Re: [R] Rf_error crashes entire program.

2008-07-28 Thread Prof Brian Ripley
Rf_error is used so often in R itself and packages that it is almost certainly not the problem -- rather something else your program has done has damaged R's internals (e.g. overrrun an array). 'Writing R Extensions' discusses how to debug R code, including foreign code. For example, I would

Re: [R] Help interpreting density().

2008-07-28 Thread Mark Difford
Hi Kevin, >> The documentation indicates that the bw is essentially the sd. >> > d <- density(rnorm(1000)) Not so. The documentation states that the following about "bw": "The kernels are scaled such that this is the standard deviation of the smoothing kernel...," which is a very different thing

Re: [R] Help interpreting density().

2008-07-28 Thread Bill.Venables
You should read the documentation more carefully. The bw is not "essentially the sd". To quote the documentation the bw is "the smoothing bandwidth to be used. The kernels are scaled such that this is the standard deviation of the smoothing kernel." That is a very different thing. You are confu

[R] list

2008-07-28 Thread Paul Adams
I have run a wilcox test on a dataframe and I have returned to me data which I am wanting to sort and/or pick the max. I have tried the following code to pick the max: v<-wilcox.test.run w<-max(v,na.rm=FALSE)   I have also tried w<-pmax(p-value,na.rm=FALSE) for the second line   and this returns t

Re: [R] Is there anyway to clip the bottom of a barplot?

2008-07-28 Thread hadley wickham
That's probably not a good idea. See the end of this article for some reasons why and an alternative: http://www.b-eye-network.com/view/2468 Hadley On Mon, Jul 28, 2008 at 11:23 PM, Arthur Roberts <[EMAIL PROTECTED]> wrote: > Hi, all, > > I need to show only values in a barplot from say 4-12. W

[R] Is there anyway to clip the bottom of a barplot?

2008-07-28 Thread Arthur Roberts
Hi, all, I need to show only values in a barplot from say 4-12. When I do this, values below 4 are not cutoff. I would appreciate any input into how I could cut the bottom part of the bar off. Best wishes, Art Roberts University of Washington Department of Medicinal Chemistry ___

[R] Help interpreting density().

2008-07-28 Thread rkevinburton
I issue the following: > d <- density(rnorm(1000)) > d and get: Call: density.default(x = rnorm(1000)) Data: rnorm(1000) (1000 obs.); Bandwidth 'bw' = 0.2235 x y Min. :-3.5157 Min. :2.416e-05 1st Qu.:-1.6892 1st Qu.:1.129e-02 Median :

Re: [R] environment question

2008-07-28 Thread Jeffrey Horner
Edna Bell wrote: Hi R users! I was looking at some of the example code for the "environment" function. Here it is: e1 <- new.env(parent = baseenv()) # this one has enclosure package:base. e2 <- new.env(parent = e1) assign("a", 3, envir=e1) ls(e1) ls(e2) exists("a", envir=e2) # this succeeds

[R] environment question

2008-07-28 Thread Edna Bell
Hi R users! I was looking at some of the example code for the "environment" function. Here it is: e1 <- new.env(parent = baseenv()) # this one has enclosure package:base. e2 <- new.env(parent = e1) assign("a", 3, envir=e1) ls(e1) ls(e2) exists("a", envir=e2) # this succeeds by inheritance exi

Re: [R] Rf_error crashes entire program.

2008-07-28 Thread Andrew Redd
Switching all of my printfs to Rprintf fixed the problem the errors now proceed correctly. I was unable to reproduce the error, but now that is irrelevant, at least to me. Thanks for the help. -Andrew [[alternative HTML version deleted]] __ R-

[R] "wave model" semivariogram

2008-07-28 Thread Alessandro
Hey All, I have a question about "Wave model" in R. I have a wave model shape, but I don't know the code in R to fit my semivariogram with "wave model". Thanks alessandro [[alternative HTML version deleted]] __ R-help@r-project.o

Re: [R] 64-bit R on Mac OS X 10.5.4

2008-07-28 Thread joseph
Hi Matt Installation of Bioconductor packages works fine with biocLite. When I tried to install an R package, RMySQL, I got an error related to tcltk: > options(pkgType="source") > install.packages(pkgs ="RMySQL",type ="source", lib > ="/Library/Frameworks/R.framework/Versions/2.8/Resources/

Re: [R] Is there a way to avoid loading dependendent packages?

2008-07-28 Thread Henrik Bengtsson
On Mon, Jul 28, 2008 at 4:29 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > On 28/07/2008 6:42 PM, [EMAIL PROTECTED] wrote: >> >> Hello R help list >> >> I have been using the smoothScatter function within the "geneplotter" >> package to make some graphs using a Sweave Rnw script called via Rscrip

Re: [R] Is there a way to avoid loading dependendent packages?

2008-07-28 Thread Duncan Murdoch
On 28/07/2008 6:42 PM, [EMAIL PROTECTED] wrote: Hello R help list I have been using the smoothScatter function within the "geneplotter" package to make some graphs using a Sweave Rnw script called via Rscript in a DOS/Windows batch file. The Rscript will ultimately be called by a web service wi

Re: [R] Mixed model question.

2008-07-28 Thread Rolf Turner
Thanks for the response. I ***think*** I'm making a bit of progress On 29/07/2008, at 10:14 AM, Douglas Bates wrote: On Sun, Jul 27, 2008 at 9:06 PM, Rolf Turner <[EMAIL PROTECTED]> wrote: What I *don't* understand is the correlation structure of the estimates produced

Re: [R] rollapply() opertation on time series

2008-07-28 Thread Gabor Grothendieck
And then lapply over out. On Mon, Jul 28, 2008 at 6:41 PM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > rollapply along an index: > > library(zoo) > z <- zoo(matrix(101:110, 5), 201:205) > tt <- time(z) > zz <- zoo(seq_along(tt), tt) > out <- rollapply(zz, 3, function(ix) list(z[ix,])) > str(ou

[R] Is there a way to avoid loading dependendent packages?

2008-07-28 Thread Paul.Rustomji
Hello R help list I have been using the smoothScatter function within the "geneplotter" package to make some graphs using a Sweave Rnw script called via Rscript in a DOS/Windows batch file. The Rscript will ultimately be called by a web service with time-out constraints, hence things need to run

Re: [R] Rf_error crashes entire program.

2008-07-28 Thread Duncan Murdoch
On 28/07/2008 6:41 PM, Andrew Redd wrote: I'm having a problem with the error and warning functions. I've tried this on multiple machine so I'm fairly sure it's not machine dependent and I've tried it on the latest versions 2.6.0-2.7.1. Whenever my program gets to an error or warning it crashes

Re: [R] rollapply() opertation on time series

2008-07-28 Thread Gabor Grothendieck
rollapply along an index: library(zoo) z <- zoo(matrix(101:110, 5), 201:205) tt <- time(z) zz <- zoo(seq_along(tt), tt) out <- rollapply(zz, 3, function(ix) list(z[ix,])) str(out) # list of zoo objects On Mon, Jul 28, 2008 at 5:03 PM, rcoder <[EMAIL PROTECTED]> wrote: > > > rcoder wrote: >> >> H

[R] Rf_error crashes entire program.

2008-07-28 Thread Andrew Redd
I'm having a problem with the error and warning functions. I've tried this on multiple machine so I'm fairly sure it's not machine dependent and I've tried it on the latest versions 2.6.0-2.7.1. Whenever my program gets to an error or warning it crashes the entire program rather than throwing the

Re: [R] Mixed model question.

2008-07-28 Thread Douglas Bates
On Sun, Jul 27, 2008 at 9:06 PM, Rolf Turner <[EMAIL PROTECTED]> wrote: > I continue to struggle with mixed models. The square zero version > of the problem that I am trying to deal with is as follows: > > A number (240) of students are measured (tested; for reading comprehension) > on 6 separate

[R] rollapply() opertation on time series

2008-07-28 Thread rcoder
rcoder wrote: > > Hi everyone, > > Is there a way to perform a rollapply operation on a time series data > matrix and preserve the time frame? Currently, when I apply rollapply in > its standart form, the date column is no longer present in the o/p matrix. > > Thanks, > > rcoder > -- View

Re: [R] help with durbin.watson

2008-07-28 Thread John Fox
Dear Tom, It is in principle possible for residuals to be autocorrelated even when the series for the response variable is not. Moreover, the DW test should be appropriate for the model you fit. On the other hand, a DW statistic of 0 suggests perfect positive autocorrelation, and so I would suspec

Re: [R] Link functions in SEM

2008-07-28 Thread John Fox
Dear Jeroen, It's true that the sem() function only handles quantitative endogenous variables, but you could use it along with functions in the polycor package to fit models with ordered or dichotomous observed variables. There's an example of a confirmatory factor analysis model with ordinal indi

Re: [R] RODBC to query an Oracle table

2008-07-28 Thread David Scott
On Mon, 28 Jul 2008, Megan J Bellamy wrote: Hello all, I am having trouble running a count function in R using RODBC to query a table I created in Oracle. It may very well be that my SQL coding is incorrect; I just started learning it. But if someone could point me in the right direction or

[R] [-->OT] was: Re: Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Ted Harding
This all got very serious, though I've read it with interest. Zerfetzen's original post reminded me of something which happened around the time "Y2K" was becoming an issue, bringing up a similar issue from 2000 years earlier. Admin etc. does not change over time ... I've copied the email exchange

Re: [R] multiv

2008-07-28 Thread Mark Difford
Hi Ileana, See this thread: http://www.nabble.com/R-package-install-td18636993.html HTH, Mark. Somesan, Ileana wrote: > >> Hello, >> >> I want to install the package "multiv" which is not maintained any >> more (found in the archive: multiv_1.1-6.tar.gz from 16 July 2003). I >> have install

Re: [R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Christos Hatzis
Just for the fun of it, here is a recursive solution to the same problem... rna <- function(z) { y <- c(NA, head(z, -1)) z <- ifelse(is.na(z), y, z) if (any(is.na(z))) Recall(z) else z } > x [1] "A" "B" NA NA "C" NA NA NA NA "D" NA NA > rna(x) [1] "A" "B" "B" "B

Re: [R] loop does not work

2008-07-28 Thread Sarah Goslee
You are missing a right paren in this line: >while (jhttp://www.functionaldiversity.org __ 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.org/posting-guide

[R] loop does not work

2008-07-28 Thread aude Valade
Hi, I am new to R and am trying to do a loop but it seems not to run after one turn. What I want to do is subset my dataframe (extract one station and one day) to calculate and store the maxima that can then be plotted. I have an error message at the end of each loop: Error: unexpected '}' in "}"

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread zerfetzen
Thanks to each of you for your excellent input. I have copied the file and will read it tonight. I haven't run into any heat from IT, but if I do, it will be in the near future. The exact legal issue was touched upon. There was a concern that anything associated with R (my code, etc.) would ha

Re: [R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Bert Gunter
Just for the record, a less efficient but certainly simple and maybe adequate way for you to do it in standard R (no zoo package required) is: for(i in seq_along(x)[-1])if(is.na(x[i])) x[i] <- x[i-1] I tried timing it on my not so fancy Windows desktop for a vector of 10,000 values, but it was in

Re: [R] How to unsubscribe?

2008-07-28 Thread Marc Schwartz
on 07/28/2008 02:36 PM Endre Domiczi wrote: Hello, I am going to be on vacation and would like to temporary unsubscribe from the list. Sending "unsubscribe" didn't help. Could you please guide me on the appropriate step? Thanks a lot in advance! Best regards, Endre Go here: https://stat.ethz

Re: [R] Case statements in R

2008-07-28 Thread Patrick Burns
(Ted Harding) wrote: On 28-Jul-08 17:52:31, Henrik Bengtsson wrote: Use '&' for vectors and '&&' for scalars. Ditto applies to the OR operator(s). /Henrik What's wrong with using "&" for scalars? Surely it gives the correct answer? Maybe it's simply a bit slower, or something?

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Marc Schwartz
on 07/28/2008 01:32 PM zerfetzen wrote: Hi, I use R at home, and am interested in using it at my work company (which is in the Fortune 100). I began the request, and our legal team has given some gruff about the open source license. Not boring you with the details here, but I used some info on

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Roland Rau
Jim Porzak wrote: All this is included in the distribution in "doc" folder: 1. see FAQ: "2.11 Can I use R for commercial purposes?" 2. Specific GNU License is in file COPYING Furthermore, the start-up message of R can (hopefully) help you in your case. It mentions to type in license() or lice

[R] How to unsubscribe?

2008-07-28 Thread Endre Domiczi
Hello, I am going to be on vacation and would like to temporary unsubscribe from the list. Sending "unsubscribe" didn't help. Could you please guide me on the appropriate step? Thanks a lot in advance! Best regards, Endre -- Endre Domiczi, CEO Sevana Oy, http://www.sevana.fi Email : [EMAIL P

Re: [R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Yasir Kaheil
maybe this is easiest way to do it: x<-c("A","B",NA,NA,"C",NA,NA,NA,NA,"D",NA,NA); x[is.na(x)]<- "D"; x thanks y Owen Jones-3 wrote: > > I have a vector of data (species names) interspersed with NA values > and I want a function to "fill in the blanks", replacing NA values > with wha

Re: [R] Is there way to multiple plots on gap.plot?

2008-07-28 Thread Yasir Kaheil
yeah, just use points twogrp<-c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22) gpcol<-c(2,2,2,2,2,3,3,3,3,3,4,4,4,4,4,5,5,5,5,5) gap.plot(twogrp,gap=c(8,12),xlab="Index",ylab="Group values", main="Plot gap on Y axis",col=gpcol) twogrp2<-c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22) points(

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Duncan Murdoch
On 7/28/2008 2:32 PM, zerfetzen wrote: Hi, I use R at home, and am interested in using it at my work company (which is in the Fortune 100). I began the request, and our legal team has given some gruff about the open source license. Not boring you with the details here, but I used some info on g

Re: [R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Dimitris Rizopoulos
try function na.locf() from package 'zoo', i.e., library(zoo) x <- c("A","B",NA,NA,"C",NA,NA,NA,NA,"D",NA,NA) na.locf(x) I hope it helps. Best, Dimitris Dimitris Rizopoulos Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, B

Re: [R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Gabor Grothendieck
Try this: library(zoo) x <- c("A","B",NA,NA,"C",NA,NA,NA,NA,"D",NA,NA) na.locf(x) On Mon, Jul 28, 2008 at 2:10 PM, Owen Jones <[EMAIL PROTECTED]> wrote: > I have a vector of data (species names) interspersed with NA values and I > want a function to "fill in the blanks", replacing NA values wi

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Patrick Burns
I'll leave it to someone else to answer the question that you asked, but I don't mind answering the question that you didn't ask: Are there alternatives ways of getting R into the company? Yes. There are now some commercially supported versions of R -- see 'What is R-plus?' in the R-FAQ for a l

Re: [R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread Jim Porzak
All this is included in the distribution in "doc" folder: 1. see FAQ: "2.11 Can I use R for commercial purposes?" 2. Specific GNU License is in file COPYING HTH, Jim Porzak Responsys, Inc. San Francisco, CA http://www.linkedin.com/in/jimporzak On Mon, Jul 28, 2008 at 11:32 AM, zerfetzen <[EMA

Re: [R] Case statements in R

2008-07-28 Thread Henrik Bengtsson
Hi. On Mon, Jul 28, 2008 at 11:21 AM, Ted Harding <[EMAIL PROTECTED]> wrote: > On 28-Jul-08 17:52:31, Henrik Bengtsson wrote: >> Use '&' for vectors and '&&' for scalars. Ditto applies to the OR >> operator(s). /Henrik > > What's wrong with using "&" for scalars? Surely it gives the > correct a

[R] Is there way to multiple plots on gap.plot?

2008-07-28 Thread Arthur Roberts
Hi, all, Does anyone now of a way to put multiple plots on gap.plot? Much appreciated, Art __ 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.org/posting-guide.html a

[R] Fill in NA values in vector with previous character/factor

2008-07-28 Thread Owen Jones
I have a vector of data (species names) interspersed with NA values and I want a function to "fill in the blanks", replacing NA values with whatever the last species name was. For example the vector: "A","B",NA,NA,"C",NA,NA,NA,NA,"D",NA,NA. should evaluate to: "A" "B" "B" "B" "C" "C" "C"

Re: [R] Case statements in R

2008-07-28 Thread David Katz
See ?cut for creating a factor based on ranges of values. Regards, Wade Wall wrote: > > Hi all, > > I am trying to convert geometric means in a matrix to cover classes. My > values are as such: > > perc<-c(0,0.025136418, 0.316227766, 1.414213562,3.16227766, 7.071067812, > 15.8113883, 35.3

[R] Legality Question about R's Open Source GNU GPL License

2008-07-28 Thread zerfetzen
Hi, I use R at home, and am interested in using it at my work company (which is in the Fortune 100). I began the request, and our legal team has given some gruff about the open source license. Not boring you with the details here, but I used some info on gnu.org as a rebuttal, and someone at the

[R] Negative Binomial Regression

2008-07-28 Thread jcarmichael
Hello. I am attempting to duplicate a negative binomial regression in R. SAS uses generalized estimating equations for model fitting in the GENMOD procedure. proc genmod data=mydata (where=(gender='F')); by agegroup; class id gender type; model count = var1 var2 var3 /dist=NB link=log offset=l

Re: [R] Case statements in R

2008-07-28 Thread Ted Harding
On 28-Jul-08 17:52:31, Henrik Bengtsson wrote: > Use '&' for vectors and '&&' for scalars. Ditto applies to the OR > operator(s). /Henrik What's wrong with using "&" for scalars? Surely it gives the correct answer? Maybe it's simply a bit slower, or something? Ted. > On Mon, Jul 28, 2008 at 1

Re: [R] Help with a loop

2008-07-28 Thread Sofia Martinez
HI the code is suppose to generate a random value selected uniformly as a time interval in seconds (that's the dT) from the range given fromdtmin<-969 dtmax<-9884. Once that value is selected the program will generate the interval (ts1, ts2, and so on. for each sampling without getting out o

Re: [R] Case statements in R

2008-07-28 Thread Stefan Evert
And you may want to consider using the 'cut' function. In your case, something like veg_mean <- cut(veg_mean, breaks=c(0,.1,1,2,5,10,25,50,75,95,100), right=FALSE) should do the trick (see ?cut for more options). Best, Stefan On 28 Jul 2008, at 19:52, Henrik Bengtsson wrote: Use '&'

Re: [R] Overlay of simple plots

2008-07-28 Thread stephen sefick
?lines On Mon, Jul 28, 2008 at 12:57 PM, Phillip R. Hunt <[EMAIL PROTECTED]>wrote: > I am trying to create a graph that puts three x-y plots (age vs rate for > three categories ) on a single plot. SAS does this with the overlay > function. I cannot find in the R documentation a method for doing

Re: [R] RStem with portuguese language

2008-07-28 Thread Duncan Temple Lang
Hi Paulo. My development version has that warning turned off. However, the Rstem package predates the encoding in R, AFAIR. So when I call wordStem() with a string which has an Encoding() of UTF-8, the resulting string has Encoding() "unknown". I'll take a look and add see if I can add support

Re: [R] Using PrettyR to produce LaTeX output

2008-07-28 Thread jcarmichael
Thank you all for your input! I was able to create my descriptive table as well as a few other things I was having trouble with. Thanks again! J. jcarmichael wrote: > > Hello everyone. I am new to R, so please bear with me. I am trying to > find an easy way to export descriptive statistics

Re: [R] Using PrettyR to produce LaTeX output

2008-07-28 Thread jcarmichael
This is EXACTLY what I needed. I suppose the only issue was that I needed to isolate the numeric output of PrettyR::describe. Thanks very much! Gabor Grothendieck wrote: > > Using the built in BOD data frame: > > library(prettyR) > str(describe(BOD)) # note Numeric component > > BOD.descri

Re: [R] Case statements in R

2008-07-28 Thread Roland Rau
Hi, maybe the following code helps to achieve what you want? It seems to me it is basically a 'recode' question. set.seed(1234) # not neccessary but this ensures we have the same #results random.values <- runif(n=30, min=0, max=100) newgrouping <- cut(x=random.values, breaks=c(0,0.1, 1, 2, 5, 10

Re: [R] Case statements in R

2008-07-28 Thread Henrik Bengtsson
Use '&' for vectors and '&&' for scalars. Ditto applies to the OR operator(s). /Henrik On Mon, Jul 28, 2008 at 10:36 AM, Wade Wall <[EMAIL PROTECTED]> wrote: > Hi all, > > I am trying to convert geometric means in a matrix to cover classes. My > values are as such: > > perc<-c(0,0.025136418, 0

[R] Case statements in R

2008-07-28 Thread Wade Wall
Hi all, I am trying to convert geometric means in a matrix to cover classes. My values are as such: perc<-c(0,0.025136418, 0.316227766, 1.414213562,3.16227766, 7.071067812, 15.8113883, 35.35533906, 61.23724357, 84.40971508, 97.46794345) cover<-c(0,1,2,3,4,5,6,7,8,9,10) This is what I am tryin

[R] Question about the SSOAP package

2008-07-28 Thread Aiste Aistike
Hello, I need to retrieve data from the internet to R using SOAP protocol. I found that SSOAP package (http://www.omegahat.org/SSOAP/) should do the work. However, I cannot install it properly. It just does not work. I am using R 2.7.1 (this was the only version on which other required packages (

[R] Overlay of simple plots

2008-07-28 Thread Phillip R. Hunt
I am trying to create a graph that puts three x-y plots (age vs rate for three categories ) on a single plot. SAS does this with the overlay function. I cannot find in the R documentation a method for doing this. Any help would be appreciated. Thanks, Phill Phillip R. Hunt, Sc.D. 24

Re: [R] in axis() suppressing axis line but keeping tick marks

2008-07-28 Thread Prof Brian Ripley
I'm pretty sure that this is not Paul's design and he usually doesn't want to touch base graphics. I've added arguments lwd.ticks and col.ticks in R-devel. The simplest way to suppress the axis line become axis(..., lwd=0, lwd.ticks=1). On Mon, 16 Jun 2008, Peter Dalgaard wrote: Andrew Yee

[R] rollapply() opertation on ts matrix

2008-07-28 Thread rcoder
Hi everyone, Is there a way to perform a rollapply operation on a time series data matrix and preserve the time frame? Currently, when I apply rollapply in its standart form, the date column is no longer present in the o/p matrix. Thanks, rcoder -- View this message in context: http://www.nab

[R] multiv

2008-07-28 Thread Somesan, Ileana
> Hello, > > I want to install the package "multiv" which is not maintained any > more (found in the archive: multiv_1.1-6.tar.gz from 16 July 2003). I > have installed an older version of R 1.4.1 on my Windows Vista in > order to match the older package. > > As no binary is distributed, is it n

[R] RStem with portuguese language

2008-07-28 Thread Paulo Cortez
Greetings, I have R 2.7.1 in MacOs and I believe UTF encoding is already installed. At least: > Sys.getenv() shows several variables, including: LANG "pt_PT.UTF-8" I installed the Rstem and tm packages and when I try the following code: > wordStem(c("aberração","aberrações"), language="por

[R] [R-pkgs] randomSurvivalForest 3.5.0 now available

2008-07-28 Thread Udaya B. Kogalur
Please find release 3.5.0 of the CRAN package "randomSurvivalForest" now posted on CRAN. Thank you. [EMAIL PROTECTED] Udaya B. Kogalur, Ph.D. Kogalur Shear Corporation 5425 Nestleway Drive, Suite L1 Clemmons, NC 27012

Re: [R] Color of box frame in Legend (Was: Matrix barplot)

2008-07-28 Thread Prof Brian Ripley
The current default for the box/frame colour is not "black" (it is par("fg")), but otherwise I've committed something very similar to the R-devel version of R earlier today. On Mon, 28 Jul 2008, Nutter, Benjamin wrote: Try sourcing in the 'new.legend' function below. It's the legend function

Re: [R] RODBC to query an Oracle table

2008-07-28 Thread Jim Porzak
Hi Megan, Marc's hint is the R way, which is needed with your original SELECT. OTOH, it may be more efficient to move the WHERE clause into the SELECT. Something like select plotnum, sampyear, sptype from density where sampyear=1995 AND plotnum=1 AND sptype IN ('S', 'H') should work i

Re: [R] Converting from char to POSIX:

2008-07-28 Thread Prof Brian Ripley
On Mon, 28 Jul 2008, Agustin Lobo wrote: Given char vector delme2: str(delme2) chr [1:1065] "30-1-08 8:48:21" "30-1-08 8:55:17" "30-1-08 9:00:22" ... I do: delme3 <- strptime(delme2,format="%d-%m-%y %H:%M:%S") But then: str(delme3) POSIXlt[1:9], format: "2008-01-30 08:48:21" "2008-01-30

Re: [R] RODBC to query an Oracle table

2008-07-28 Thread Prof Brian Ripley
It's your R syntax that is faulty: Use "" (not ') to delimit the R string which contains single quotes for use by SQL. On Mon, 28 Jul 2008, Megan J Bellamy wrote: Hello all, I am having trouble running a count function in R using RODBC to query a table I created in Oracle. It may very well b

[R] Bootstrapping

2008-07-28 Thread laila khalfan
HiI would like to use the parametric bootstrap confidence intervals. The problem is that I am using a step stress model based on a gamma distributed data. So, first I need to generate a spacial data and then find the MLE`s then I must find the bootstrap confidence interval.I dont know how to us

Re: [R] how to add notes to the graph?

2008-07-28 Thread Dieter Menne
rlearner309 gmail.com> writes: > x <- c(1,2,3) > plot(x, pch=16,type="b") > > I would like to add some notes just beside these 3 dots, and the notes are > stored in a vector: > > a <- c(12,54,84) > > So the result will be: there should be a "12" below the first dot (or next > to it, but not

[R] how to add notes to the graph?

2008-07-28 Thread rlearner309
Hi, I have a simple graph: x <- c(1,2,3) plot(x, pch=16,type="b") I would like to add some notes just beside these 3 dots, and the notes are stored in a vector: a <- c(12,54,84) So the result will be: there should be a "12" below the first dot (or next to it, but not replacing the solid dot

[R] Converting from char to POSIX:

2008-07-28 Thread Agustin Lobo
Given char vector delme2: > str(delme2) chr [1:1065] "30-1-08 8:48:21" "30-1-08 8:55:17" "30-1-08 9:00:22" ... I do: > delme3 <- strptime(delme2,format="%d-%m-%y %H:%M:%S") But then: > str(delme3) POSIXlt[1:9], format: "2008-01-30 08:48:21" "2008-01-30 08:55:17" ... > length(delme3) [1] 9 wh

[R] Help with yaImpute

2008-07-28 Thread Wesley Roberts
Dear fellow R-users I am trying to do some imputation using K-NN with the yaImpute library. All seems to be going well until I try to use AsciiGridImpute. All my data are correctly formatted and I am able to run and view the results of yai. Below is my code:

Re: [R] how to export ".xls" file with colorful cells?

2008-07-28 Thread Kevin Wright
Xin Meng, Ignore all the "you didn't tell us your operating system" comments--I will show you a simple, although very tedious way to do what you want that is totally free of any operating system limitations. Began by formatting a very simple Excel file with colored cells, then save the file as a

Re: [R] RODBC to query an Oracle table

2008-07-28 Thread Marc Schwartz
on 07/28/2008 09:44 AM Megan J Bellamy wrote: Hello all, I am having trouble running a count function in R using RODBC to query a table I created in Oracle. It may very well be that my SQL coding is incorrect; I just started learning it. But if someone could point me in the right direction or te

Re: [R] writing the plots

2008-07-28 Thread stephen sefick
?pdf and copy and write whatever notes you want i a note pad On Mon, Jul 28, 2008 at 10:54 AM, Rajasekaramya <[EMAIL PROTECTED]>wrote: > > hi there, > > I want to write the plots in the pdfs and the details about the graph in a > seperate notepad. > > plot(as.numeric(lapply(resultgenes,length)),

[R] RODBC to query an Oracle table

2008-07-28 Thread Megan J Bellamy
Hello all, I am having trouble running a count function in R using RODBC to query a table I created in Oracle. It may very well be that my SQL coding is incorrect; I just started learning it. But if someone could point me in the right direction or tell me if I am going about this the correct wa

Re: [R] speeding up loop and dealing wtih memory problems

2008-07-28 Thread Prof Brian Ripley
We were not told this was a matrix, rather a 'dataset'. If it is matrix, logical indexing via is.na(x) is pretty good, although it will create an index equal in size to the dataset (but logical). If 'dataset' means a data frame, you will use less memory using a for() loop over columns, e.g.

[R] writing the plots

2008-07-28 Thread Rajasekaramya
hi there, I want to write the plots in the pdfs and the details about the graph in a seperate notepad. plot(as.numeric(lapply(resultgenes,length)), main= "Geneset.gene#.bias.test",xlab="Top.Ranked.Genesets", ylab="gene.number.per.geneset") lines(loess.smooth(c(1:1000),as.numeric(lapply(resultge

Re: [R] product of successive rows

2008-07-28 Thread Patrizio Frederic
this works too: n = 6 # number of rows m = 4 # number of coloumns nm = n*m mat = matrix(1:nm,n) # your matrix pf = function(Col){ ind = rep(1:(n/2),each=2) out = tapply(Col,ind,prod) out } # pf performs forall vecotr x: x[i]*x[i-1], i=2,4,6

Re: [R] speeding up loop and dealing wtih memory problems

2008-07-28 Thread jim holtman
If your matrix is 835353x86, then if it is numeric, then it will take about 550MB for a single copy. You should therefore have at least 2GB (so you can have a couple of copies as part of some processing) of real memory on your system. If you want to replace NAs with zero, then this is how you mig

Re: [R] S4 : setGeneric for classical methods

2008-07-28 Thread cgenolin
Martin Maechler <[EMAIL PROTECTED]> a écrit : "CG" == Christophe Genolini <[EMAIL PROTECTED]> on Sun, 27 Jul 2008 09:27:34 +0200 writes: CG> Martin Maechler <[EMAIL PROTECTED]> a écrit : >>> "CG" == Christophe Genolini <[EMAIL PROTECTED]> >>> on Sat, 26 Jul 2008 12:12:

Re: [R] speeding up loop and dealing wtih memory problems

2008-07-28 Thread ONKELINX, Thierry
Dear Denise, It looks like you want to replace all NA with 0 in the dataset? The code below should do that trick without loops. And it will be rather fast. dat[is.na(dat)] <- 0 > dat <- matrix(rbinom(40, 1, 0.75), ncol = 4, nrow = 10) > dat[dat == 0] <- NA > dat [,1] [,2] [,3] [,4] [1,]

Re: [R] speeding up loop and dealing wtih memory problems

2008-07-28 Thread David Hajage
Is it what you want ? > x <- matrix(c(1:3, NA, NA, 4, 1:2, NA), 3, 3) > x [,1] [,2] [,3] [1,]1 NA1 [2,]2 NA2 [3,]34 NA > x[is.na(x)] <- 0 > x [,1] [,2] [,3] [1,]101 [2,]202 [3,]340 2008/7/28 Denise Xifara <[EMAIL PROTECT

[R] speeding up loop and dealing wtih memory problems

2008-07-28 Thread Denise Xifara
Dear All and Mark, Given a dataset that I have called dat, I was hoping to speed up the following loop: for(i in 1:835353){ for(j in 1:86){ if (is.na(dat[i,j])==TRUE){dat[i,j]<-0 }}} Actually I am also having a memory problem. I get the following: Error: cannot allocate vector of size 3.2 Mb

Re: [R] Color of box frame in Legend (Was: Matrix barplot)

2008-07-28 Thread Nutter, Benjamin
Try sourcing in the 'new.legend' function below. It's the legend function with a new argument called 'box.col'. The argument will change the color of the box surrounding the legend. If I understand what it is you are looking for, this should work. Also, I didn't see a way to change the axis bar

Re: [R] product of successive rows

2008-07-28 Thread jim holtman
Does this do what you want: > x <- matrix(1:36,6) > x [,1] [,2] [,3] [,4] [,5] [,6] [1,]17 13 19 25 31 [2,]28 14 20 26 32 [3,]39 15 21 27 33 [4,]4 10 16 22 28 34 [5,]5 11 17 23 29 35 [6,]6 12 18 24 30 36

[R] Rv: Chi-square parameter estimation

2008-07-28 Thread Julio Rojas
Hi. I have made 100 experiments of an M/M/1 queue, and for each one I have calculated both, mean and variance of the queue size. Now, a professor has told me that variance is usually chi-squared distributed. Is there a way in R that I can find the parameter that best fits a chi-square to the var

[R] parametric bootstrap

2008-07-28 Thread laila khalfan
Hi I am using the boot function in boot package. I am facing a problem in getting the values of bias and st.error in the output. r<-36 n<-40 shape<-2 theta11<-exp(1) # (=2.718282) theta21<-exp(.5) #( =1.648721) m0<- function(Ti,Tj) #a function that generates the MLestimates { loglik<-function(ti

Re: [R] Using stop ( ) from a Text Editor

2008-07-28 Thread Paulo Cardoso
> I see no condition object in your example Isn't if(length(content[content%in%folders])!=4) a condition? > stop() breaks execution of a block of code that source()d -- maybe that is what you are looking for? Yes > I don't know what you mean by 'TINN' and 'Winedit' (what exact program, how ar

Re: [R] Using stop ( ) from a Text Editor

2008-07-28 Thread Prof Brian Ripley
On Mon, 28 Jul 2008, Paulo Cardoso wrote: When using stop clause with a condition, its documented that "If a condition object is supplied it should be the only argument, and further arguments will be ignored, with a warning". I see no condition object in your example. This will not be the ca

Re: [R] Using stop ( ) from a Text Editor

2008-07-28 Thread jim holtman
If you are using Tinn-R, then I am assuming that you are using the 'send selection' which basically minics the keyboard. On the keyboard, after a 'stop' you can type in the next command without any problems. Here is a script I was using with Tinn-R: x <- 1 stop('error') cat('continue processing'

Re: [R] axis.break on Date-x-axis in lattice xyplot

2008-07-28 Thread Jim Lemon
On Mon, 2008-07-28 at 12:19 +0200, Henning Wildhagen wrote: > Dear list, > > i am using the following code to produce a lattice xyplot, but the > axis.break-function is seemingly not executed. > > Date<-seq(as.Date("2006-08-29"), as.Date("2007-08-28"), by="2 weeks") > Period<- > var1<-rnorm(27,

Re: [R] axis.break on Date-x-axis in lattice xyplot

2008-07-28 Thread Ben Bolker
Henning Wildhagen gmx.de> writes: > > Dear list, > > i am using the following code to produce  a lattice xyplot, but the > axis.break-function is seemingly not executed. axis.break (from plotrix) won't work at all on lattice graphics -- you can look to see what it does and try to replicate

[R] Using stop ( ) from a Text Editor

2008-07-28 Thread Paulo Cardoso
When using stop clause with a condition, its documented that "If a condition object is supplied it should be the only argument, and further arguments will be ignored, with a warning". This will not be the case when running codes from Winedit or TINN? When I do something like: if(length(content[c

Re: [R] Converting english words to numeric equivalents

2008-07-28 Thread Hans-Joerg Bibiko
On 28 Jul 2008, at 12:23, Hans-Joerg Bibiko wrote: How about this? unletter <- function(word) { gsub('-64',' ',paste(sprintf("%02d",utf8ToInt(tolower(word)) - 96),collapse='')) } unletter("abc") [1] "010203" unletter("Aw") [1] "0123" unletter("I walk to school") [1] "09 23011211 2015 1903

[R] axis.break on Date-x-axis in lattice xyplot

2008-07-28 Thread Henning Wildhagen
Dear list, i am using the following code to produce  a lattice xyplot, but the axis.break-function is seemingly not executed. Date<-seq(as.Date("2006-08-29"), as.Date("2007-08-28"), by="2 weeks") Period<- var1<-rnorm(27, 9000, 3000) var2<-rnorm(27, 5,25000) var3<-rnorm(27, 10

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