[R] Help on read in a txt file
Dear list, Hello! I had a problem of reading in a txt file and need your help. The txt file, called A, comprises of 592 columns and 34179 rows. I need to note that for some cells of A , A[i,j], are blank. I used read.table() and got the warning message: A-read.table(file=A.txt,sep=\t) Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns dim(A) [1] 33623 592 However, as some rows were missed because the original number of rows is 34179, after read.table(), it was decreased to 33623. I have no idea whether it has anything to do with the warning message. Do you have any suggestions for this problem? Thanks much, Alex [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of survreg.distributions
Dear R-user: I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=gaussian, data=y.data, scale=0, weights=w) my.gaussian-survreg.distributions$gaussian my.gaussian$name=lognormal my.gaussian$dist-my.gaussian tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=my.gaussian, data=y.data, scale=0, weights=w) If I run these codes then I got the following error message, Error in survreg(Surv(y, y = -5, type = left) ~ x + : Invalid distribution object Does anybody can help me in identifying the error(s) in these code please? Advance thanks for your time. Abdus Sattar [EMAIL PROTECTED] [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] request for Unsubscribe
Dear Please unsubscribe my email from mailing list of R-Help. Thanks Amir Kavousi [EMAIL PROTECTED] - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using image function to plot character values
Eric Bell eric at ericjbell.com writes: A secondary problem is that after I do the conversion, I need to know what codes were converted to what numeric values. Column-wise factor conversion can be handy, but often it bites. # Assume you have the data file m1 m2 A B B C C D #--- # make sure that no column-wise factor conversion is done dv - read.csv( a.txt, header=TRUE,sep= ,stringsAsFactors=FALSE) # find unique levels in the whole data set faklevels = unique(unlist(dv)) dv[] = lapply(dv,function(x) factor(x,levels=faklevels)) # now we have common levels for all columns, we can convert to numerics dv[] = lapply(dv,as.numeric) # or combine the two above #dv[] = lapply(dv,function(x) as.numeric(factor(x,levels=faklevels))) Dieter __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] request for Unsubscribe
Amir Kavousi wrote: Dear Please unsubscribe my email from mailing list of R-Help. Please use the unsubscription mechanism at https://stat.ethz.ch/mailman/listinfo/r-help (near the bottom) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Constructing dummy variables for months for a time series object
I have a TS of monthly observations. head(data4) 1991(1) 1991(2) 1991(3) 1991(4) 1991(5) 1991(6) 12.00864 11.94203 11.98386 12.01900 12.19226 12.15488 Now I want to make 11 dummy variables indicating months. Therefore I did followings : For Jan : rep(c(rep(0,0), 1, rep(0, 11)), 17) For Feb : rep(c(rep(0,1), 1, rep(0, 10)), 17) and so on But my question is there any way to aumate this? Or I have to do the above thing for all 11 months? - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to overlap two density plots?
Hi, How can I overlap two density plots? A - c(8,10,10,11,11,11,12,12,12,12,11,11,11,10,10,7) B - c(11,13,13,14,14,14,15,15,15,15,14,14,14,13,13,10) plot(density(A)) plot(density(B)) Regards, Emre P.S. There's a overlap.density function in package DAAG Is there another way to do this? -- --- Emre ÜNAL http://www.geocities.com/dusemre [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] force glm estimates to be nonnegative
You could use the BRugs package and formulate your prior knowledge about slopes in terms of a probability distribution. Michele Christina Itten kirjoitti: Is there a way to force certain formula parameters to be nonnegative? What I want to do is to estimate student capacity over time, namely by capacity ~ Student + Student:Day I add this formula to a glm call and obtain negative learning slope estimates (Student:Day) in some cases. However, I don't want to allow for that. In such a case, glm should solve capacity ~ Student and I will set the slope to zero. Is there an option to constrain a parameter set to nonnegative values? Many thanks in advance! Michele Itten, BS. Carnegie Mellon __ 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 and provide commented, minimal, self-contained, reproducible code. -- -- Samu Mäntyniemi Researcher Fisheries and Environmental Management Group (FEM) Department of Biological and Environmental Sciences Biocenter 3, room 4414 Viikinkaari 1 P.O. Box 65 FIN-00014 University of Helsinki Phone: +358 9 191 58710 Fax: +358 9 191 58257 email: [EMAIL PROTECTED] personal webpage: http://www.helsinki.fi/people/samu.mantyniemi/ FEM webpage: http://www.helsinki.fi/science/fem/ __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] make check errors with R 2.7.0
On Fri, 25-Apr-2008 at 06:12AM +0100, Prof Brian Ripley wrote:
Note that the problem is not that you got the message, but an apparent
whitespace issue in the output. That's clearer in this version: note that
the output for reg-IO.Rout.save is shifted left one column. But I don't
trust email to transmit these things faithfully (especially after the last
two days of encoding issues).
So the problem is most likely either the way reg-IO.Rout.save got unpacked
or your 'diff' function.
That was well-spotted. I notice that according to Emacs,
reg-IO.Rout.save is a DOS text file. Can't say I've seen that before.
You don't mention an OS, but my recollection is that you usually use Linux.
I *have* seen an error in this test on Cygwin, where the issue was the
unpacking by tar.
This is Fedora 8 (32 bit). Previously, I'd used FC6 (64 bit) which
had a problem unpacking the gz file. That was simply fixed by redoing
it -- so much for the deterministic nature of that machine.
[]
Do I have any cause for concern?
Some, but with your toolset.
Thanks for the hint. On the strength of it, I checked and noticed
that there were, indeed, updates for make, diffutils and unzip. So I
updated them and retried the installation. Everything went fine as
I'm accustomed to seeing (and Emacs doesn't think it's reading DOS
text files).
Brian, you're a genius.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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Re: [R] Constructing dummy variables for months for a time series object
GenDummyVar - function (NumMonth) rep(c(rep(0, NumMonth-1), 1, rep(0, 12-NumMonth)), 17) NameDummy - c(DJan, DFeb, DMar, DApr, DMay, DJun, DJul, DAug, DSep, DOct, DNov, DDec) for (NumMonth in 1:12) assign(NameDummy, GenDummyVar (NumMonth)) DJan [1] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 [74] 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 [147] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 DFeb [1] 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 [74] 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 [147] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 Is this what you need ? Why 11 (and not 12) months ? Nael On Fri, Apr 25, 2008 at 9:40 AM, Megh Dal [EMAIL PROTECTED] wrote: I have a TS of monthly observations. head(data4) 1991(1) 1991(2) 1991(3) 1991(4) 1991(5) 1991(6) 12.00864 11.94203 11.98386 12.01900 12.19226 12.15488 Now I want to make 11 dummy variables indicating months. Therefore I did followings : For Jan : rep(c(rep(0,0), 1, rep(0, 11)), 17) For Feb : rep(c(rep(0,1), 1, rep(0, 10)), 17) and so on But my question is there any way to aumate this? Or I have to do the above thing for all 11 months? - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing dummy variables for months for a time series object
Oops.. the last line should have been : for (NumMonth in 1:12) assign(NameDummy[NumMonth], GenDummyVar (NumMonth)) On Fri, Apr 25, 2008 at 10:18 AM, N. Lapidus [EMAIL PROTECTED] wrote: GenDummyVar - function (NumMonth) rep(c(rep(0, NumMonth-1), 1, rep(0, 12-NumMonth)), 17) NameDummy - c(DJan, DFeb, DMar, DApr, DMay, DJun, DJul, DAug, DSep, DOct, DNov, DDec) for (NumMonth in 1:12) assign(NameDummy, GenDummyVar (NumMonth)) DJan [1] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 [74] 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 [147] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 DFeb [1] 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 [74] 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 [147] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 Is this what you need ? Why 11 (and not 12) months ? Nael On Fri, Apr 25, 2008 at 9:40 AM, Megh Dal [EMAIL PROTECTED] wrote: I have a TS of monthly observations. head(data4) 1991(1) 1991(2) 1991(3) 1991(4) 1991(5) 1991(6) 12.00864 11.94203 11.98386 12.01900 12.19226 12.15488 Now I want to make 11 dummy variables indicating months. Therefore I did followings : For Jan : rep(c(rep(0,0), 1, rep(0, 11)), 17) For Feb : rep(c(rep(0,1), 1, rep(0, 10)), 17) and so on But my question is there any way to aumate this? Or I have to do the above thing for all 11 months? - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] request for Unsubscribe
Amir Kavousi schrieb: Dear Please unsubscribe my email from mailing list of R-Help. Thanks Amir Kavousi [EMAIL PROTECTED] you can unsubsribe at the following page by yourself. (including password reminder) https://stat.ethz.ch/mailman/listinfo/r-help Regards Knut __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Non-linear system of equations
Hello R users, I am trying to estimate the parameters of a bimodal normal distribution using moments matching, so I have to solve a non-linear system of equations. How can I solve the following simple example? x^2 - y^2 = 6 x – y = 3 I heard about nlsystemfit, but I don’t know how to run it exactly. I have tried the following code, but it doesn’t really work: f1 -y~ x[1]^2-x[2]^2-6 f2 -z~ x[1]-x[2]-3 f - list(f1=0,f2=0) nlsystemfit(OLS,f,startvals=c(0,0)) Thank You in advance for your help. Evgeniq Petrova __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using image function to plot character values
Eric Bell wrote: Hello. I am a newbie to R. If I should be reading some FAQ or manual that could help answer my question please tell me and I will go there. Problem: I have a spreadsheet that contains a character code in each cell. The columns in the spreadsheet represent time and the rows represent people. I want to use the image function to display this information, but the image function requires numeric data. I know how to read in the spreadsheet into a data frame, but if I use data.matrix to convert data frame into a numeric matrix, each column gets converted separately, so that the same character code may get converted to a different numeric code depending on the column. How do I apply the character to numeric conversion so that each character gets converted to the same numeric value? A secondary problem is that after I do the conversion, I need to know what codes were converted to what numeric values. Hi Eric, Using your example data frame, matrix(as.numeric(unlist(dv)),nrow=dim(dv)[1]) gives you the matrix you want, and levels(unlist(dv)) unique(as.numeric(unlist(dv))) gives you the correspondence between character codes and numbers. Jim __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] grid() : start values?
Hi, is not there any way to tell grid() the starting value? With nx,ny I get the right number of grid cells, but not on the exact values I would like them. (I know I can do it with abline(), just asking for an easier way, i.e. grid(nx,nx,start.x,start.y)) An alternative way (which would solve another problem) would be making the axes coincident with the rectangular plot region, that is, if ploting plot(0:10,0:10) get (0,0) just on the bottom down corner of the rectangle. I've tried with several par() and could not find the way. Thanks Agus -- Dr. Agustin Lobo Institut de Ciencies de la Terra Jaume Almera (CSIC) LLuis Sole Sabaris s/n 08028 Barcelona Spain Tel. 34 934095410 Fax. 34 934110012 email: [EMAIL PROTECTED] http://www.ija.csic.es/gt/obster __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
I am trying to estimate the parameters of a bimodal normal distribution
using moments matching, so I have to solve a non-linear system of equations.
How can I solve the following simple example?
x^2 - y^2 = 6
x – y = 3
I heard about nlsystemfit, but I don't know how to run it exactly. I have
tried the following code, but it doesn't really work:
f1 -y~ x[1]^2-x[2]^2-6
f2 -z~ x[1]-x[2]-3
f - list(f1=0,f2=0)
nlsystemfit(OLS,f,startvals=c(0,0))
You could try the recent package BB by Ravi Varadhan. The code could
be the following:
library(BB)
f - function(x) {
x1 - x[1]
x2 - x[2]
F - rep(NA, 2)
F[1] - x1^2 - x2^2 - 6
F[2] - x1 - x2 - 3
return(F)
}
p0 - c(1,2)
dfsane(par=p0, fn=f,control=list(maxit=3000))
I got the solution:
x1 = 2.5
x2 = -0.5
Paul
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to overlap two density plots?
Emre Unal [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Hi, How can I overlap two density plots? A - c(8,10,10,11,11,11,12,12,12,12,11,11,11,10,10,7) B - c(11,13,13,14,14,14,15,15,15,15,14,14,14,13,13,10) plot(density(A)) Instead: lines(density(B)) -- David Winsemius plot(density(B)) Regards, Emre P.S. There's a overlap.density function in package DAAG Is there another way to do this? __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
Hello Paul,
Thank you for your quick answer. I have tried to use your advice and to
estimate the parameters of beta distribution with moments matching. This is my
code:
ex - 0.3914877
ex2 - 0.2671597
my.mm - function(x){
p - x[1]
q - x[2]
p - .Machine$double.eps
q - .Machine$double.eps
F - rep(NA,2)
F[1] - p/(p + q)
F[2]- (p*q + (p + q + 1)*p^2)/((p + q + 1)*(p + q)^2)
return(F)
}
p0 - c(ex,ex2)
dfsane(par=p0, fn=my.mm,control=list(maxit=5))
and I became the following output:
…
iteration: 3640 ||F(xn)|| = 0.7071068
iteration: 3641 ||F(xn)|| = 0. 7071068
…
iteration: 49990 ||F(xn)|| = 0. 7071068
iteration: 5 ||F(xn)|| = 0. 7071068
$par
[1] -446.2791 -446.4034
$residual
[1] 0.5
$fn.reduction
[1] 0
$feval
[1] 828495
$iter
[1] 50001
$convergence
[1] 1
$message
[1] Maximum limit for iterations exceeded
I have tried maxiter=10 but the output is the same. I know that ex and ex2
are bringing the problems, but I am stuck with them. How can I make it
convergent?
Thank you,
Evgeniq
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
I am trying to estimate the parameters of a bimodal normal distribution
using moments matching, so I have to solve a non-linear system of
equations. How can I solve the following simple example?
x^2 - y^2 = 6
x – y = 3
I heard about nlsystemfit, but I don't know how to run it exactly. I have
tried the following code, but it doesn't really work:
f1 -y~ x[1]^2-x[2]^2-6
f2 -z~ x[1]-x[2]-3
f - list(f1=0,f2=0)
nlsystemfit(OLS,f,startvals=c(0,0))
You could try the recent package BB by Ravi Varadhan. The code could
be the following:
library(BB)
f - function(x) {
x1 - x[1]
x2 - x[2]
F - rep(NA, 2)
F[1] - x1^2 - x2^2 - 6
F[2] - x1 - x2 - 3
return(F)
}
p0 - c(1,2)
dfsane(par=p0, fn=f,control=list(maxit=3000))
I got the solution:
x1 = 2.5
x2 = -0.5
Paul
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] grid() : start values?
On 4/25/2008 5:32 AM, Agustin Lobo wrote: Hi, is not there any way to tell grid() the starting value? With nx,ny I get the right number of grid cells, but not on the exact values I would like them. (I know I can do it with abline(), just asking for an easier way, i.e. grid(nx,nx,start.x,start.y)) See the help page: If more fine tuning is required, use 'abline(h = ., v = .)' directly. Just use abline(h=seq(starty, stopy, len=ny), v=seq(startx, stopx, len=nx)) Duncan Murdoch An alternative way (which would solve another problem) would be making the axes coincident with the rectangular plot region, that is, if ploting plot(0:10,0:10) get (0,0) just on the bottom down corner of the rectangle. I've tried with several par() and could not find the way. Thanks Agus __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to overlap two density plots?
On Fri, Apr 25, 2008 at 10:57:27AM +0300, Emre Unal wrote: How can I overlap two density plots? A - c(8,10,10,11,11,11,12,12,12,12,11,11,11,10,10,7) B - c(11,13,13,14,14,14,15,15,15,15,14,14,14,13,13,10) plot(density(A)) lines(density(B)) cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany and Institut für Bioinformatik und Systembiologie / MIPS Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] No rule to make target 'R/Copy'
Dear all, I am currently building a package with C code (in scr folder). Everything was ok, but now, I get the following error message when compiling the package using R CMD INSTALL: make[2]: *** No rule to make target 'R/Copy', needed in [...] What does that mean? I can still compile other packages containing C code, but not that one. No 00UNLOCK directory has been created . I am on a IBM PC, and use windows XP. Thanks for your help -- David Ardia H-building, room 11-26 Econometric Institute Erasmus University PO Box 1738 NL 3000 DR Rotterdam The Netherlands Phone: +31 (0)10 408 2269 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of survreg.distributions
--begin included message --- I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=gaussian, data=y.data, scale=0, weights=w) my.gaussian-survreg.distributions$gaussian my.gaussian$name=lognormal my.gaussian$dist-my.gaussian tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=my.gaussian, data=y.data, scale=0, weights=w) If I run these codes then I got the following error message, Error in survreg(Surv(y, y = -5, type = left) ~ x + : Invalid distribution object Does anybody can help me in identifying the error(s) in these code please? --- end include Can you tell us what you are trying to do? Your first model was a fit of y ~ x + eps, eps ~ Gaussian. If what you want is log(y) ~ x + eps, then all that you need do is use dist=loggaussian in the survreg call. (Or 'lognormal'; which is the same distribution.) Terry Therneau __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
x^2 - y^2 = 6
x – y = 3
You can also try this
# function
f - function(x) {
y - numeric(2)
y[1] - x[1]^2-x[2]^2-6
y[2] - x[1]-x[2]-3
y
}
# function values transformed to scalar
# minimising fnorm this way is not the best method of finding a solution for
f(x)=0
# there may be values for x which minimise fnorm but do not set f(x) = 0
# but you can always try
fnorm - function(z) {p - f(z);return(crossprod(p))}
#starting values
xstart - c(0,0)
# You can use nlm or nlminb
nlm(fnorm,xstart)
nlminb(xstart,fnorm)
Sometimes minpack.lm can be used to find roots.
Do
library(minpack.lm)
nls.lm(xstart,f)
and in this case you'll see that it doesn't work.
In this case stick to nlm and/or nlminb.
Berend
--
View this message in context:
http://www.nabble.com/Non-linear-system-of-equations-tp16893056p16895541.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
Try to change the initial values of the parameters with, for instance,
p0 - rnorm(2)
But you sure that your system has a solution, Evgeniq?
Paul
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
Hello Paul,
Thank you for your quick answer. I have tried to use your advice and to
estimate the parameters of beta distribution with moments matching. This is
my code:
ex - 0.3914877
ex2 - 0.2671597
my.mm - function(x){
p - x[1]
q - x[2]
p - .Machine$double.eps
q - .Machine$double.eps
F - rep(NA,2)
F[1] - p/(p + q)
F[2]- (p*q + (p + q + 1)*p^2)/((p + q + 1)*(p + q)^2)
return(F)
}
p0 - c(ex,ex2)
dfsane(par=p0, fn=my.mm,control=list(maxit=5))
and I became the following output:
…
iteration: 3640 ||F(xn)|| = 0.7071068
iteration: 3641 ||F(xn)|| = 0. 7071068
…
iteration: 49990 ||F(xn)|| = 0. 7071068
iteration: 5 ||F(xn)|| = 0. 7071068
$par
[1] -446.2791 -446.4034
$residual
[1] 0.5
$fn.reduction
[1] 0
$feval
[1] 828495
$iter
[1] 50001
$convergence
[1] 1
$message
[1] Maximum limit for iterations exceeded
I have tried maxiter=10 but the output is the same. I know that ex and
ex2 are bringing the problems, but I am stuck with them. How can I make it
convergent?
Thank you,
Evgeniq
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
I am trying to estimate the parameters of a bimodal normal distribution
using moments matching, so I have to solve a non-linear system of equations.
How can I solve the following simple example?
x^2 - y^2 = 6
x – y = 3
I heard about nlsystemfit, but I don't know how to run it exactly. I
have tried the following code, but it doesn't really work:
f1 -y~ x[1]^2-x[2]^2-6
f2 -z~ x[1]-x[2]-3
f - list(f1=0,f2=0)
nlsystemfit(OLS,f,startvals=c(0,0))
You could try the recent package BB by Ravi Varadhan. The code could
be the following:
library(BB)
f - function(x) {
x1 - x[1]
x2 - x[2]
F - rep(NA, 2)
F[1] - x1^2 - x2^2 - 6
F[2] - x1 - x2 - 3
return(F)
}
p0 - c(1,2)
dfsane(par=p0, fn=f,control=list(maxit=3000))
I got the solution:
x1 = 2.5
x2 = -0.5
Paul
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] No rule to make target 'R/Copy'
Do you have a space in some file name? Starting 'Copy '? On Fri, 25 Apr 2008, Ardia David wrote: Dear all, I am currently building a package with C code (in scr folder). Everything was ok, but now, I get the following error message when compiling the package using R CMD INSTALL: make[2]: *** No rule to make target 'R/Copy', needed in [...] What does that mean? I can still compile other packages containing C code, but not that one. No 00UNLOCK directory has been created . I am on a IBM PC, and use windows XP. Thanks for your help -- David Ardia H-building, room 11-26 Econometric Institute Erasmus University PO Box 1738 NL 3000 DR Rotterdam The Netherlands Phone: +31 (0)10 408 2269 __ 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 and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Newbie Question/Data Model
[EMAIL PROTECTED] wrote: Given a data set and a set of predictors and a response in the data, we would like to find a model that fits the data set best. Suppose that we do not know what kind of model (linear, polynomial regression,... ) might be good, we are wondering if there is R-package(s) can auctomatically do this. Otherwise, can you direct me, or point out reference(s), basic steps to do this. Thanks. -james The best-fitting model for any data is a model with a lot of parameters, so maybe the best fitting model for any data is a model with an infinite number of parameters. However, any model with more parameters than data will have a negative number of degrees of freedom, and you do not want that. The best-fitting model for any data subject to the constraint that the number of degrees of freedom is non-negative, is the data itself, with zero degrees of freedom. The AIC tells you this too. The AIC for the model formed by the data itsel is 2n, whereas the AIC for any model with negative degrees of freedom is 2n. But I guess you want to make inference from sample to population. If that is indeed the case, then you should consider changing your focus from finding a model that fits the data set best to a model that best summarizes the information contained in your sample about the population the sample comes from. To do that, start by defining the nature of your response variable. What is the nature of the natural process generating this response variable? Is it continuous or discrete? Is it univariate or multivariate? Can it take negative and positive values? Can it take values of zero? After you have clarified the probabilistic model for the response variable, then you can start thinking about the mathematical relation between the response variable and the predictors. Is it linear or nonlinear? Are the predictors categorical or continuous? Read the posting guide, formulate a clear question, and maybe you will be given more specific help. Rubén __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] package compilation: including external libraries in windows compilation
Dear R package developers: I need help on getting a package compiled for windows. I am trying to use definitions and routines from a set of libraries in that are in LINUX under #include netdb.h #include sys/socket.h #include netinet/in.h #include arpa/inet.h but these are unavailable in windows. I found that we can get these by including, in windows these includes: #include winsock2.h #include io.h My problem is I do not know how to instruct the preprocessor to include the linux .h files when in linux and the windows one in windows. I thought I found a solution online by using: #if defined(Win32) #include winsock2.h #include io.h #else #ifdef HAVE_UNISTD_H #include unistd.h #endif #ifdef HAVE_BSD_NETWORKING #include netdb.h #include sys/socket.h #include netinet/in.h #include arpa/inet.h #endif #endif But I still get an error when these are compiled on the R-distribution. I do not understand where I am supposed to set the Win32 flag so that it will be ignored in LINUX but used in windows. where is Win32 HAVE_UNISTD_H and HAVE_BSD_NETWORKING set? It seems that Makevars.win would be logical place, but I do not see how to do this. Thanks for any help. Jonathan Lees -- Making package WINRPACK adding build stamp to DESCRIPTION making DLL ... making win2R.d from win2R.c making win2asc.d from win2asc.c gcc-sjlj -std=gnu99 -Id:/Rcompile/recent/R-26~1.2/include -O3 -Wall -c win2R.c -o win2R.o win2R.c:21:24: error: sys/socket.h: No such file or directory win2R.c:22:24: error: netinet/in.h: No such file or directory win2R.c:23:23: error: arpa/inet.h: No such file or directory win2R.c: In function 'read_data': win2R.c:591: warning: implicit declaration of function 'ntohl' win2R.c: In function 'read_one_sec': win2R.c:723: warning: implicit declaration of function 'ntohs' make[3]: *** [win2R.o] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-WINRPACK] Error 2 *** Installation of WINRPACK failed *** -- == Prof. Jonathan M. Lees Department of Geological Sciences CB #3315, Mitchell Hall University of North Carolina Chapel Hill, NC 27599-3315 (919) 962-0695 FAX (919) 966-4519 [EMAIL PROTECTED] http://www.unc.edu/~leesj __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
Hi Radka,
The problem lies in your function my.mm(). Especially, the following lines:
p - .Machine$double.eps
q - .Machine$double.eps
Even if you take out these 2 lines, still the definition is not correct, I
think, since there is a trivial answer x* = c(0, q).
I am not sure how you intended to use these, but they are the problem.
Therefore, you need to define your function correctly.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Radka Pancheva
Sent: Friday, April 25, 2008 8:13 AM
To: R-help@r-project.org
Subject: Re: [R] Non-linear system of equations
Hello Paul,
Thank you for your quick answer. I have tried to use your advice and to
estimate the parameters of beta distribution with moments matching. This is
my code:
ex - 0.3914877
ex2 - 0.2671597
my.mm - function(x){
p - x[1]
q - x[2]
p - .Machine$double.eps
q - .Machine$double.eps
F - rep(NA,2)
F[1] - p/(p + q)
F[2]- (p*q + (p + q + 1)*p^2)/((p + q + 1)*(p + q)^2)
return(F)
}
p0 - c(ex,ex2)
dfsane(par=p0, fn=my.mm,control=list(maxit=5))
and I became the following output:
.
iteration: 3640 ||F(xn)|| = 0.7071068
iteration: 3641 ||F(xn)|| = 0. 7071068
.
iteration: 49990 ||F(xn)|| = 0. 7071068
iteration: 5 ||F(xn)|| = 0. 7071068
$par
[1] -446.2791 -446.4034
$residual
[1] 0.5
$fn.reduction
[1] 0
$feval
[1] 828495
$iter
[1] 50001
$convergence
[1] 1
$message
[1] Maximum limit for iterations exceeded
I have tried maxiter=10 but the output is the same. I know that ex and
ex2 are bringing the problems, but I am stuck with them. How can I make it
convergent?
Thank you,
Evgeniq
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
I am trying to estimate the parameters of a bimodal normal distribution
using moments matching, so I have to solve a non-linear system of equations.
How can I solve the following simple example?
x^2 - y^2 = 6
x - y = 3
I heard about nlsystemfit, but I don't know how to run it exactly. I
have tried the following code, but it doesn't really work:
f1 -y~ x[1]^2-x[2]^2-6
f2 -z~ x[1]-x[2]-3
f - list(f1=0,f2=0)
nlsystemfit(OLS,f,startvals=c(0,0))
You could try the recent package BB by Ravi Varadhan. The code could
be the following:
library(BB)
f - function(x) {
x1 - x[1]
x2 - x[2]
F - rep(NA, 2)
F[1] - x1^2 - x2^2 - 6
F[2] - x1 - x2 - 3
return(F)
}
p0 - c(1,2)
dfsane(par=p0, fn=f,control=list(maxit=3000))
I got the solution:
x1 = 2.5
x2 = -0.5
Paul
__
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
and provide commented, minimal, self-contained, reproducible code.
__
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
and provide commented, minimal, self-contained, reproducible code.
__
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
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Non-linear system of equations
Radka,
Generally, there is no need to increase `maxit' to beyond default. If you
are unable to obtain a reasonable approximation to your system within
`maxit', then you should do the following (not necessarily in that order):
1. Try a few different starting values and see if you can obtain a residual
closer to zero.
2. Try a different method within dfsane, try method=1 or method=3.
3. If neither (1) nor (2) works, then try a different algorithm, sane.
4. If none of the above steps is successful, then check your function
definition carefully for possible errors.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Radka Pancheva
Sent: Friday, April 25, 2008 8:13 AM
To: R-help@r-project.org
Subject: Re: [R] Non-linear system of equations
Hello Paul,
Thank you for your quick answer. I have tried to use your advice and to
estimate the parameters of beta distribution with moments matching. This is
my code:
ex - 0.3914877
ex2 - 0.2671597
my.mm - function(x){
p - x[1]
q - x[2]
p - .Machine$double.eps
q - .Machine$double.eps
F - rep(NA,2)
F[1] - p/(p + q)
F[2]- (p*q + (p + q + 1)*p^2)/((p + q + 1)*(p + q)^2)
return(F)
}
p0 - c(ex,ex2)
dfsane(par=p0, fn=my.mm,control=list(maxit=5))
and I became the following output:
.
iteration: 3640 ||F(xn)|| = 0.7071068
iteration: 3641 ||F(xn)|| = 0. 7071068
.
iteration: 49990 ||F(xn)|| = 0. 7071068
iteration: 5 ||F(xn)|| = 0. 7071068
$par
[1] -446.2791 -446.4034
$residual
[1] 0.5
$fn.reduction
[1] 0
$feval
[1] 828495
$iter
[1] 50001
$convergence
[1] 1
$message
[1] Maximum limit for iterations exceeded
I have tried maxiter=10 but the output is the same. I know that ex and
ex2 are bringing the problems, but I am stuck with them. How can I make it
convergent?
Thank you,
Evgeniq
2008/4/25 Radka Pancheva [EMAIL PROTECTED]:
I am trying to estimate the parameters of a bimodal normal distribution
using moments matching, so I have to solve a non-linear system of equations.
How can I solve the following simple example?
x^2 - y^2 = 6
x - y = 3
I heard about nlsystemfit, but I don't know how to run it exactly. I
have tried the following code, but it doesn't really work:
f1 -y~ x[1]^2-x[2]^2-6
f2 -z~ x[1]-x[2]-3
f - list(f1=0,f2=0)
nlsystemfit(OLS,f,startvals=c(0,0))
You could try the recent package BB by Ravi Varadhan. The code could
be the following:
library(BB)
f - function(x) {
x1 - x[1]
x2 - x[2]
F - rep(NA, 2)
F[1] - x1^2 - x2^2 - 6
F[2] - x1 - x2 - 3
return(F)
}
p0 - c(1,2)
dfsane(par=p0, fn=f,control=list(maxit=3000))
I got the solution:
x1 = 2.5
x2 = -0.5
Paul
__
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
and provide commented, minimal, self-contained, reproducible code.
__
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
and provide commented, minimal, self-contained, reproducible code.
__
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
and provide commented, minimal, self-contained, reproducible code.
[R] Extracting coefficients' standard errors from linear model
Dear all, Hope this question is not too trivial... In order to correct standard errors from an estimation of a fixed effects regression model y need to extract the vector of standard errors of the coefficients of a simple linear model estimated using lm(var1~var2+var3+var4) Unfortunately I can't find out the corresponding function. Thank you very much for your help. Uli -- Uli Kleinwechter Department of Agricultural Economics and Social Sciences Faculty of Agriculture and Horticulture Humboldt University of Berlin Unter den Linden 6 D-10099 Berlin, Germany Phone: (+49) 30 2093 6124, Fax. (+49) 30 2093 6301 E-mail: [EMAIL PROTECTED] __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] remarks on function pnbeta
Dear Developers, The pnbeta function has been reviewed recently in the article of A. Baharev, S. Kemény, On the computation of the noncentral F and noncentral beta distribution, Statistics and Computing, 2008, in press. Preprint of the paper is available here: http://reliablecomputing.eu/publications.html and the article here http://dx.doi.org/10.1007/s11222-008-9061-3 I suggest increasing the itrmax to (at least) 2000, since practically important values cannot be computed with the current value. For example: pnbeta(0.2057, 25.0, 0.5, 34012.98, 1, 0); needs 1649 iterations on my machine, and returns 0.0752037 instead of the true value 0.10. This is not a bug, i got a warning, however i think it would be better to increase the iteration limit. According to my experience the users tend to ignore warning messages and would use the incorrect values that is why i think it would be better if pnbeta called exit(EXIT_FAILURE) or throw an exception than returning a completely incorrect value and let the user use that. This is my personal opinion, i do not know more about the design and application logic of R. The source file pnbeta.c refers to the paper of Frick (1990, AS R84) giving a FORTRAN implementation. That paper contains typos; those were corrected by Lam (1995, AS R95). Lam also made some remarks that are worth considering. The R implementation is a revised C code, and it seems to me that the pnbeta's implementation is not influenced by the typos in the paper of Frick. However it would be better to indicate that the pnbeta is a revised implementation compared to AS 226 and AS R84, and is not influenced by AS R95. Cancellation may occur during the recursion in the do while loop, we failed to produce an example using practically meaningful parameter values where serious cancellation occurs. We suspect it may be an issue where the corresponding probability is small (less then 1.0E-30). We plan to contribute a C implementation of our algorithm where cancellation cannot occur, and newton iteration for the noncentrality parameter is included. The computation of the noncentrality parameter is need for ANOVA purposes. Best regards, Ali Baharev __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] package compilation: including external libraries in windows compilation
The standard C define is WIN32, not Win32 (which R uses as private define). You could have PKG_CPPFLAGS=-DWin32 in Makevars.win, but this is unnecessary. See e.g. Rmath.h. On Fri, 25 Apr 2008, Jonathan Lees wrote: Dear R package developers: I need help on getting a package compiled for windows. I am trying to use definitions and routines from a set of libraries in that are in LINUX under #include netdb.h #include sys/socket.h #include netinet/in.h #include arpa/inet.h but these are unavailable in windows. I found that we can get these by including, in windows these includes: #include winsock2.h #include io.h My problem is I do not know how to instruct the preprocessor to include the linux .h files when in linux and the windows one in windows. I thought I found a solution online by using: You mean in the R sources? #if defined(Win32) #include winsock2.h #include io.h #else #ifdef HAVE_UNISTD_H #include unistd.h #endif #ifdef HAVE_BSD_NETWORKING #include netdb.h #include sys/socket.h #include netinet/in.h #include arpa/inet.h #endif #endif But I still get an error when these are compiled on the R-distribution. I do not understand where I am supposed to set the Win32 flag so that it will be ignored in LINUX but used in windows. where is Win32 HAVE_UNISTD_H and HAVE_BSD_NETWORKING set? In config.h. It seems that Makevars.win would be logical place, but I do not see how to do this. Thanks for any help. Jonathan Lees -- Making package WINRPACK adding build stamp to DESCRIPTION making DLL ... making win2R.d from win2R.c making win2asc.d from win2asc.c gcc-sjlj -std=gnu99 -Id:/Rcompile/recent/R-26~1.2/include -O3 -Wall -c win2R.c -o win2R.o win2R.c:21:24: error: sys/socket.h: No such file or directory win2R.c:22:24: error: netinet/in.h: No such file or directory win2R.c:23:23: error: arpa/inet.h: No such file or directory win2R.c: In function 'read_data': win2R.c:591: warning: implicit declaration of function 'ntohl' win2R.c: In function 'read_one_sec': win2R.c:723: warning: implicit declaration of function 'ntohs' make[3]: *** [win2R.o] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-WINRPACK] Error 2 *** Installation of WINRPACK failed *** -- == Prof. Jonathan M. Lees Department of Geological Sciences CB #3315, Mitchell Hall University of North Carolina Chapel Hill, NC 27599-3315 (919) 962-0695 FAX (919) 966-4519 [EMAIL PROTECTED] http://www.unc.edu/~leesj __ 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 and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting coefficients' standard errors from linear model
Uli Kleinwechter [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Dear all, Hope this question is not too trivial... In order to correct standard errors from an estimation of a fixed effects regression model y need to extract the vector of standard errors of the coefficients of a simple linear model estimated using lm(var1~var2+var3+var4) Unfortunately I can't find out the corresponding function. See if vcov() suits. From the lm() help page an example: ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight - c(ctl, trt) lm.D9 - lm(weight ~ group) Then look at summary(lm.D9) and these results: vcov(lm.D9)[2,2] [1] 0.09699167 vcov(lm.D9)[2,2]^(1/2) [1] 0.3114349 diag(vcov(lm.mdl))^(1/2) may be needed to get the vector you seek. -- David Winsemius __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Documentation General Comments
I realize the R developers are probably overwhelmed and have little time for this, but the documentation really needs some serious reorganizaton. My reply: I'm quite new to R and so have spent a lot of time in the last few days reading documentation both online and text. I'm incredibly impressed by the language and, overall, by the documentation - the documentation tools are so well integrated into the program, and in most cases the documentation does a good job of balancing brevity and completeness. The original poster noted a need for reorganization (not revision) and I think that's key. Several people have posted about potential projects in several threads - so I'll try combining those thoughts in a new response thread. Summary: 1) New users have questions based on common tasks, which don't necessarily reflect the structure of the language 2) There's a lot of good documentation out there already, both official and unofficial 3) It doesn't break intellectual property laws to create an annotated bibliography of existing references, with a task-based topic structure. 4) I suspect new and old users would contribute to such a project if it allowed external contributions - as in, suggest a resource (under an existing topic) along with a brief explanation about why that resource was helpful. Detailed comments: One thing I notice in the official documentation is that it's organized around the R language structure. The help table of contents does include a listing of natural-language titles, but they're listed alphabetically rather than organized by task-based concept. But when you look at the forums, the new users are searching for information by task or by concept - what are the classes of object? How do I manipulate a data frame? What are my tools for regular expressions? Many of my texts (and some independent web pages) seem to try to organize by task, but all are incomplete - perhaps because of space limitations, perhaps because the language is so dynamic that useful functions hadn't yet been developed when a text was published. Also, most of my books actually only introduce the R language then move on to discussing the use of R for specific statistical functions. Yet, most of the forum questions seem to be about things like loading and manipulating the data to get it into the appropriate format for the desired analysis. So I really like the suggestion to try creating some cross-indexing for the materials that are out there already. Perhaps a wiki-based annotated bibliography with a task-based structure. I'm tempted to suggest that we just expand on the wikipedia content for R! The structure of such a thing should have categories like managing regular expressions or manipulating data in dataframes - and often a particular topic might be cross-referenced to more than one category, I'd think. By annotated bibliography I mean that most of the entries under a topic would be here's a link or reference to a source that seems to explain this topic well - and here's why I like it. And - I have to run to a meeting. So I will stop brainstorming now. -- View this message in context: http://www.nabble.com/Documentation-General-Comments-tp16821085p16895859.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] join chars in loops
Hi, Is it possible to create new vars in a loop For instance: for (i in 1:11) var'i' - assign something output = var1 var2 ... var11 Is there a way to combine/join the value of 'i' to the string/char var in de loop. -- View this message in context: http://www.nabble.com/join-chars-in-loops-tp16895854p16895854.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] join chars in loops
for (i in 1:11){
assign(paste('var', i, sep=''), value)
}
On Fri, Apr 25, 2008 at 10:40 AM, Dirkheld [EMAIL PROTECTED] wrote:
Hi,
Is it possible to create new vars in a loop
For instance:
for (i in 1:11)
var'i' - assign something
output =
var1
var2
...
var11
Is there a way to combine/join the value of 'i' to the string/char var in de
loop.
--
View this message in context:
http://www.nabble.com/join-chars-in-loops-tp16895854p16895854.html
Sent from the R help mailing list archive at Nabble.com.
__
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
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting coefficients' standard errors from linear model
Try: summary(lm.D9)[[coefficients]][,2] On Fri, Apr 25, 2008 at 10:55 AM, Uli Kleinwechter [EMAIL PROTECTED] wrote: Dear all, Hope this question is not too trivial... In order to correct standard errors from an estimation of a fixed effects regression model y need to extract the vector of standard errors of the coefficients of a simple linear model estimated using lm(var1~var2+var3+var4) Unfortunately I can't find out the corresponding function. Thank you very much for your help. Uli -- Uli Kleinwechter Department of Agricultural Economics and Social Sciences Faculty of Agriculture and Horticulture Humboldt University of Berlin Unter den Linden 6 D-10099 Berlin, Germany Phone: (+49) 30 2093 6124, Fax. (+49) 30 2093 6301 E-mail: [EMAIL PROTECTED] __ 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 and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] join chars in loops
look at ?assign(), e.g.,
for (i in 1:11) {
assign(paste(var, i, sep = ), i)
}
var1
var2
var10
but I'd prefer to use a list. I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Dirkheld [EMAIL PROTECTED]
To: r-help@r-project.org
Sent: Friday, April 25, 2008 4:40 PM
Subject: [R] join chars in loops
Hi,
Is it possible to create new vars in a loop
For instance:
for (i in 1:11)
var'i' - assign something
output =
var1
var2
...
var11
Is there a way to combine/join the value of 'i' to the string/char
var in de
loop.
--
View this message in context:
http://www.nabble.com/join-chars-in-loops-tp16895854p16895854.html
Sent from the R help mailing list archive at Nabble.com.
__
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
and provide commented, minimal, self-contained, reproducible code.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] matrix from list
You may want to read the help page for '[' and '[[' a few more times (the differencese can be subtle). The '[[' only returns a single element from a data structure (but in the case of a list, that single element can be quite complex). So something like list[[1:2]] does not make sense because you are asking something that returns 1 thing to return 2. You can do list[1:2] which will return a list consisting of the 1st 2 elements of the original list. If you list happens to be a data frame as well, then you can subset it like a matrix: mydf[1:2, 3:4] gives the 1st 2 rows of columns 3 and 4, mydf[,1:2] gives the first 2 columns. These will continue to be data frames (since '[' returns the same type of object), but tools like as.matrix can convert this into a matrix. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Olivier Lefevre Sent: Thursday, April 24, 2008 4:16 PM To: [EMAIL PROTECTED] Subject: Re: [R] matrix from list Yes, unlist is the magic wand I was looking for. Thanks a million! Having said that, I find it rather arbitrary that you can write mat[1:4] but not list[[1:2]]; IMO there should be no need for a magic operator like unlist: list[[1:length(list)]] could do the job. -- O.L. __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] No rule to make target 'R/Copy'
No... don't think so. I rerun my computer, moved some folders (I deleted the folder with .C file), rerun the compilation, and it worked... Not sure to understand why. Any idea? Prof Brian Ripley wrote: Do you have a space in some file name? Starting 'Copy '? On Fri, 25 Apr 2008, Ardia David wrote: Dear all, I am currently building a package with C code (in scr folder). Everything was ok, but now, I get the following error message when compiling the package using R CMD INSTALL: make[2]: *** No rule to make target 'R/Copy', needed in [...] What does that mean? I can still compile other packages containing C code, but not that one. No 00UNLOCK directory has been created . I am on a IBM PC, and use windows XP. Thanks for your help -- David Ardia H-building, room 11-26 Econometric Institute Erasmus University PO Box 1738 NL 3000 DR Rotterdam The Netherlands Phone: +31 (0)10 408 2269 __ 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 and provide commented, minimal, self-contained, reproducible code. -- David Ardia H-building, room 11-26 Econometric Institute Erasmus University PO Box 1738 NL 3000 DR Rotterdam The Netherlands Phone: +31 (0)10 408 2269 __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting coefficients' standard errors from linear model
Or use: mod - lm(var1 ~ var2 + var3 + var4) coef(summary(mod))[, 2] or coef(summary(lm.D9))[, Std. Error] if you prefer using column names. coef() extracts the model coefficients from the lm object and the additional content in a summary.lm object. There are accessor functions for model objects and these are referenced in An Introduction to R and in the See Also section of ?lm. HTH, Marc Schwartz Henrique Dallazuanna wrote: Try: summary(lm.D9)[[coefficients]][,2] On Fri, Apr 25, 2008 at 10:55 AM, Uli Kleinwechter [EMAIL PROTECTED] wrote: Dear all, Hope this question is not too trivial... In order to correct standard errors from an estimation of a fixed effects regression model y need to extract the vector of standard errors of the coefficients of a simple linear model estimated using lm(var1~var2+var3+var4) Unfortunately I can't find out the corresponding function. Thank you very much for your help. Uli __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sum of random values
You might want to look at the distr package (and its relatives). It provides methods for calculating the distribution function of combinations (the sum is one) of other distributions. I'm not sure how you would convert your percentiles to a distribution function, but there may be a way in the documentation for distr and friends. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ricardo Bessa Sent: Thursday, April 24, 2008 5:12 PM To: r-help@r-project.org Subject: [R] Sum of random values Hello, I have two random variables with their percentiles which correspond to their probability distribution function. My objective is to sum these two random variables. There exists any algorithm or procedure in R capable of converting the percentiles to a probability density function? is the fast Fourier transform function of R(fft) capable of doing the sum with a convolution? I'm just starting with this specific problem, so any help it will be very useful. Best regards, Ricardo Bessa _ [[elided Hotmail spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] join chars in loops
...
That is, use the construction
thelist - lapply(1:11,function(i){...return something})
I would go further then Dmitris and say that this should be the canonical
answer to this frequently asked question and that perhaps in 7.21 in the R
FAQ (Version 2.6.2 -- I haven't yet upgraded) -- How can I turn a string
into a variable? -- this could be explicitly stated (it's in there, but
not quite so explicitly). Or perhaps it might be a separate FAQ
question:How to create new variables from their character string names in a
loop? This might make it a little easier for people to find and a little
less likely that the question will get asked on the list -- though I must
agree with those who have lamented that it often seems pointless to make
such efforts because people don't bother to use the resources anyway. Ah,
but that's just the grumbling of an old reprobate...
Cheers,
Bert
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Dimitris Rizopoulos
Sent: Friday, April 25, 2008 8:07 AM
To: Dirkheld
Cc: r-help@r-project.org
Subject: Re: [R] join chars in loops
look at ?assign(), e.g.,
for (i in 1:11) {
assign(paste(var, i, sep = ), i)
}
var1
var2
var10
but I'd prefer to use a list. I hope it helps.
Best,
Dimitris
Dimitris Rizopoulos
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
- Original Message -
From: Dirkheld [EMAIL PROTECTED]
To: r-help@r-project.org
Sent: Friday, April 25, 2008 4:40 PM
Subject: [R] join chars in loops
Hi,
Is it possible to create new vars in a loop
For instance:
for (i in 1:11)
var'i' - assign something
output =
var1
var2
...
var11
Is there a way to combine/join the value of 'i' to the string/char
var in de
loop.
--
View this message in context:
http://www.nabble.com/join-chars-in-loops-tp16895854p16895854.html
Sent from the R help mailing list archive at Nabble.com.
__
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
and provide commented, minimal, self-contained, reproducible code.
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] fix variance parameter values for lmer estimation
Dear list-members, a model is fit with lmer, but I want to force the variance parameter values to be as defined by me I thought, use 'start' to specify initial values and only allow for one iteration ? my question is how to do that ? to specify the 2x2 matrix of variance parameter values: start=list(groups=array(2,-0.5,1),dim=c(2,2)) now I need to make sure the mean structure is estimated, while the variance parameter values are kept constant ?? e.g. lmer(resp~pred1+pred2+(1 + pred1|groups),start=list(groups=array(2,-0.5,1),dim=c(2,2)),) cheers, Wilfried Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] FASeg
Hi All, I was using FASeg package. Now when I am trying to install this library I get the message Warning message: package 'FASeg' is not available Can someone please suggest something. Thank you vidhu [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rows assignment
Hi to all members, i encountered a weird problem when trying to assign subset of rows in a matrix. Simple example works fine: z-matrix(NA,ncol=3,nrow=10) z[,1]-1:10 y-matrix(1:30,ncol=3,nrow=10) y[,1]-5:14 z[z[,1]%in%y[,1],2]-y[y[,1]%in%z[,1],2] z z[z[,1]%in%y[,1],]-y[y[,1]%in%z[,1],] z When i try it on a bigger matrix it works fine when i try to assign 1 element, but converts original matrix to a list when trying to assign 2 or 3 columns for example. What can be a problem, as it seems that matrices are both numbers only? Thanks -- View this message in context: http://www.nabble.com/Rows-assignment-tp16896591p16896591.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] fix variance parameter values for lmer estimation
On 4/25/08, Wilfried Cools [EMAIL PROTECTED] wrote: Dear list-members, a model is fit with lmer, but I want to force the variance parameter values to be as defined by me I thought, use 'start' to specify initial values and only allow for one iteration ? my question is how to do that ? to specify the 2x2 matrix of variance parameter values: start=list(groups=array(2,-0.5,1),dim=c(2,2)) Well, the problem is that if you are going to decide what the arguments to the function should be and how they should be interpreted you are going to need to write the function yourself. There is nothing in the lmer documentation that says it will fit a model with the variance parameter values as defined by you and there is nothing to say that you can specify a list with arbitrary names as the value of the start parameter and somehow lmer will magically infer what you mean by these starting values and do the right thing. Sorry but I don't write mind-reading software. You are going to have to write it yourself. now I need to make sure the mean structure is estimated, while the variance parameter values are kept constant ?? e.g. lmer(resp~pred1+pred2+(1 + pred1|groups),start=list(groups=array(2,-0.5,1),dim=c(2,2)),) cheers, Wilfried Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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 and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Use of survreg.distributions
Hello Dr. Therneau: Thank you for your response. Let me explain to you want I want. My y variable(time) is normal and would like to fit the model on logarithmic transformation of y (log(y)). I tried to run codes according to your suggestion: tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=lognormal, data=y.data, scale=0, weights=w) The following error message is giving: Error in survreg(Surv(y, y = -5, type = left) ~ x + : Invalid survival times for this distribution In addition: Warning messages: 1: In log(dlist$dtrans(Y[exactsurv, 1])) : NaNs produced 2: In log(y) : NaNs produced Note, the data file y.data does not contain any missing data! Do you know why it is giving me such an error message please? Thank you again for your helpful comment/suggestion. Best Regards, Abdus Sattar [EMAIL PROTECTED] - Original Message From: Terry Therneau [EMAIL PROTECTED] To: [EMAIL PROTECTED] Cc: r-help@R-project.org Sent: Friday, April 25, 2008 8:46:45 AM Subject: Re: [R] Use of survreg.distributions --begin included message --- I am using survreg(Surv()) for fitting a Tobit model of left-censored longitudinal data. For logarithmic transformation of y data, I am trying use survreg.distributions in the following way: tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=gaussian, data=y.data, scale=0, weights=w) my.gaussian-survreg.distributions$gaussian my.gaussian$name=lognormal my.gaussian$dist-my.gaussian tfit=survreg(Surv(y, y=-5, type=left)~x + cluster(id), dist=my.gaussian, data=y.data, scale=0, weights=w) If I run these codes then I got the following error message, Error in survreg(Surv(y, y = -5, type = left) ~ x + : Invalid distribution object Does anybody can help me in identifying the error(s) in these code please? --- end include Can you tell us what you are trying to do? Your first model was a fit of y ~ x + eps, eps ~ Gaussian. If what you want is log(y) ~ x + eps, then all that you need do is use dist=loggaussian in the survreg call. (Or 'lognormal'; which is the same distribution.) Terry Therneau [[elided Yahoo spam]] =Ahu06i62sR8HDtDypao8Wcj9tAcJ [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] making a dll for windows eviornment for R
Hi All, I have a .c file and I need to make a dll so that it could be called by R. I have successfully made .so from .c file and its working great. But i have no clue of making dll. I tried googling for help ...but not much of use Please suggest something regards Vidhu [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Documentation General Comments
Each pdf reference manual includes an index of functions classified according to keywords. I wonder why indexes in on-line documentation do not include similar categorisation. It would be much easier to figure out all related functions and topics. Thanks, Vitalie. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] making a dll for windows eviornment for R
On 4/25/2008 1:12 PM, Vidhu Choudhary wrote: Hi All, I have a .c file and I need to make a dll so that it could be called by R. I have successfully made .so from .c file and its working great. But i have no clue of making dll. I tried googling for help ...but not much of use Please suggest something Take a look at the Writing R Extensions manual. Lots of detail there. Quick version: Install Rtools, put Rtools/bin first on your path, the other tools somewhere on it, then just do as you do anywhere else. Duncan Murdoch __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtaining correlation parameters for multiple rows
Hi Jorge,
That was great! Thank you very much for the suggestion.
I just had to make a couple of minor changes (e.g., pearson vs. spearman)
and it worked perfectly.
Thanks,
Joao Pedro
Hi,
I'm sure it could be better but try this:
# F statistics based on lm
FSTAT=function(y,x) summary(lm(y~x))$f[1]
# Correlation and p-value
CORR=function(y,x){
tc=cor.test(x,y,method=spearman,alternative=two.sided)
temp=matrix(c(tc$estimate,tc$p.value),ncol=2)
colnames(temp)=c('rho','pvalue')
temp
}
# 1000 variables and 100 samples
set.seed(124)
X=matrix(rnorm(1000*100),ncol=100)
# Correlation coefficient, p-value and F statistics
corr=t(apply(X[-1,],1,CORR,x=X[1,])) # Your reference is X[1,]
fs=apply(X[-1,],1,FSTAT,x=X[1,]) # Your reference is X[1,]
# Report
temp=data.frame(fstats=fs,rho=corr[,1],pvalue=corr[,2])
rownames(temp)=paste(X,2:nrow(X),sep=)
dim(temp)
[1] 999 3
temp[1:10,]
fstats rho pvalue
X2 1.421307790 -0.05038104 0.61807912
X3 0.051423768 -0.04614461 0.64795111
X4 0.128000634 0.01795380 0.85902211
X5 0.990235820 -0.06540654 0.51730942
X6 5.569006085 0.24232823 0.01532172
X7 0.001862766 -0.01436544 0.88703532
X8 1.025363077 -0.10628263 0.29206908
X9 0.679794149 0.06509451 0.51927479
X10 1.296034903 0.09492949 0.34686211
X11 0.126636867 0.05137714 0.61110106
HTH,
Jorge
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Re: [R] Differentiate alphanumeric vs numeric strings
This is fantastic. As a future note to myself and to others who may stumble upon this: further documentation for all one's heart could desire is in the base help system at. Regular Expressions as used in R - regexp Pattern Matching and Replacement - grep Split the Elements of a Character Vector - strsplit The following worked in my situation: channel2007-odbcConnectAccess(filename for 2007 data) tables -sqlTables(channel2007)[,3] tables -grep([[:digit:]],tables,value=TRUE) all2007 -sqlFetch(channel2007, tables[1]) for (f in tables[-1]) all2007-rbind(all2007, sqlFetch(channel2007, f)) Thanks for your help On Thu, Apr 24, 2008 at 11:34 PM, jim holtman [EMAIL PROTECTED] wrote: The following will return the indices or the values of character strings that are all numeric: x - c(12345, 123AS23, A123, 398457) grep(^[[:digit:]]*$, x) # index [1] 1 4 grep(^[[:digit:]]*$, x, value=TRUE) # values [1] 12345 398457 On Thu, Apr 24, 2008 at 10:39 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: I have a bunch of tables in a Microsoft Access database. An updated database is sent to me every week containing a new table. I know that is inefficient and weird but welcome to my life. I want to read the tables whose names are something such as 040207 but not the ones that have alphanumeric names such as everyone. Using RODBC I am easily able to create a character vector of the names of the tables. Is there a function that can differentiate values consisting only of digits (numerics) as opposed to ones that contain letters (and perhaps digts as well)? I am sure there is. What is it and where should I have found it? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] hist densities
This is a reply to Luke Spadavecchia's question about hist densities. If you want to construct a histogram where the bar heights are the percentage of observations in the intervals you can use this code: x-rnorm(n=5000,mean=1.5,sd=0.25) h-hist(x) h$density-h$counts/sum(h$counts) plot(h,freq=F,ylab=Percentage) Sarah Hardy [EMAIL PROTECTED] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing dummy variables for months for a time series object
The simplest way is probably to generate them as the columns of a matrix. Let's suppose you have data from Jan 1991 up to Mar 2008. X - outer(rep(month.abb, length = 16*12+3), month.abb, ==) + 0 ## the + 0 will convert logical to numeric dim(X) [1] 195 12 dimnames(X)[[2]] - month.abb head(X) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec [1,] 1 0 0 0 0 0 0 0 0 0 0 0 [2,] 0 1 0 0 0 0 0 0 0 0 0 0 [3,] 0 0 1 0 0 0 0 0 0 0 0 0 [4,] 0 0 0 1 0 0 0 0 0 0 0 0 [5,] 0 0 0 0 1 0 0 0 0 0 0 0 [6,] 0 0 0 0 0 1 0 0 0 0 0 0 To get the July indicators, use X[, Jul], c Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Megh Dal Sent: Friday, 25 April 2008 5:40 PM To: [EMAIL PROTECTED] Subject: [R] Constructing dummy variables for months for a time series object I have a TS of monthly observations. head(data4) 1991(1) 1991(2) 1991(3) 1991(4) 1991(5) 1991(6) 12.00864 11.94203 11.98386 12.01900 12.19226 12.15488 Now I want to make 11 dummy variables indicating months. Therefore I did followings : For Jan : rep(c(rep(0,0), 1, rep(0, 11)), 17) For Feb : rep(c(rep(0,1), 1, rep(0, 10)), 17) and so on But my question is there any way to aumate this? Or I have to do the above thing for all 11 months? - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Equivalent of Excel pivot tables in R
Can somebody tell me how to do the equivalent of a pivot table in R ? For example, if I have : var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 I could have : x y z a1 0 2 b0 1 2 where entries in the table are counts of var3. x y z a10 0 20 b0 20 40 where entries are sums of var3. I would expect it to be tapply(), but I can't see how it would be done. Any suggestions please. -- View this message in context: http://www.nabble.com/Equivalent-of-Excel-pivot-tables-in-R-tp16906289p16906289.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent of Excel pivot tables in R
Hi, Try this: x=var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 yourdata=read.table(textConnection(x),header=TRUE) attach(yourdata) res=tapply(var3,yourdata[,-3],sum) # With tapply! res[is.na(res)]-0 res var2 var1 x y z a 10 0 20 b 0 20 40 See also ?tapply. HTH, Jorge On Fri, Apr 25, 2008 at 5:54 PM, ppaarrkk [EMAIL PROTECTED] wrote: Can somebody tell me how to do the equivalent of a pivot table in R ? For example, if I have : var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 I could have : x y z a1 0 2 b0 1 2 where entries in the table are counts of var3. x y z a10 0 20 b0 20 40 where entries are sums of var3. I would expect it to be tapply(), but I can't see how it would be done. Any suggestions please. -- View this message in context: http://www.nabble.com/Equivalent-of-Excel-pivot-tables-in-R-tp16906289p16906289.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent of Excel pivot tables in R
See Hadley's reshape package http://had.co.nz/reshape/ and on CRAN. On Fri, Apr 25, 2008 at 2:54 PM, ppaarrkk [EMAIL PROTECTED] wrote: Can somebody tell me how to do the equivalent of a pivot table in R ? For example, if I have : var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 I could have : x y z a1 0 2 b0 1 2 where entries in the table are counts of var3. x y z a10 0 20 b0 20 40 where entries are sums of var3. I would expect it to be tapply(), but I can't see how it would be done. Any suggestions please. -- View this message in context: http://www.nabble.com/Equivalent-of-Excel-pivot-tables-in-R-tp16906289p16906289.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code. -- HTH, Jim Porzak Responsys, Inc. San Francisco, CA http://www.linkedin.com/in/jimporzak [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent of Excel pivot tables in R
Try: with(x, tapply(var3, list(var1, var2), length)) with(x, tapply(var3, list(var1, var2), sum)) Or with xtabs xtabs(as.logical(var3) ~ var1 + var2, data = x) xtabs(var3 ~ var1 + var2, data = x) On 4/25/08, ppaarrkk [EMAIL PROTECTED] wrote: Can somebody tell me how to do the equivalent of a pivot table in R ? For example, if I have : var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 I could have : x y z a1 0 2 b0 1 2 where entries in the table are counts of var3. x y z a10 0 20 b0 20 40 where entries are sums of var3. I would expect it to be tapply(), but I can't see how it would be done. Any suggestions please. -- View this message in context: http://www.nabble.com/Equivalent-of-Excel-pivot-tables-in-R-tp16906289p16906289.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] matrix from list
Greg Snow wrote: The '[[' only returns a single element from a data structure I know but that is precisely what I find arbitrary. Anyway you are right that it would still return the kind of object, only subsetted, which is not I want. As someone kindly pointed out to me offline, besides the unlist trick posted before, you can also achieve the desired result with m - as.matrix(l) dimnames(m) - NULL -- O.L. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] Ubuntu vs Mac OS X
Hi ! I have installed R-2.7.0 64-bits on a computer where the new Ubuntu version (8.04) was installed. This computer is a 3.2 GHz Dual-core with 2 Gb of RAM. To test how fast (I though !) this machine is, I compared two simple matrix manipulations between Ubuntu and my laptop (a MacBook Pro 2.2 GHz with also 2 Gb of RAM under Mac OS X 10.5.2). By the way, I install the normal version of R on my MacBook Pro (32-bits) I decided to use the following matrix manipulation because they are typical manipulation that I was planning to do repetitively and with much larger matrices for my PhD project. First matrix manipulation: coco-matrix(rnorm(100),1000,1000) system.time(coco2-eigen(coco)) Results on the Mac: user system elapsed 7.301 0.974 7.376 Results on Ubuntu: user system elapsed 20.573 0.088 20.766 Second matrix manipulation: coco-matrix(rnorm(100),1000,1000) system.time(coco3-coco%*%coco) Results on the Mac: user system elapsed 0.360 0.024 0.224 Results on Ubuntu: user system elapsed 2.756 0.000 2.758 If I understand these results right, my MacBook Pro is far better than this Desk computer. I know Macs are good but that difference of performance is surprising me, did I do something wrong considering the large difference in processor? Thanks in advance Guillaume Blanchet __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent of Excel pivot tables in R
Hi, I forgot the first part (I'm sorry): table(var1,var2) var2 var1 x y z a 1 0 2 b 0 1 2 HTH, Jorge On Fri, Apr 25, 2008 at 7:25 PM, Jorge Ivan Velez [EMAIL PROTECTED] wrote: Hi, Try this: x=var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 yourdata=read.table(textConnection(x),header=TRUE) attach(yourdata) res=tapply(var3,yourdata[,-3],sum) # With tapply! res[is.na(res)]-0 res var2 var1 x y z a 10 0 20 b 0 20 40 See also ?tapply. HTH, Jorge On Fri, Apr 25, 2008 at 5:54 PM, ppaarrkk [EMAIL PROTECTED] wrote: Can somebody tell me how to do the equivalent of a pivot table in R ? For example, if I have : var1var2 var3 a x10 b y20 a z10 b z20 a z10 b z20 I could have : x y z a1 0 2 b0 1 2 where entries in the table are counts of var3. x y z a10 0 20 b0 20 40 where entries are sums of var3. I would expect it to be tapply(), but I can't see how it would be done. Any suggestions please. -- View this message in context: http://www.nabble.com/Equivalent-of-Excel-pivot-tables-in-R-tp16906289p16906289.html Sent from the R help mailing list archive at Nabble.com. __ 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 and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constructing dummy variables for months for a time series object
First generate a factor and then calculate its model matrix: month. - factor(cycle(x), labels = month.abb) model.matrix(~ month.)[,-1] Actually you may not even need the dummy variables at all if your purpose is to do a regression. You can use the factor directly: lm(x ~ month.) By the way, be sure to check out ?monthplot On Fri, Apr 25, 2008 at 3:40 AM, Megh Dal [EMAIL PROTECTED] wrote: I have a TS of monthly observations. head(data4) 1991(1) 1991(2) 1991(3) 1991(4) 1991(5) 1991(6) 12.00864 11.94203 11.98386 12.01900 12.19226 12.15488 Now I want to make 11 dummy variables indicating months. Therefore I did followings : For Jan : rep(c(rep(0,0), 1, rep(0, 11)), 17) For Feb : rep(c(rep(0,1), 1, rep(0, 10)), 17) and so on But my question is there any way to aumate this? Or I have to do the above thing for all 11 months? - [[elided Yahoo spam]] [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ubuntu vs Mac OS X
On Apr 25, 2008, at 4:34 PM, Guillaume Blanchet wrote: Hi ! I have installed R-2.7.0 64-bits on a computer where the new Ubuntu version (8.04) was installed. This computer is a 3.2 GHz Dual-core with 2 Gb of RAM. To test how fast (I though !) this machine is, I compared two simple matrix manipulations between Ubuntu and my laptop (a MacBook Pro 2.2 GHz with also 2 Gb of RAM under Mac OS X 10.5.2). By the way, I install the normal version of R on my MacBook Pro (32-bits) A guess to get that big a difference is that one has an optimized BLAS and the other doesn't. Try something not so heavily dependent on BLAS and see what the times are. -Roy M ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: [EMAIL PROTECTED] (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] R question about prediction from a fitted model
Hi, I have a question about predicting new values from a fitted model in R. For example, if i fit a linear model fit-lm(y~x) predict(fit) will give the fitted values for each x. I am wondering if there is a way to do some prediction of the fitted for some new values of x that are not in the data points? for example, x=0.5 is not in the original data (not a datapoint), is there a way to predict the fitted value corresponding to x=0.5 easily? Thank you! [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R question about prediction from a fitted model
Hi Lisa, See examples in ?predict.lm HTH, Jorge On Fri, Apr 25, 2008 at 7:47 PM, Lisa [EMAIL PROTECTED] wrote: Hi, I have a question about predicting new values from a fitted model in R. For example, if i fit a linear model fit-lm(y~x) predict(fit) will give the fitted values for each x. I am wondering if there is a way to do some prediction of the fitted for some new values of x that are not in the data points? for example, x=0.5 is not in the original data (not a datapoint), is there a way to predict the fitted value corresponding to x=0.5 easily? Thank you! [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Summarize data for MCA (FactoMineR)
Hi :-) I'm new to R and I started using it for a project (I'm the CS guy in a group of statisticians helping them find out how to solve issues as they come out). This is my first post to the list and I am starting to learn R. Well, they were used to doing MCA analysis in other programs where the data seems to be preprocessed automatically before running MCA. So, they need to process a data set that comes with N=100 of elements, but there are really about N/100 distinct elements over all the variables, so the MCA can be run in reasonable time summarizing data. So, the question is: How can I turn x from: x - structure(list(weight = c(1, 1, 2, 1, 2), var1 = structure(c(1L, 1L, 1L, 1L, 2L), .Label = c(A, C), class = factor), var2 = structure(c(1L, 1L, 1L, 1L, 2L), .Label = c(B, D), class = factor)), .Names = c(weight, var1, var2), row.names = c(NA, 5L), class = data.frame) to: y - structure(list(weihgt = c(5L, 2L), var1 = structure(1:2, .Label = c(A, C), class = factor), var2 = structure(1:2, .Label = c(B, D), class = factor)), .Names = c(weihgt, var1, var2 ), class = data.frame, row.names = c(NA, -2L)) using R? That is, from: x weight var1 var2 1 1AB 2 1AB 3 2AB 4 1AB 5 2CD to: y weihgt var1 var2 1 5AB 2 2CD The idea is that there is one occurrence of A B repeated 4 times in the original table, and it is summarized in the second table, computing the sum of the weights. I solved the problem using Perl, but I'd like to know what I have to read in order to do it in R. Regards, Nelson.- -- http://arhuaco.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.html and provide commented, minimal, self-contained, reproducible code.
[R] Details regarding the nnet package
Hello, I've recently been using the nnet package to do some basic forecast predictions. I've found the package to be quite useful and I am getting some good results. However, I am in the midst of writing a small paper on the results I am getting and wish to clarify some things about the nnet package that are not made clear in the documentation. In particular I would like to know the following: 1) Is it a standard feed forward network trained using gradient descent (I am assuming this is the case, seems like a no brainer but just to be sure)? 2) What is the sigmoidal function used for the activation/firing of a node in the network? 3) What exactly does the output value consist of at each iteration? Is this the value of the Least Mean Square function of the difference between the output layer and the target values or is it something else? 4) Will this package ever be updated to allow for multiple layers instead of just one? (just out of curiousity) I have to present this paper on Friday May 2nd so I would greatly appreciate a timely response. Thanks, -Colin __ 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 and provide commented, minimal, self-contained, reproducible code.
[R] function clogit
Hello, I am using the clogit (conditional logistic regression) on a simple data set which is not related to survivorship, which I understand to be fine. I have trouble understanding the output. I would like to find parameter estimates of the logistic models I am constructing with R, and am unclear as to what the coefficients represent that are provided. The below is a copy of my output. summary(clogit(Pluv~Clay+ Veg+ Grav+ Cobb+ strata(Site), data=microsite1))Call:coxph(formula = Surv(rep(1, 50L), Pluv) ~ Clay + Veg + Grav + Cobb + strata(Site), data = microsite1, method = exact) n= 50coef exp(coef) se(coef) z pClay -14.15 7.16e-07 8.43 -1.679 0.093Veg -4.13 1.60e-0213.04 -0.317 0.750Grav -6.93 9.76e-04 8.63 -0.803 0.420Cobb 17.70 4.89e+0715.37 1.152 0.250 exp(coef) exp(-coef) lower .95 upper .95Clay 7.16e-07 1.40e+06 4.79e-14 1.07e+01Veg 1.60e-02 6.23e+01 1.27e-13 2.02e+09Grav 9.76e-04 1.02e+03 4.42e-11 2.16e+04Cobb 4.89e+07 2.05e-08 4.03e-06 5.93e+20 Rsquare= 0.397 (max possible= 0.5 )Likelihood ratio test= 25.3 on 4 df, p=4.46e-05Wald test= 3.8 on 4 df, p=0.434Score (logrank) test = 14.3 on 4 df, p=0.00625 Any help is greatly appreciated, Thank you, Carmen _ n more at SignInAndWIN.ca [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R question about prediction from a fitted model
Hi Jorge, thank you very much for your reply. I checked and have got the prediction of new values for lm or glm or nls, the new question is, is there any prediction for the cox model? I tried predict(Surv(y~x),newdata), it only gave the fitted values. Any clue on this? thanks a lot! On 4/25/08, Jorge Ivan Velez [EMAIL PROTECTED] wrote: Hi Lisa, See examples in ?predict.lm HTH, Jorge On Fri, Apr 25, 2008 at 7:47 PM, Lisa [EMAIL PROTECTED] wrote: Hi, I have a question about predicting new values from a fitted model in R. For example, if i fit a linear model fit-lm(y~x) predict(fit) will give the fitted values for each x. I am wondering if there is a way to do some prediction of the fitted for some new values of x that are not in the data points? for example, x=0.5 is not in the original data (not a datapoint), is there a way to predict the fitted value corresponding to x=0.5 easily? Thank you! [[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.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
