Re: [R] Optimisation and NaN Errors using clm() and clmm()

2013-04-20 Thread Rune Haubo
On 18 April 2013 18:38, Thomas Foxley wrote: > Rune, > > Thank you very much for your response. > > I don't actually have the models that failed to converge from the first > (glmulti) part as they were not saved with the confidence set. glmulti > generates thousands of models so it seems reasonabl

Re: [R] Spider Plot

2013-04-20 Thread Jim Lemon
On 04/20/2013 06:29 AM, XINLI LI wrote: Does any one have a sample code for a Spider Plot as attached? Hi Xing, Have a look at the third example in the radial.plot function (plotrix). Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mai

[R] how to set the row name of a specific row

2013-04-20 Thread Simone Gabbriellini
Hello, I am adding rows to a matrix using rbind() and I would like to also add a row name to the added row in order to do some sorting after the adding rows part is finished. is this possible? Best, Simone -- Simone Gabbriellini, PhD PostDoc@DISI, University of Bologna mobile: +39 340 39 75 62

[R] MOS-test using package vegan

2013-04-20 Thread Elaine Kuo
Dear all, I am using MOStest in vegan to examine the hump-shaped of a quadratic regression model. In the manual of vegan, it mentions that the value of MOStest include isHump. My result showed the quadratic regression is hump-shaped according to the p-value (nearly 0). However, the value isHump di

Re: [R] how to set the row name of a specific row

2013-04-20 Thread Rui Barradas
Hello, It is possible, but do the other rows have names? x <- matrix(1:12, 4) x <- rbind(x, c(13:15)) rownames(x)[5] <- "abcd" x Hope this helps, Rui Barradas Em 20-04-2013 10:58, Simone Gabbriellini escreveu: Hello, I am adding rows to a matrix using rbind() and I would like to also add

Re: [R] how to set the row name of a specific row

2013-04-20 Thread Simone Gabbriellini
Hi Rui, yes, all the other rows have names! Thanks, works perfecty 2013/4/20 Rui Barradas > Hello, > > It is possible, but do the other rows have names? > > x <- matrix(1:12, 4) > > x <- rbind(x, c(13:15)) > rownames(x)[5] <- "abcd" > x > > > Hope this helps, > > Rui Barradas > > Em 20-04-2013

[R] R CMD build

2013-04-20 Thread Knut Krueger
I have no idea where I must R CMD build... I am using Windows 7 wiht pearl installed http://stat.ethz.ch/R-manual/R-patched/library/utils/html/PkgUtils.html its completely unclear for me ... sorry Knut __ R-help@r-project.org mailing list https://st

Re: [R] R CMD build

2013-04-20 Thread Knut Krueger
I was looking for the problem at least two days.. and just after writing to the list I found rcmd.exe in the C:\Program Files\R\R-2.15.2\bin\i386 directory. install http://sourceforge.net/projects/mingw/?source=dlp chage the path variable of windows and set the path in front of the others C:\Min

[R] Assigning factor to character vector

2013-04-20 Thread Milan Bouchet-Valat
Hi! Yesterday I accidentally discovered this: > a <- LETTERS[1:5] > a [1] "A" "B" "C" "D" "E" > > a[1] <- factor(a[1]) > a [1] "1" "B" "C" "D" "E" BUT: > b <- factor(LETTERS[1:5]) > b [1] A B C D E Levels: A B C D E > b[1] <- factor(b[1]) > b [1] A B C D E Levels: A B C D E > b[1] <- as.characte

Re: [R] possible loop problem

2013-04-20 Thread MHwk79
Wow - thanks a lot for your help. Sorry it's taken a while to answer, but honestly, didn't expect a reply so soon. Sorry I hadn't provided enough information at the beginning, but you'd correctly figured it was a csv file (actually exported from Excel). I had figured that there was a more stream

Re: [R] R CMD build

2013-04-20 Thread Gabor Grothendieck
On Sat, Apr 20, 2013 at 8:09 AM, Knut Krueger wrote: > I was looking for the problem at least two days.. and just after writing to > the list I found rcmd.exe in the > C:\Program Files\R\R-2.15.2\bin\i386 directory. > install > http://sourceforge.net/projects/mingw/?source=dlp > chage the path var

[R] Editing data sheet issue with write.table append

2013-04-20 Thread Vinny Moriarty
I'm running R 2.15.2 on Max OS X 10.6.8 If I write a simple file Data1<-1 DF<-data.frame(Data1) colnames(DF)<-"Col1" and write to a csv file write.table(DF,file="Data.csv",sep=",",row.names=FALSE,col.names=TRUE) I can then append to it no problem Data2<-2 Data3<-4 DF2<-data.frame(Data2) DF

Re: [R] Multiple Multivariate regression in R with 50 independentvariables

2013-04-20 Thread Nilesh Gupta
Thanks to all , I solved the problem using William's suggestion. Peter I agree with the theory issue and I will deal with that subsequently, but I wanted to run this once . Regards The woods are lovely, dark and deep But I have promises to keep And miles to go before I sleep And miles to go befor

Re: [R] Assigning factor to character vector

2013-04-20 Thread Bert Gunter
Sorry, I failed to cc: the list. I also added a slight edit below to clarify my final statement. -- Bert On Sat, Apr 20, 2013 at 7:17 AM, Bert Gunter wrote: > Milan: > > 1. The R Inferno was written by Pat Burns and is not in any way an > "official" R document. So it is a "Pat Burns" not an "R"

Re: [R] Editing data sheet issue with write.table append

2013-04-20 Thread Jeff Newmiller
a) Your terminology "data sheet" is foreign to R (and this mailing list). It implies a computing model that R does not use. b) You appear to be complaining about the behavior of software other than R on the R-help mailing list, which is pointless. c) I think the chances of adding code to base R

Re: [R] Assigning factor to character vector

2013-04-20 Thread Milan Bouchet-Valat
Le samedi 20 avril 2013 à 07:22 -0700, Bert Gunter a écrit : > Sorry, I failed to cc: the list. > > I also added a slight edit below to clarify my final statement. -- Bert > > On Sat, Apr 20, 2013 at 7:17 AM, Bert Gunter wrote: > > Milan: > > > > 1. The R Inferno was written by Pat Burns and is

Re: [R] Editing data sheet issue with write.table append

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 1:29 AM, Vinny Moriarty wrote: > I'm running R 2.15.2 on Max OS X 10.6.8 > > > If I write a simple file > > Data1<-1 > DF<-data.frame(Data1) > colnames(DF)<-"Col1" > > and write to a csv file > > write.table(DF,file="Data.csv",sep=",",row.names=FALSE,col.names=TRUE) > >

Re: [R] Editing data sheet issue with write.table append

2013-04-20 Thread William Dunlap
R is nice because it can deal with other less flexible software and many people must use Excel at their jobs. You can write a function that detects if your file ends with a newline and use it to add a newline exactly when needed. E.g., the following compares the last few bytes in the file to the

Re: [R] Spider Plot

2013-04-20 Thread Hall, Mark
Check the archives. About 4 years ago, I asked on help with doing spider-plots used in geologic literature and got a bunch of helpful results. Best, Mark Hall Winnemucca BLM On Fri, Apr 19, 2013 at 1:41 PM, Janesh Devkota wrote: > Xing, > I cannot open the attachment. Can you attach the "png"

[R] Reshape or Plyr?

2013-04-20 Thread Bruce Miller
H all, I have relative abundance data from >100 sites. This is from acoustic monitoring and usually the data is for 2-3 nights but in some cases my be longer like months or years for each location.. The data output from my management data base is proved by species by night for each location so

Re: [R] Editing data sheet issue with write.table append

2013-04-20 Thread Vinny Moriarty
Thanks Bill , that works great. It occurred to me upon reading the other responses that rather than try and work around this issue with excel, another option would be to just always append to the top line of the data sheet (1 line below the header). That way I would be assured a proper carriage re

[R] Calculate confidence intervals in mgcv for unconditional on the, smoothing parameters

2013-04-20 Thread Alexander März
Dear R-Help members, I am using Simon Wood`s mgcv package version1.7-22and R version 3.0.0 (2013-04-03) for fitting a GAM-Model to the LIDAR Data contained in the "SemiPar" package. Here is the code for fitting the model and for plotting the result: data("lidar") attach(lidar) ### # mgcv fitt

[R] creating dummy variables

2013-04-20 Thread shyam basnet
Hello R-users,   The below is a snippet of my data:   fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349   Here,

[R] R copying script code to clipboard

2013-04-20 Thread Thomas Hansen
Hi everyone I am trying to figure out why, and how to stop R, from copying my entire script text to the clipboard when I either select the "run all" option or select the entire script and ctrl+r. Since my script imports data from the clipboard it is non-functional when R overwrites the data I sav

Re: [R] how to subtotal by rows

2013-04-20 Thread shyam basnet
Dear All,   Thanks for helping me to redress the problem.    Cheers,   Shyam Basnet Nepal - Original Message - > From: arun > To: Janesh Devkota > Cc: R help ; shyam basnet > Sent: Saturday, April 20, 2013 12:52 AM > Subject: Re: [R] how to subtotal by rows > > HI, > > If you wanted

Re: [R] creating dummy variables

2013-04-20 Thread Bert Gunter
Dummy variables are not needed in R. Bert Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet wrote: > Hello R-users, > > The below is a snippet of my data: > > > fid crop year value > 5_1_1 SWHE 1995 171 > 5_1_1 SWHE 1997 696 > 5_1_1

[R] matrix of size 30^5

2013-04-20 Thread Benjamin Caldwell
Dear R helpers Reproducible example: #warning - this causes a hard freeze on the machines I've tried it on matrix.holder<- matrix(rnorm(150), nrow=30, ncol=5) Out= expand.grid(matrix.holder[,1],matrix.holder[,2],matrix.holder[,3],matrix.holder[,4], matrix.holder[,5]) Problem: I'm running an an

Re: [R] creating dummy variables

2013-04-20 Thread Patrick Coulombe
Hello Shyam, if your data is stored in variable "dataset", for example, the following code will create the desired dummy-coded variables and attach them to the dataset: ## #init vars SWHE=BARL <- vector(length=nrow(dataset)) SWHE[]=BARL[] <- 0 #initialize dummy-coded vars wi

Re: [R] R CMD build

2013-04-20 Thread Knut Krueger
Am 20.04.2013 15:50, schrieb Gabor Grothendieck: Note that there is a separate directory for the 64-bit R executables. Does it make any difference to check and pack the source files iwth 32 or 64 bit? Also, downloading MinGW should not be needed. Rtools already contains the needed UNIX utilitie

[R] Source Code

2013-04-20 Thread Eva Prieto Castro
Dear all, How can I get the source code of text function? Regards Eva [[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.

Re: [R] matrix of size 30^5

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 2:19 PM, Benjamin Caldwell wrote: > Dear R helpers > > Reproducible example: > > #warning - this causes a hard freeze on the machines I've tried it on > matrix.holder<- matrix(rnorm(150), nrow=30, ncol=5) > > Out= > expand.grid(matrix.holder[,1],matrix.holder[,2],matrix.hol

Re: [R] Source Code

2013-04-20 Thread R. Michael Weylandt
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro wrote: > Dear all, > > How can I get the source code of text function? > What is the 'text function'? Try typing the name of the function at the prompt without any parentheses after it. If its written in R, then it should be visible. Michael

Re: [R] Source Code

2013-04-20 Thread Eva Prieto Castro
This is what I get when typing text: > text function (x, ...) UseMethod("text") The text function let you add text in a plot. How can I obtain the source code?. Thanks. Eva --- El dom, 21/4/13, R. Michael Weylandt escribió: De: R. Michael Weylandt Asunto: Re: [R] Source Code Para:

Re: [R] creating dummy variables

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 2:03 PM, Bert Gunter wrote: > Dummy variables are not needed in R. > > Bert > Bert is correct on this point, but if you what to know how the regression functions in R do this "behind the scenes" then you could always look at: ?model.matrix # where _some_ of the the au

Re: [R] Source Code

2013-04-20 Thread Rui Barradas
Hello, The output you got means that text is generic, so you need something like text.default > text.default function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL, offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL, ...) { if (!missing(y) && (is.character(

Re: [R] Source Code

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 3:34 PM, R. Michael Weylandt wrote: > > > On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro wrote: > >> Dear all, >> >> How can I get the source code of text function? >> > > What is the 'text function'? > > Try typing the name of the function at the prompt without any

Re: [R] creating dummy variables

2013-04-20 Thread Eva Prieto Castro
Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. Thanks, Eva --- El dom, 21/4/13, David Winsemius escribió: De: David Winsemius Asunto: Re: [R] creating dummy variables Para: "Bert Gunter" CC: "r-help@R-project.org" , "shyam basnet" Fecha: do

Re: [R] Source Code

2013-04-20 Thread Eva Prieto Castro
Thanks!. The problem is that I can't see the source code in .Internal(txt... > text.default function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL,     offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL,     ...) {     if (!missing(y) && (is.character(y) || is.expressi

Re: [R] Source Code

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 4:05 PM, Eva Prieto Castro wrote: > > Thanks!. The problem is that I can't see the source code in .Internal(txt... Exactly which was why I provided the link to Ligges' article. (So now you _are_ expected to do some self-study.) -- David. > > > > text.default > funct

Re: [R] creating dummy variables

2013-04-20 Thread David Winsemius
On Apr 20, 2013, at 3:56 PM, Eva Prieto Castro wrote: > > Hi, > > Why do you write that dummy variables are not needed in R?. I would like you > explain it. I suppose you might want individual instruction, but Rhelp was established with certain principles (expressed in the Posting Guide), on

Re: [R] creating dummy variables

2013-04-20 Thread Bert Gunter
To all who ask about dummy variables in R: Please please read the "Introduction to R" section on "Statistical Models in R" or other tutorial (there are many on the web) on regression modeling in R. (For that matter -- please read all of this or other basic R tutorial before posting here!). An exce

Re: [R] Source Code

2013-04-20 Thread R. Michael Weylandt
On Apr 20, 2013, at 7:13 PM, David Winsemius wrote: > > On Apr 20, 2013, at 4:05 PM, Eva Prieto Castro wrote: > >> >> Thanks!. The problem is that I can't see the source code in .Internal(txt... > > Exactly which was why I provided the link to Ligges' article. (So now you > _are_ expec

[R] Foundation for Open Access Statistics

2013-04-20 Thread Jan de Leeuw
The Foundation for Open Access Statistics is a nonprofit public benefit corporation registered in California. We have applied for federal tax-exempt status under Internal Revenue Section 501(c)(3). FOAS has a worldwide mission to promote free software, open access publishing, and reproducible re

Re: [R] creating dummy variables

2013-04-20 Thread Rolf Turner
On 21/04/13 10:56, Eva Prieto Castro wrote: Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. As others have said --- do some self-study. But a brief answer is that in any "reasonable" modelling problem in which dummy variables might arise, R crea

Re: [R] R CMD build

2013-04-20 Thread Henrik Bengtsson
On Sat, Apr 20, 2013 at 3:10 PM, Knut Krueger wrote: > Am 20.04.2013 15:50, schrieb Gabor Grothendieck: > >> Note that there is a separate directory for the 64-bit R executables. > > Does it make any difference to check and pack the source files iwth 32 or 64 > bit? > >> Also, downloading MinGW sh

Re: [R] R CMD build

2013-04-20 Thread Gabor Grothendieck
On Sat, Apr 20, 2013 at 10:14 PM, Henrik Bengtsson wrote: > On Sat, Apr 20, 2013 at 3:10 PM, Knut Krueger wrote: >> Am 20.04.2013 15:50, schrieb Gabor Grothendieck: >> >>> Note that there is a separate directory for the 64-bit R executables. >> >> Does it make any difference to check and pack th

[R] The secret of wisdom, power and knowledge is humility.

2013-04-20 Thread Eva Prieto Castro
Dear all, Thank for your friendliness. I have read several documents and I'm sure that if I have time to read ALL documents in the world I would not need to be part of this list, because of my capabilities... I have used this idea (factors) in several cases in which dummy variables arise, b

Re: [R] creating dummy variables

2013-04-20 Thread Santosh
R is for dummies (like me, but I don't use dummy variables) or for the non-Dummies like all experts who help us all the time@@.. so dummy variables are not needed! :) QED... On Sat, Apr 20, 2013 at 6:16 PM, Rolf Turner wrote: > On 21/04/13 10:56, Eva Prieto Castro wrote: > >> Hi, >> >> Why do y

[R] cluster gene list

2013-04-20 Thread Sudhir Singh
Hi, I have created a heatmap using heatmap.2 having 7 clusters. I would like to extract the list of genes that are in these 7 clusters. Is there any function that can be used to extract genes for each cluster? Cheers, Sudhir -- __ SA