) Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish & Wildlife Service California, USA --- On Thu, 12/10/09, smu wrote: > From: smu > Subje

Re: [R] heatmap/image from csv data

2009-12-10 Thread Liat
I have looked at the help for data.matrix. But didn't find a solution. data.matrix only gets two arguments the data and a logical rownames.force - I have tried to change this logical to TRUE but that doesn't help. Any advice would be greatly appreciated. Thanks!! Liat wrote: > > Hi all, > I'm tr

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