Re: [R] Multiple hist(ograms) - One plot

2008-10-01 Thread Dieter Menne
Michael Just gmail.com> writes: > I am trying to plot multiple histograms with the same scales, etc into one > plot. The commands below produce a 3 page PDF with each histogram occupying > the upper right quadrant. And use slightly different scales on the X and Y > axes. I suggest that you forge

Re: [R] fft inverse display help

2008-10-01 Thread Dieter Menne
charter.net> writes: > > ff <- complex(length(fs)) > ff[9] <- fs[9] > ff[5] <- fs[5] > > Include the DC component: > > ff[1] <- fs[1] > > Take the inverse > > fi <- fft(ff, inverse=TRUE) / length(ff) > > Plot > > plot(fi) > > Notice that the plot is the Re vs. Im on the x and y axis' res

[R] How do one suggest a patch for the Foreign package

2008-10-01 Thread fsando
Hi I believe I have long time solution to the problems with the read.spss() funtion. In non-ascii locales the import of spss files into R has consistently produced errors and sometimes wouldn't allow import at all. I've made a custom version of the read.spss() function that appear to solv

Re: [R] Bug or feature with finding a list element?

2008-10-01 Thread Chunhao Tu
Hi, I have tried this with R-2.7.2 then I got > alist[['goodbye']] NULL > alist[['hi']] NULL > alist[['hello']] [1] 10 The results make sense to me thus you might want to update your R version. chunhao B Fox wrote: > > This seems odd. When I try to look up a list element which has a space

Re: [R] using bquote to construct function

2008-10-01 Thread Sundar Dorai-Raj
Thanks, Gabor! This workaround fixes my immediate needs. --sundar Gabor Grothendieck said the following on 10/1/2008 10:42 PM: That may be a bug in R but I think there is another problem on top of that as I don't think bquote descends into function bodies: z <- 2 bquote(function(x) {x^.(z)})

Re: [R] using bquote to construct function

2008-10-01 Thread Gabor Grothendieck
That may be a bug in R but I think there is another problem on top of that as I don't think bquote descends into function bodies: > z <- 2 > bquote(function(x) {x^.(z)}) function(x) {x^.(z)} > bquote(function(x, y) { x^.(z) + y}) function(x, y) { x^.(z) + y} > R.version.string # Vista [1] "R ver

[R] matrix with different type of column [SEC=UNCLASSIFIED]

2008-10-01 Thread ZHU, Justin
Hi, I would like to create a matrix. Say 5*4. The first column is integer, the second column is date, the third column is character and the rest columns are integers. So it's a combination of different types. I am wondering how can I do that? "matrix" command only allow one type. **

Re: [R] an unsophisticated question about recoding in a data frame with control structure if {}

2008-10-01 Thread Kenn Konstabel
if expects just one condition (no vectors); see ?ifelse dataframe$thevector <- ifelse(dataframe$factor=="3", a.mean, dataframe$thevector) K On Wed, Oct 1, 2008 at 12:05 PM, Whitt Kilburn <[EMAIL PROTECTED]> wrote: > Hello all, > > I apologize for a terribly simple question. I'm used to using

[R] Multiple hist(ograms) - One plot

2008-10-01 Thread Michael Just
Hello, I am trying to plot multiple histograms with the same scales, etc into one plot. The commands below produce a 3 page PDF with each histogram occupying the upper right quadrant. And use slightly different scales on the X and Y axes. > s21 <- dat[dat$sc_recov=="21",] > s21.ED <- subset(s21, s

[R] using bquote to construct function

2008-10-01 Thread Sundar Dorai-Raj
Hi, R-help, (sessionInfo at the end) I'm trying to construct a function using bquote and running into a strange error message. As an example, what I would like to do is this: z <- 2 eval(bquote(function(x, y) { x^.(z) + y }))(2, 3) However, I get the following: Error in eval(expr, envir, en

Re: [R] lapply where each list object has multiple parts

2008-10-01 Thread Chunhao Tu
Hi Eric, > data<-list(x1 <- c(0,1,2,3),x2 <- c(7,8),x3 <- c(2,6,6,8), x4 <- c(4,8)) > lapply(X=data, mean) [[1]] [1] 1.5 [[2]] [1] 7.5 [[3]] [1] 5.5 [[4]] [1] 6 Hope it helps Chunhao eric lee-8 wrote: > > Hi. I have a list where each object in the list has multiple parts. I'd > like to

Re: [R] movie3d function in the rgl package

2008-10-01 Thread Daniel McGlinn
Dear Duncan, Thanks for your quick response! I really like the rgl package. First a clarification. I was not using IMDisplay to try to view the .gif file. I apologize for that confusion. I attempted to open the file with Mozilla firefox which works but unfortunately only displays a black box.

[R] pvals.fnc in lme4 and languageR

2008-10-01 Thread Daniela Reicheneder
Hi everybody! I was using the function pvals.fnc from package 'languageR' until April. I do not know which version. Yesterday I updated all my packages and tried to run my loop again. Now I get the following error message: error in pvals.fnc(mm, nsim = 1000) : MCMC sampling is not yet implemen

[R] Bug or feature with finding a list element?

2008-10-01 Thread B Fox
This seems odd. When I try to look up a list element which has a space in the name using just the first word (i.e. no spaces), it will sometimes return the element with a space in the name and sometimes it will return NULL. Try this: alist <- list( 'hello'=10, bye=20, 'hello world'=30, 'goodbye

Re: [R] Running source() on a file in another directory

2008-10-01 Thread Gabor Grothendieck
Suppose p is a vector of paths, e.g., p <- c("~/dir1", "~/dir2/dir3") Then the following will return the full pathname of the first found location: Find(file.exists, file.path(p, "prog.R")) so you can source that. On Wed, Oct 1, 2008 at 6:09 PM, Gang Chen <[EMAIL PROTECTED]> wrote: > Suppose

Re: [R] writeMat error

2008-10-01 Thread Henrik Bengtsson
Hi. On Sat, Sep 27, 2008 at 5:17 AM, Steele, Dr Douglas <[EMAIL PROTECTED]> wrote: > Hi > > I am using Ubuntu 8.04 64 bit, R as below, Matlab 7.6.0. I would like to > transfer mat files back and forward between R and Matlab. Whilst I have used > Matlab for years its been a long time since I ha

Re: [R] shifting ticks to left or right

2008-10-01 Thread Schreiber, Stefan
Thank you very much! That's the way to go! Cheers, Stefan -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 01, 2008 10:52 AM To: Schreiber, Stefan Cc: r-help@r-project.org; [EMAIL PROTECTED] Subject: Re: [R] shifting ticks to left or right

Re: [R] Bivariate normal

2008-10-01 Thread Ravi Varadhan
I think it is meaningful to ask for a non-trivial Pr (X < x, Y=y) when you are writing down the likelihood for parameter estimation. This is commonly the case in likelihood estimation in bivariate failure time models. If one interprets Pr(Y=y) as the density evaluated y then: Pr(Xhttp://www.jh

[R] Running source() on a file in another directory

2008-10-01 Thread Gang Chen
Suppose I have a file prog.R stored in a directory under ~/dirname, and ~/dirname is set in a shell script file (e.g. .cshrc) as one of the accessible paths on terminal. On a different directory I could run prog.R interactively by executing source("~/dirname/prog.R") It seems that source() does n

Re: [R] Bivariate normal

2008-10-01 Thread Rolf Turner
On 2/10/2008, at 11:02 AM, Ravi Varadhan wrote: I think it is meaningful to ask for a non-trivial Pr (X < x, Y=y) when you are writing down the likelihood for parameter estimation. This is commonly the case in likelihood estimation in bivariate failure time models. If one interprets P

[R] lapply where each list object has multiple parts

2008-10-01 Thread eric lee
Hi. I have a list where each object in the list has multiple parts. I'd like to take the mean of just one part of each object. Is it possible to do this with lapply? If not, can you recommend another function? Thanks. eric > x1 <- c(0,1,2,3) > x2 <- c(7,8) > x3 <- c(2,6,6,8) > x4 <- c(4,8) >

[R] Error: cannot allocate vector of size 117.3 Mb

2008-10-01 Thread ram basnet
Dear R users,   I am using RandomForest package. While using this package, i got "Error: cannot allocate vector of size 117.3 Mb" .message. I had this problem earlier too but could not manage. Is there any way to solve this problem or to increase vector size ? My data set

[R] Aggregate issues with subset

2008-10-01 Thread Michael Just
Hello, I used the aggregate function with success on my data frame "all". > aggregate(all, list(sc_recov), mean) I then made a subset of this data frame: >s.all <-subset(all, select= c(3,4,5,6,7,8,9,10,11,23)) but when I tried to to run the aggregate function on this subset: > aggregate(s.all,

Re: [R] Bias in sample - Logistic Regression

2008-10-01 Thread Wensui Liu
Hi, Shiva, The idea of reject inference is very simple. Let's assume a credit card environment. There are 100 applicants, out of which 50 will be approved and booked in. Therefore, we can only observe the adverse behavior, such as default and delinquency, of 50 booked accounts. Again, let's assume

[R] extracting diagonal from dist()

2008-10-01 Thread stephen sefick
h <- structure(list(V1 = c(-0.351714766, 0.188298251, 0.042951816, -0.072490327, -0.691885485, -0.816169763, -0.7066502, -0.856286332, -0.839723411, -0.427242353, -0.372911996, 0.326707494, 0.07847893, 0.687447841, 0.516105863, 0.267076547, 0.727867663, 0.432699191, 0.258610632), V2 = c(0.256636068

Re: [R] 1-SE rule in mvpart

2008-10-01 Thread Kunio takezawa
R-users E-mail: r-help@r-project.org Hi! >I interprete this as following: the simplest tree with xerror under >min(xerror) + its own xstd >Neverthless, in some article I read the following rule: >the simplest tree with xerror under min(xerror) + xstd corresponding to the >min(xerror) >Is this a m

Re: [R] Bivariate normal

2008-10-01 Thread Rolf Turner
On 2/10/2008, at 4:43 AM, Sasha Pustota wrote: Package mvtnorm provides dmvnorm, pmvnorm that can be used to compute Pr(X=x,Y=y) and Pr(X Yes: foo <- function(x,y) { 0 } I'm currently using "integrate" with dmvnorm but it is too slow. Words fail me

Re: [R] Looking for position of character in a string

2008-10-01 Thread Doran, Harold
> s1 <- "Hello.World" > which(strsplit(s1, '')[[1]]=='.') [1] 6 > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of phoebe kong > Sent: Wednesday, October 01, 2008 2:56 PM > To: r-help@r-project.org > Subject: [R] Looking for position of character in

Re: [R] Looking for position of character in a string

2008-10-01 Thread Henrique Dallazuanna
Try this: gregexpr("\\.", X) On Wed, Oct 1, 2008 at 3:56 PM, phoebe kong <[EMAIL PROTECTED]> wrote: > Hi all, > > I would like to check if a string contains "." in it. If yes, I would like > to know the position of "." in the string. > > Eg: X<-"NM1236.3" > > In above example, "." is at position

[R] Looking for position of character in a string

2008-10-01 Thread phoebe kong
Hi all, I would like to check if a string contains "." in it. If yes, I would like to know the position of "." in the string. Eg: X<-"NM1236.3" In above example, "." is at position 7. I tried functions grep() and match(). It seems they couldn't detect ".". Thanks in advance for your help, Sit

Re: [R] Bivariate normal

2008-10-01 Thread Sasha Pustota
P.S. just "pnorm(x, mean=m, sd=s)", not "1-pnorm(x, mean=m, sd=s) + pnorm(-x, mean=m, sd=s)" On Wed, Oct 1, 2008 at 2:04 PM, Sasha Pustota <[EMAIL PROTECTED]> wrote: > Thanks Jay. I realized that I was doing it a silly way shortly after I > posted and that the answer i was looking for is simply >

Re: [R] changing 'https' to 'http' when using download.file(), any side effects or just use RCurl?

2008-10-01 Thread Tony Breyal
Dear R-help, I have just been informed that I must not rewrite the 'https' as 'http' as some web pages may not download (I think I just got lucky on the ones I've tried thus far). Therefore I would ask if some kind individual could let me know where I can post questions about the RCurl package (Om

[R] changing 'https' to 'http' when using download.file(), any side effects or just use RCurl?

2008-10-01 Thread Tony Breyal
Dear R-Help, >From reading the help file, it is my understanding the the download.file() function does not support HTTPS connections. So therefore, understandably, the follow produces an error: ### R Code > url <- "https://stat.ethz.ch/pipermail/r-help/2008-October/thread.html"; > destfile <- "//

[R] plotting several yearly/monthly time series on the same plotting several yearly/monthly time series on the same graph

2008-10-01 Thread Maximilian Rausch
I have searched the forums but I am having trouble trying accomplish two specific plots. I am not sure if this is a very basic task but I am having a lot of trouble Here is my data frame: dateprod_daily price 1 2003-08-15 12050 4.83 2 2003-08-18 12050

Re: [R] Bivariate normal

2008-10-01 Thread Sasha Pustota
Thanks Jay. I realized that I was doing it a silly way shortly after I posted and that the answer i was looking for is simply condXY(y, x, my, mx, r) * dnorm(y, my) condXY <- function(y, x, my, mx, r) { m <- mx + r*(y - my) s <- sqrt(1-r^2) p <- 1 - pnorm(x, mean=m, sd=s) + pnorm(-x, mean=m

Re: [R] knn class probabilities

2008-10-01 Thread Max Kuhn
On Tue, Sep 30, 2008 at 8:06 PM, Mike Fugate <[EMAIL PROTECTED]> wrote: > Good Day, > > I'm using the knn function in the package class. With k set to 3, the > function returns proportions of 1/3, 0.5, 0.6, 2/3, 3/4, and 1.0 for the > test cases. I don't understand how with k set to 3 the proport

Re: [R] Surprising randomForest Results

2008-10-01 Thread Rodney Barnett
For the sake of anyone else asking this questionas Andy Liaw explained to me, yes, this is expected because predict() uses all the trees in the forest, including the ones based on any particular item in the input data frame. Rodney -Original Message- From: [EMAIL PROTECTED] [mailto:[E

[R] family gamma (GAM fit)

2008-10-01 Thread Marina Laborde
Hello,   Im am trying to fit a GAM (mgcv) using the family gamma and get the followinr error message:   Error in gamma(link = "identity") :   Non-numeric argument to mathematical function   Does anyone know why do i get this? I tried to check in R-help already but I couldn't find anything alike.

[R] Multiple histograms one graphic device & groupings

2008-10-01 Thread Michael Just
Hello, I am trying to produce some graphics to visualize my data. I think I want histograms. I have a grouping variable that has 48 different groups. I would like to produce a graphic that contains three of of these groups in the same device (they are time steps). I would like create graphics for

[R] spectum

2008-10-01 Thread Bill Szkotnicki
Hi, In the help for spectrum it says: " If available, a confidence interval will be plotted by 'plot.spec': this is asymmetric, and the width of the centre mark indicates the equivalent bandwidth. " What you get is a blue bar on the right side of the plot. I can understand the width o

Re: [R] Logistic regression problem

2008-10-01 Thread Pedro.Rodriguez
Hi Bernardo, Do you have to use logistic regression? If not, try Random Forests... It has worked for me in past situations when I have to analyze huge datasets. Some want to understand the DGP with a simple linear equation; others want high generalization power. It is your call... See, e.g.,

Re: [R] Bivariate normal

2008-10-01 Thread G. Jay Kerns
Dear Sasha, On Wed, Oct 1, 2008 at 11:43 AM, Sasha Pustota <[EMAIL PROTECTED]> wrote: > Package mvtnorm provides dmvnorm, pmvnorm that can be used to compute > Pr(X=x,Y=y) and Pr(X > Are there functions that would compute Pr(X I'm currently using "integrate" with dmvnorm but it is too slow. Stri

Re: [R] Negative Binomial Predictions

2008-10-01 Thread Achim Zeileis
On Wed, 1 Oct 2008, Donald Catanzaro, PhD wrote: Good Day All, I have a negative binomial model which I have developed using the MASS library. I now would like to develop some predictions from it. Running the predict.glm (stats library) using type="response" gives me a non-integer value whi

[R] time segments intersection

2008-10-01 Thread [Ricardo Rodriguez] Your XEN ICT Team
Hi all, Please, how could I calculate the time that two time segments has in common? Is there any function to perform this calculation? For instance, given four POSIXlt objects... endPeriod<-as.POSIXlt("2008-09-30") startPeriod<-as.POSIXlt("2007-10-01") endProject<-as.POSIXlt("2007-05-31") st

Re: [R] shifting ticks to left or right

2008-10-01 Thread Richard . Cotton
> Does anybody knows a command to centre the tick mark labels exactly > between the tick points (right shift)? > And then to exclude the last tick label on the right? > > I know one can shift them using the 'hadj' option in par. But I am > wondering if there is a more convenient command! A littl

Re: [R] shifting ticks to left or right

2008-10-01 Thread Duncan Murdoch
Schreiber, Stefan wrote: Hey list, Does anybody knows a command to centre the tick mark labels exactly between the tick points (right shift)? And then to exclude the last tick label on the right? I know one can shift them using the 'hadj' option in par. But I am wondering if there is a more co

Re: [R] movie3d function in the rgl package

2008-10-01 Thread Duncan Murdoch
Daniel McGlinn wrote: Dear list, I am attempting to utilize the function "movie3d" in the package "rgl" to create a .gif animation of a 3d graphic. I understand that this function requires that the program "ImageMagik" is installed, and I have recently downloaded and installed this program.

Re: [R] "group by" functionality in R

2008-10-01 Thread Henrique Dallazuanna
Try this also; xtabs(volume ~ day, data = x) On Wed, Oct 1, 2008 at 10:58 AM, Max Rausch <[EMAIL PROTECTED]> wrote: > I have a data frame with the following information > > day hourvolume > 1 2003-07-18 10 836700 > 2 2003-07-18 11 375000 > 3 2003-07-18 12

Re: [R] question about working with workspaces

2008-10-01 Thread Duncan Murdoch
Daniel Rabczenko wrote: Hello everybody, Two - I hope Simple questions about working with workspaces. Is there a way to force R to start in "clean" workspace / avoid "previously saved workspace restored"? Start with --no-restore. (Start with --help for the full list of command line optio

Re: [R] shifting ticks to left or right

2008-10-01 Thread Peter Dalgaard
Schreiber, Stefan wrote: Hey list, Does anybody knows a command to centre the tick mark labels exactly between the tick points (right shift)? And then to exclude the last tick label on the right? I know one can shift them using the 'hadj' option in par. But I am wondering if there is a more co

Re: [R] "group by" functionality in R

2008-10-01 Thread hadley wickham
On Wed, Oct 1, 2008 at 8:58 AM, Max Rausch <[EMAIL PROTECTED]> wrote: > I have a data frame with the following information > > day hourvolume > 1 2003-07-18 10 836700 > 2 2003-07-18 11 375000 > 3 2003-07-18 12 6 > 4 2003-07-188 102 > 5

Re: [R] question about working with workspaces

2008-10-01 Thread Mark Lyman
Daniel Rabczenko iestat.pl> writes: > > Hello everybody, > > Two - I hope Simple questions about working with workspaces. > > Is there a way to force R to start in "clean" workspace / avoid "previously > saved workspace restored"? When you start R, use the option --no-restore. If you are work

[R] Negative Binomial Predictions

2008-10-01 Thread Donald Catanzaro, PhD
Good Day All, I have a negative binomial model which I have developed using the MASS library. I now would like to develop some predictions from it. Running the predict.glm (stats library) using type="response" gives me a non-integer value which was rather puzzling. I would like to confirm

Re: [R] Change color of plot points based on values of a variable

2008-10-01 Thread Josip Dasovic
Thank you, Dieter: I apologize to all of those who tried to help and who couldn't get my code to work. I now know three things: 1) stop working at midnight; 2) always provide the correct package name (I meant arm(), not car(); and 3) when testing code make sure you do it in a new R window. Die

Re: [R] "group by" functionality in R

2008-10-01 Thread John Kane
Two approaches ?aggregate or the reshape package aggregate(xx$volume, list(day=xx$day), sum) library(reshape) names(xx)[3] <- "value" cast(xx, day ~ ., sum) --- On Wed, 10/1/08, Max Rausch <[EMAIL PROTECTED]> wrote: > From: Max Rausch <[EMAIL PROTECTED]> > Subject: [R] "group by" functionalit

Re: [R] "tapply versus by" in function with more than 1 arguments

2008-10-01 Thread hadley wickham
On Wed, Oct 1, 2008 at 7:21 AM, Cézar Freitas <[EMAIL PROTECTED]> wrote: > Hi. I searched the list and didn't found nothing similar to this. I > simplified my example like below: > > #I need calculate correlation (for example) between 2 columns classified by a > third one at a data.frame, like be

Re: [R] "tapply versus by" in function with more than 1 arguments

2008-10-01 Thread Gabor Grothendieck
The first tapply in your question subsets V1 but not V2 so they are of different length. To subset both tapply over the row names and perform the subsetting in the function: tapply(rownames(dataf), dataf$class, function(r) cor(dataf[r, "V1"], dataf[r, "V2"])) or tapply(rownames(dataf), dataf$cl

Re: [R] Logistic regression problem

2008-10-01 Thread Liaw, Andy
From: Frank E Harrell Jr > > Bernardo Rangel Tura wrote: > > Em Ter, 2008-09-30 às 18:56 -0500, Frank E Harrell Jr escreveu: > >> Bernardo Rangel Tura wrote: > >>> Em Sáb, 2008-09-27 às 10:51 -0700, milicic.marko escreveu: > I have a huge data set with thousands of variable and one binary > >

[R] shifting ticks to left or right

2008-10-01 Thread Schreiber, Stefan
Hey list, Does anybody knows a command to centre the tick mark labels exactly between the tick points (right shift)? And then to exclude the last tick label on the right? I know one can shift them using the 'hadj' option in par. But I am wondering if there is a more convenient command! Thanks a

Re: [R] "group by" functionality in R

2008-10-01 Thread Gábor Csárdi
tapply(data$volume, data$day, sum) would do I think. But I haven't tried, was to lazy to type in some data, I'm sorry. Gabor On Wed, Oct 1, 2008 at 3:58 PM, Max Rausch <[EMAIL PROTECTED]> wrote: > I have a data frame with the following information > > day hourvolume > 1 2003

Re: [R] add labelled contour lines to filled.contour plot

2008-10-01 Thread Alain Guillet
Look at contourplot in the lattice library. There is an example doing what you want. Alain Guillet Mark wrote: Is it possible to add labelled contour lines to filled.contour plot ? [[alternative HTML version deleted]] __ R-help@r-project.o

Re: [R] Logistic regression problem

2008-10-01 Thread Robert A LaBudde
It would not be possible to answer your original question until you specify your goal. Is it to develop a model with external validity that will generalize to new data? (You are not likely to succeed, if you are starting with a "boil the ocean" approach with 44,000+ covariates and millions o

Re: [R] "tapply versus by" in function with more than 1 arguments

2008-10-01 Thread Henrique Dallazuanna
Try this: sapply(by(dataf[,c("V1","V2")], dataf$class, cor), '[', 3) On Wed, Oct 1, 2008 at 9:21 AM, Cézar Freitas <[EMAIL PROTECTED]> wrote: > Hi. I searched the list and didn't found nothing similar to this. I > simplified my example like below: > > #I need calculate correlation (for example

Re: [R] "group by" functionality in R

2008-10-01 Thread jim holtman
?aggregate day hour volume 1 2003-07-18 10 836700 2 2003-07-18 11 375000 3 2003-07-18 12 6 4 2003-07-188 102 5 2003-07-189 39 > aggregate(x$volume, list(x$day), sum) Group.1 x 1 2003-07-18 2681700 On Wed, Oct 1, 2008 at 9:58 AM, Max Rausch <[EM

Re: [R] Surprising randomForest Results

2008-10-01 Thread Liaw, Andy
If you read the help page for randomForest(), you would expect this behavior... In the "Value" section of that help page, it says: predicted the predicted values of the input data based on out-of-bag samples. Andy From: Rodney Barnett > > Is it expected that predict.randomForest() prod

[R] "group by" functionality in R

2008-10-01 Thread Max Rausch
I have a data frame with the following information day hourvolume 1 2003-07-18 10 836700 2 2003-07-18 11 375000 3 2003-07-18 12 6 4 2003-07-188 102 5 2003-07-189 39 I have been trying create a new data frame with the

Re: [R] How to get the day of the year

2008-10-01 Thread Solene Goy
Thanks a lot to all of you, it works now Cheers, Solène Goy> Subject: Re: [R] How to get the day of the year> From: [EMAIL PROTECTED]> To: [EMAIL PROTECTED]> CC: r-help@r-project.org> Date: Wed, 1 Oct 2008 13:52:09 +0100> > On Wed, 2008-10-01 at 08:42 +, Solene Goy wrote:> > Hello,> > I

[R] movie3d function in the rgl package

2008-10-01 Thread Daniel McGlinn
Dear list, I am attempting to utilize the function "movie3d" in the package "rgl" to create a .gif animation of a 3d graphic. I understand that this function requires that the program "ImageMagik" is installed, and I have recently downloaded and installed this program. The R console does not

[R] "tapply versus by" in function with more than 1 arguments

2008-10-01 Thread Cézar Freitas
Hi. I searched the list and didn't found nothing similar to this. I simplified my example like below: #I need calculate correlation (for example) between 2 columns classified by a third one at a data.frame, like below: #number of rows nr = 10 #the third column is to enforce that I need correla

[R] Bivariate normal

2008-10-01 Thread Sasha Pustota
Package mvtnorm provides dmvnorm, pmvnorm that can be used to compute Pr(X=x,Y=y) and Pr(Xhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

[R] Vertex enumeration and center of mass for convex polytops

2008-10-01 Thread Serguei Kaniovski
Dear All! I am looking for a package that contains routines for vertex enumeration and center of mass computation for convex polytops. Thanks in advance, Serguei Kaniovski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-he

[R] Simulating random draws

2008-10-01 Thread Ken Williams
Hi, I have a data frame containing a column of human judgments, some of which are missing: > pr[3] label 1 4 2 4 3 4 4 4 5 NA 6 3 7 3 8 3 9 3 10NA 11NA 12NA 13 2 14 2 15 2 16NA 17 1 18-1 19-1 20-1 Accompan

[R] ploting Lcross fonction

2008-10-01 Thread Lassana TOURE
Hi. I am using the ripley multivariate function Lcross to caracterise the spatial interactions of two factors using monte carlo simulation. envelope(B1, Lcross, nsim=100, rank=1, global=TRUE)->E1 My problem is that My confidence Interval (CI) is not parallel to the X axis when I plot the re

[R] question about working with workspaces

2008-10-01 Thread Daniel Rabczenko
Hello everybody, Two - I hope Simple questions about working with workspaces. Is there a way to force R to start in "clean" workspace / avoid "previously saved workspace restored"? When I load workspace"2" working in workspace"1" everything from "1" is written into "2" is there a way to avoid it

[R] Installing RWeka package in CentOS 5: problems with JAVA?

2008-10-01 Thread Paulo Cortez
Hi, I am a R user, with some experience in MacOS, Linux, etc, but I am having a problem that I cannot solve: I have a linux server (CentOS 5) and I installed sun jdk1.6. For instance: $ java -version Java version "1.6.0_10-rc2" Java(TM) SE Runtime Environment (build 1.6.0_10-rc2-b32) Java Hot

[R] Problem with nesting in lmer

2008-10-01 Thread swertie
Hello, I would like to run a model with nesting design in lmer but I always got the error message "Matrices must have same number of columns in rbind2(..1, r)". My model is: model_3R <- lmer(N~Bareground+Habitat_type_simple+Presence+(1|Region/Ref_lmer),family = "poisson") of course it doesn't sa

[R] add labelled contour lines to filled.contour plot

2008-10-01 Thread Mark
Is it possible to add labelled contour lines to filled.contour plot ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.or

[R] Surprising randomForest Results

2008-10-01 Thread Rodney Barnett
Is it expected that predict.randomForest() produces the response vector when given the same data frame as provided to randomForest()? See below. Thanks. Rodney > rf <- randomForest (Species ~ ., iris) > pc <- predict (rf, iris) > confusion (pc, iris$Species) true object setosa

Re: [R] fft inverse display help

2008-10-01 Thread rkevinburton
Generate the square wave: genseq <- function() { x <- numeric(4*365) s <- seq(as.Date("2005-01-01"), as.Date("2008-12-31"), by="month") ob <- as.vector(s[c(10,22,34,46)] - as.Date("2005-01-01")) oe <- as.vector(s[c(11,23,35,47)] - as.Date("2005-01-01")) for(.index in 1:length(ob)) {

[R] Linear Regression in R

2008-10-01 Thread bioinformatics_guy
I've attached below the output of a program I am running. What I want to do is, get the equation for each of the lines and determine what the overall equation is that is applicable to every scenario (I know that each line is of multiple of the proceeding line; as in the bottom's coefficient is 1x

[R] Minimizing both AIC and df in model selection

2008-10-01 Thread Christoph Scherber
Dear R users, Suppose I have a set of 10 candidate models, and these all differ by a delta-AIC of 5. Would it be sensible, then, to choose the best-fit model as the one that has *both* minimal AIC *and* minimal number of d.f.? Are there any references for such an approach? Many thanks for y

Re: [R] Weibull distribution

2008-10-01 Thread Terry Therneau
>I would like to calculate and plot a Weibull distribution (Weibull best-fit >line, accuracy curves left and right beside the best-fit line) for a simple >set >of data points. I need the shape and the scale parameter for the best-fit and >values like B5, B10, B50, B90, B95. You can use the sur

Re: [R] for loop question Documentation and its application for calculating euclidean distance on MDS ordination axis scores

2008-10-01 Thread Ben Bolker
> I will post data probably tonight, but here is my problem. I have > preformed an MDS on a set of data. I have the scores of the four axes > that > are the optimal solution. I want to calculate the euclidean distance > between time steps of the ordination. See ?dist for a much faster sol

Re: [R] merging a list and data frame

2008-10-01 Thread Mark Lyman
eric lee gmail.com> writes: > > Hi, > > I'd like to merge the following list and data frame by matching the first > column in the data frame to the first number in each object of the list. > I'd also like the merged object to be a list. Any suggestions? Thanks. > > eric > > a <- list(c(1,11

Re: [R] for loop question Documentation and its application for calculating euclidean distance on MDS ordination axis scores

2008-10-01 Thread Gábor Csárdi
Actually, help.search("for") finds Control(base) Control Flow which is exactly where 'for' is documented. In general, if you want the manual page of reserved words, then you'll have to quote them: ?"for" Gabor On Wed, Oct 1, 2008 at 3:39 PM, stephen sefick <[EMAIL PROTECTED]> wrote:

[R] "grep" argument not working in "getGrob"?

2008-10-01 Thread Pedro Barros
Hi All, I have a gTree (x1) produced by ggplot, with the following structure (output from grid.ls, edited): viewport[GRID.VP.15] frame[plot-surrounds] viewport[GRID.VP.16] cellGrob[GRID.cellGrob.137] rect[background] upViewport[1] viewport[GRID.VP.17] cellGrob

Re: [R] for loop question Documentation and its application for calculating euclidean distance on MDS ordination axis scores

2008-10-01 Thread Gabor Grothendieck
One must write ?"for" presumably since for is a reserved word in R. On Wed, Oct 1, 2008 at 9:39 AM, stephen sefick <[EMAIL PROTECTED]> wrote: > ?for doesn't return anything help.search("for") doesn't return anything- > Is the for loop so prevelant in computer programing that the > documentation is

Re: [R] How to label a "vector"

2008-10-01 Thread Henrique Dallazuanna
Use dimnames: dimnames(Z) <- list(c("X1", "X2"), c("X1", "X2", "X3")) On Wed, Oct 1, 2008 at 10:38 AM, cruz <[EMAIL PROTECTED]> wrote: > Hi, > > I have an object, Z: > >> typeof(Z) > [1] "list" > > It looks like: > > [,1] [,2] [,3] > [1,] 111 > [2,] 111 > > How can it label

[R] for loop question Documentation and its application for calculating euclidean distance on MDS ordination axis scores

2008-10-01 Thread stephen sefick
?for doesn't return anything help.search("for") doesn't return anything- Is the for loop so prevelant in computer programing that the documentation is implicit or is R paradigm to discourage the use of the for loop. I will post data probably tonight, but here is my problem. I have preformed an MD

[R] How to label a "vector"

2008-10-01 Thread cruz
Hi, I have an object, Z: > typeof(Z) [1] "list" It looks like: [,1] [,2] [,3] [1,] 111 [2,] 111 How can it label the Rows and Columns with Text? so that it looks like: Y1 Y2 Y3 X1 111 X2 111 Thanks, cruz ___

Re: [R] cryptic error message: "Error in embed(y, lag) : wrong embedding dimension"

2008-10-01 Thread Ben Bolker
jpmorgan.com> writes: > > Dear R Users, > > I've been hit with a cryptic error message: > > "Error in embed(y, lag) : wrong embedding dimension" > > My configuration is: > - R 2.7.2 > - Windows XP Sp2 > > Google returns nothing for this. Could someone suggest what this might > mean ? >

Re: [R] maximum likelihood with constraints in R

2008-10-01 Thread Ben Bolker
Plat, H.J. uva.nl> writes: > There is lots of information about maximum likelihood estimation in R. > However, I didn't came across anything about maximum likelihood > with constraints. > For example, estimation of parameters k(1) to k(20) with > maximum likelihood, where sum(k(i)) = 0. If the

Re: [R] Lattice: don't draw unlabled tick marks

2008-10-01 Thread Dieter Menne
Philipp Pagel wzw.tum.de> writes: > If I only want axis labels on the left and bottom I can set > alternating=F like in the following example: > > Depth <- equal.count(quakes$depth, number=8, overlap=.1) > xyplot(lat ~ long | Depth, data = quakes, scales=list(alternating=F) > > I also would l

Re: [R] Please help me to produce smoothed contour plots

2008-10-01 Thread Simon Wood
One approach would be to smooth the data using `gam' from package `mgcv'. `vis.gam' will contour the resulting smoothed fit if you select `plot.type="contour"'. If the results look ok but you want finer control of what the plot looks like then `predict.gam' can be used to predict from the fitte

Re: [R] fft inverse display help

2008-10-01 Thread Dieter Menne
charter.net> writes: > > So iis what you are saying n plotting the list of compliex numbers 'R' recognizes the non-symmery and plots > it differently (Re vs. Im) rather than versus Time? Mmm... don't fully understand what you mean, mainly because your program example did not run and I had do s

Re: [R] How to get the day of the year

2008-10-01 Thread Gavin Simpson
On Wed, 2008-10-01 at 08:42 +, Solene Goy wrote: > Hello, > I am new to R and I would like to get the day of the year from > numerous data in the following form: %a %d/%b/%Y %H:%M:%S (for > example from Tu 10/Jul/2007 21:59:13 I would like to get 191) > > Whatever I try, I get NAs. Tu isn't

Re: [R] Simon Wood GAMsetup

2008-10-01 Thread Simon Wood
Michela, Thanks for the email. I'm still not completely clear what parts of H you need. Are you just wanting to extract a model matrix for a smooth (i.e. the matrix of basis functions evaluated at the covariate values), or do you need other things, like the smoothing penalty matrix, as well?

[R] maximum likelihood with constraints in R

2008-10-01 Thread Plat, H.J.
Hi R-experts, There is lots of information about maximum likelihood estimation in R. However, I didn't came across anything about maximum likelihood with constraints. For example, estimation of parameters k(1) to k(20) with maximum likelihood, where sum(k(i)) = 0. Is there any standard functi

[R] cryptic error message: "Error in embed(y, lag) : wrong embedding dimension"

2008-10-01 Thread tolga . i . uzuner
Dear R Users, I've been hit with a cryptic error message: "Error in embed(y, lag) : wrong embedding dimension" My configuration is: - R 2.7.2 - Windows XP Sp2 Google returns nothing for this. Could someone suggest what this might mean ? Thanks in advance, Tolga Generally, this communicatio

[R] Lattice: don't draw unlabled tick marks

2008-10-01 Thread Philipp Pagel
If I only want axis labels on the left and bottom I can set alternating=F like in the following example: Depth <- equal.count(quakes$depth, number=8, overlap=.1) xyplot(lat ~ long | Depth, data = quakes, scales=list(alternating=F) I also would like to get rid of the unlabeled tick marks (top a

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